Publications: Difference between revisions

From OxDNA
Jump to navigation Jump to search
No edit summary
No edit summary
 
(216 intermediate revisions by the same user not shown)
Line 107: Line 107:
# Q.Y. Yeo, I.Y. Loh, S.R. Tee, Y.H. Chiang, J. Cheng, M.H. Liu and Z.S. Wang, ''Nanoscale'' '''9''', 12142-12149 (2017)
# Q.Y. Yeo, I.Y. Loh, S.R. Tee, Y.H. Chiang, J. Cheng, M.H. Liu and Z.S. Wang, ''Nanoscale'' '''9''', 12142-12149 (2017)
#:[https://doi.org/10.1039/C7NR03809G A DNA bipedal nanowalker with a piston-like expulsion stroke]
#:[https://doi.org/10.1039/C7NR03809G A DNA bipedal nanowalker with a piston-like expulsion stroke]
# G. Chatterjee, N. Dalchau, R.A. Muscat, A. Phillips and G. Seelig, ''Nat. Nanotechnol.'' '''12''', 920–927 (2017)
#: [https://doi.org/10.1038/nnano.2017.127 A spatially localized architecture for fast and modular DNA computing]
# Q. Wang, R.N. Irobalieva, W. Chiu, M.F. Schmid, J.M. Fogg, L. Zechiedrich, B.M. Pettitt, ''Nucleic Acids Res.'' '''45''' 7633-7642 (2017)
# Q. Wang, R.N. Irobalieva, W. Chiu, M.F. Schmid, J.M. Fogg, L. Zechiedrich, B.M. Pettitt, ''Nucleic Acids Res.'' '''45''' 7633-7642 (2017)
#: [https://doi.org/10.1093/nar/gkx516 Influence of DNA sequence on the structure of minicircles under torsional stress]  
#: [https://doi.org/10.1093/nar/gkx516 Influence of DNA sequence on the structure of minicircles under torsional stress]  
Line 135: Line 137:
# E. Locatelli and L. Rovigatti, ''Polymers'' '''10''', 447 (2018)
# E. Locatelli and L. Rovigatti, ''Polymers'' '''10''', 447 (2018)
#: [https://doi.org/10.3390/polym10040447 An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids] ([https://www.preprints.org/manuscript/201803.0203/v1 preprints])
#: [https://doi.org/10.3390/polym10040447 An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids] ([https://www.preprints.org/manuscript/201803.0203/v1 preprints])
# E. Spruijt, S.E. Tusk and H. Bayley, ''Nature Nanotechnology'' '''13''', 739-745 (2018)
# E. Spruijt, S.E. Tusk and H. Bayley, ''Nat. Nanotechnol.'' '''13''', 739-745 (2018)
#: [http://dx.doi.org/10.1038/s41565-018-0139-6 DNA scaffolds support stable and uniform peptide nanopores]
#: [http://dx.doi.org/10.1038/s41565-018-0139-6 DNA scaffolds support stable and uniform peptide nanopores]
# L. Coronel, A. Suma and C. Micheletti, ''Nucleic Acids Res.'' '''46''',7522–7532 (2018)
# L. Coronel, A. Suma and C. Micheletti, ''Nucleic Acids Res.'' '''46''',7522–7532 (2018)
Line 209: Line 211:
# A. Bader and S.L. Cockroft, ''Chem. Commun.'' '''56''', 5135-5138 (2020)
# A. Bader and S.L. Cockroft, ''Chem. Commun.'' '''56''', 5135-5138 (2020)
#: [https://doi.org/10.1039/D0CC00882F Conformational enhancement of fidelity in toehold-sequestered DNA nanodevices]
#: [https://doi.org/10.1039/D0CC00882F Conformational enhancement of fidelity in toehold-sequestered DNA nanodevices]
# J.P.K. Doye, H. Fowler, D. Prešern, J. Bohlin, L. Rovigatti, F. Romano, P. Šulc, C.K. Wong, A.A. Louis, J.S. Schreck and M.C. Engel, M. Matthies, E. Benson, E. Poppleton and B.E.K. Snodin, ''Methods in Molecular Biology'', submitted.  
# J.P.K. Doye, H. Fowler, D. Prešern, J. Bohlin, L. Rovigatti, F. Romano, P. Šulc, C.K. Wong, A.A. Louis, J.S. Schreck and M.C. Engel, M. Matthies, E. Benson, E. Poppleton and B.E.K. Snodin, ''Methods in Molecular Biology'' ''2639'', 93-112 (2023).  
#: The oxDNA coarse-grained model as a tool to simulate DNA origami ([http://arxiv.org/abs/2004.05052 arXiv]) ([http://dx.doi.org/10.5287/bodleian:vgqKg0rYo data])
#: [https://doi.org/10.1007/978-1-0716-3028-0_6 The oxDNA coarse-grained model as a tool to simulate DNA origami] ([http://arxiv.org/abs/2004.05052 arXiv]) ([http://dx.doi.org/10.5287/bodleian:vgqKg0rYo data])
# J. Lee, J.-H. Huh, S. Lee, ''Langmuir'' '''36''', 5118–5125 (2020)
# J. Lee, J.-H. Huh, S. Lee, ''Langmuir'' '''36''', 5118–5125 (2020)
#: [https://doi.org/10.1021/acs.langmuir.0c00239 DNA Base Pair-Stacking Crystallization of Gold Colloids]
#: [https://doi.org/10.1021/acs.langmuir.0c00239 DNA Base Pair-Stacking Crystallization of Gold Colloids]
Line 295: Line 297:
# Z. Yu, M. Centola, J. Valero, M. Matthies, P. Šulc, and M. Famulok, ''J. Am. Chem. Soc.'' '''143''', 13292–13298 (2021)
# Z. Yu, M. Centola, J. Valero, M. Matthies, P. Šulc, and M. Famulok, ''J. Am. Chem. Soc.'' '''143''', 13292–13298 (2021)
#: [https://doi.org/10.1021/jacs.1c06226 A Self-Regulating DNA Rotaxane Linear Actuator Driven by Chemical Energy]
#: [https://doi.org/10.1021/jacs.1c06226 A Self-Regulating DNA Rotaxane Linear Actuator Driven by Chemical Energy]
# T. Lee, S. Do, J.G. Lee, D.-N. Kim and Y. Shin, ''Nanoscale'' '''13''', 17638-17647 (2021)
#: [https://doi.org/10.1039/D1NR03495B The flexibility-based modulation of DNA nanostar phase separation]
# Y. Wang, J. V. Le, K. Crocker, M.A. Darcy, P.D. Halley, D. Zhao, N. Andrioff, C. Croy, M.G Poirier, R. Bundschuh, C.E Castro, ''Nucleic Acids Res.'' '''49''', 8987–8999 (2021)
# Y. Wang, J. V. Le, K. Crocker, M.A. Darcy, P.D. Halley, D. Zhao, N. Andrioff, C. Croy, M.G Poirier, R. Bundschuh, C.E Castro, ''Nucleic Acids Res.'' '''49''', 8987–8999 (2021)
#: [https://doi.org/10.1093/nar/gkab656 A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules]
#: [https://doi.org/10.1093/nar/gkab656 A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules]
# F. Liu, X. Liu, Q. Shi, C. Maffeo, M. Kojima, L. Dong, A. Aksimentiev, Q. Huang, T. Fukuda and  T. Arai, ''Nanoscale'' '''13''', 15552-15559 (2021)
# F. Liu, X. Liu, Q. Shi, C. Maffeo, M. Kojima, L. Dong, A. Aksimentiev, Q. Huang, T. Fukuda and  T. Arai, ''Nanoscale'' '''13''', 15552-15559 (2021)
#: [https://doi.org/10.1039/D1NR02757C A tetrahedral DNA nanorobot with conformational change in response to molecular trigger]
#: [https://doi.org/10.1039/D1NR02757C A tetrahedral DNA nanorobot with conformational change in response to molecular trigger]
# J. Appeldorn, S. Lemcke, T. Speck and A. Nikoubashman, submitted.
# J. Appeldorn, S. Lemcke, T. Speck and A. Nikoubashman, ''J. Phys. Chem. B'' '''126''', 5007–5016 (2022).
#: Employing artificial neural networks to find reaction coordinates and pathways for self-assembly ([https://doi.org/10.33774/chemrxiv-2021-9t07w ChemRxiv])
#: [https://doi.org/10.1021/acs.jpcb.2c02232 Employing artificial neural networks to find reaction coordinates and pathways for self-assembly] ([https://doi.org/10.33774/chemrxiv-2021-9t07w ChemRxiv])
# H. Jun, X. Wang, M.F. Parsons, W.P. Bricker, T. John, S. Li, S. Jackson, W. Chiu, M. Bathe, ''Nucleic Acids Res.'' '''49''', 10265–10274 (2021)
# H. Jun, X. Wang, M.F. Parsons, W.P. Bricker, T. John, S. Li, S. Jackson, W. Chiu, M. Bathe, ''Nucleic Acids Res.'' '''49''', 10265–10274 (2021)
#:[https://doi.org/10.1093/nar/gkab762 Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami]
#:[https://doi.org/10.1093/nar/gkab762 Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami]
# C.K. Wong, C. Tang, J.S. Schreck and J.P.K. Doye, ''Nanoscale'', submitted.
# C.K. Wong, C. Tang, J.S. Schreck and J.P.K. Doye, ''Nanoscale'' '''14''', 2638–2648 (2022).
#: Characterizing the free-energy landscapes of DNA origamis ([https://arxiv.org/abs/2108.06517 arXiv])
#: [https://doi.org/10.1039/D1NR05716B  Characterizing the free-energy landscapes of DNA origamis] ([https://arxiv.org/abs/2108.06517 arXiv])
# W. Lim, F. Randisi, J.P.K. Doye and A.A. Louis, ''Nucleic Acids Res.'' submitted.
# W. Lim, F. Randisi, J.P.K. Doye and A.A. Louis, ''Nucleic Acids Res.'' '''50''', 2480–2492 (2022).
#: The interplay of supercoiling and thymine dimers in DNA ([https://doi.org/10.1101/2021.09.27.461905 bioRxiv])
#: [https://doi.org/10.1093/nar/gkac082 The interplay of supercoiling and thymine dimers in DNA] ([https://doi.org/10.1101/2021.09.27.461905 bioRxiv])
# W.T. Kaufhold, W. Pfeifer, C.E. Castro and L. Di Michele, submitted.
# W.T. Kaufhold, W. Pfeifer, C.E. Castro and L. Di Michele, ''ACS Nano'' '''16''', 8784–8797 (2022).
#: Probing the mechanical properties of DNA nanostructures with metadynamics ([https://arxiv.org/abs/2110.01477 arXiv])
#: [https://doi.org/10.1021/acsnano.1c08999 Probing the mechanical properties of DNA nanostructures with metadynamics] ([https://arxiv.org/abs/2110.01477 arXiv])
# H. Su, J.M. Brockman, Y. Duan, N. Sen, H. Chhabra, A. Bazrafshan, A.T. Blanchard, T. Meyer, B. Andrews, J.P.K. Doye, Y. Ke, R.B. Dyer and K. Salaita, ''J. Am. Chem. Soc.'' accepted.
# H. Su, J.M. Brockman, Y. Duan, N. Sen, H. Chhabra, A. Bazrafshan, A.T. Blanchard, T. Meyer, B. Andrews, J.P.K. Doye, Y. Ke, R.B. Dyer and K. Salaita, ''J. Am. Chem. Soc.'' '''43''', 19466–19473 (2021).
#: [https://doi.org/10.1021/jacs.1c08796 Massively parallelized molecular force manipulation with on demand thermal and optical control]
#: [https://doi.org/10.1021/jacs.1c08796 Massively parallelized molecular force manipulation with on demand thermal and optical control]
# L. Yang, C. Cullin and J. Elezgaray, submitted.
# L. Yang, C. Cullin and J. Elezgaray, ''ChemPhysChem'' '''23''', e202200021 (2022).
#: Detection of short DNA sequences with DNA nanopores ([https://arxiv.org/abs/2110.11642 arXiv])
#: [https://doi.org/10.1002/cphc.202200021 Detection of short DNA sequences with DNA nanopores] ([https://arxiv.org/abs/2110.11642 arXiv])
# Y. Pan, R. Weng, L. Zhang, J. Qiu, X. Wang, G. Liao, Z. Qin, R. Liu, X. Dai, Y. Qian, X. Su, submitted.
# Y. Pan, R. Weng, L. Zhang, J. Qiu, X. Wang, G. Liao, Z. Qin, L. Zhang, H. Xiao, Y. Qian, X. Su, ''Nano Today'' '''46''' 101573 (2022).
#: Intramolecular Orthogonal Reporters for Dissecting Oxidative Stress and Response ([https://doi.org/10.21203/rs.3.rs-917337/v1 Research Square])
#: [https://doi.org/10.1016/j.nantod.2022.101573 Simulation guided intramolecular orthogonal reporters for dissecting cellular oxidative stress and response] ([https://doi.org/10.21203/rs.3.rs-917337/v1 Research Square])
# X. Wang, S. Li, H. Jun, T. John, K. Zhang, H. Fowler, J.P.K. Doye, W. Chiu and M. Bathe, submitted.
# X. Wang, S. Li, H. Jun, T. John, K. Zhang, H. Fowler, J.P.K. Doye, W. Chiu and M. Bathe, ''Sci. Adv.'' '''8''', eabn0039 (2022).
#: Planar 2D wireframe DNA origami
#: [https://doi.org/10.1126/SCIADV.ABN0039 Planar 2D wireframe DNA origami]
# E. Poppleton, A. Mallya, S. Dey, J. Joseph, P. Šulc, ''Nucleic Acids Res.'', accepted.
# E. Poppleton, A. Mallya, S. Dey, J. Joseph, P. Šulc, ''Nucleic Acids Res.'' '''50''', D246–D252 (2022)
#: [https://doi.org/10.1093/nar/gkab1000 Nanobase.org: a repository for DNA and RNA nanostructures]
#: [https://doi.org/10.1093/nar/gkab1000 Nanobase.org: a repository for DNA and RNA nanostructures]
# R. Foffi, F. Sciortino, J. M. Tavares, P. I. C. Teixeira, ''Soft Matter'' accepted (2021)
# R. Foffi, F. Sciortino, J. M. Tavares, P. I. C. Teixeira, ''Soft Matter'' '''17''', 10736-10743 (2021)
#: [https://doi.org/10.1039/D1SM01130H Building up DNA, bit by bit: a simple description of chain assembly] ([https://arxiv.org/abs/2111.03978 arXiv])
#: [https://doi.org/10.1039/D1SM01130H Building up DNA, bit by bit: a simple description of chain assembly] ([https://arxiv.org/abs/2111.03978 arXiv])
# J. Yoo, S. Park, C. Maffeo, T. Ha, A. Aksimentiev, ''Nucleic Acids Res.'' '''49''', 11459–11475 (2021).
# J. Yoo, S. Park, C. Maffeo, T. Ha, A. Aksimentiev, ''Nucleic Acids Res.'' '''49''', 11459–11475 (2021).
#: [https://doi.org/10.1093/nar/gkab967 DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles]
#: [https://doi.org/10.1093/nar/gkab967 DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles]
# E. Lin-Shiao,  W.G. Pfeifer, B.R. Shy, M. Saffari Doost, E. Chen, V.S. Vykunta,  J.R. Hamilton,  E.C. Stahl, D.M. Lopez,  C.R. Sandoval Espinoza, A.E. Dejanov, R.J. Lew, M.G. Poirer, A. Marson,  C.E. Castro,  J.A. Doudna, submitted
# E. Lin-Shiao,  W.G. Pfeifer, B.R. Shy, M. Saffari Doost, E. Chen, V.S. Vykunta,  J.R. Hamilton,  E.C. Stahl, D.M. Lopez,  C.R. Sandoval Espinoza, A.E. Dejanov, R.J. Lew, M.G. Poirer, A. Marson,  C.E. Castro,  J.A. Doudna, ''Nucleic Acids Res.'' '''50''', 1256–1268 (2022)
#: CRISPR-Cas9 mediated nuclear transport and genomic integration of nanostructured genes in human primary cells ([https://doi.org/10.1101/2021.11.08.467750 bioRxiv])
#: [https://doi.org/10.1093/nar/gkac049 CRISPR-Cas9 mediated nuclear transport and genomic integration of nanostructured genes in human primary cells] ([https://doi.org/10.1101/2021.11.08.467750 bioRxiv])
# J.P.K. Doye, A.A. Louis, J.S. Schreck, F. Romano, R.M. Harrison, M. Mosayebi, M.C. Engel, T.E. Ouldridge, to appear in ``[https://www.elsevier.com/books/energy-landscapes-of-nanoscale-systems/wales/978-0-12-824406-7 Energy Landscapes of Nanoscale Systems]'', ed. D.J. Wales, ``Frontiers of Nanoscience'' Vol. 21 (Elsevier)
# J.P.K. Doye, A.A. Louis, J.S. Schreck, F. Romano, R.M. Harrison, M. Mosayebi, M.C. Engel, T.E. Ouldridge, in ''[https://www.elsevier.com/books/energy-landscapes-of-nanoscale-systems/wales/978-0-12-824406-7 Energy Landscapes of Nanoscale Systems]'', ed. D.J. Wales, ''Frontiers of Nanoscience'' (Elsevier) Vol. 21, Chapter 9, pp 195-210 (2022)
#: Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling
#: [https://doi.org/10.1016/B978-0-12-824406-7.00016-6 Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling] ([https://arxiv.org/abs/2111.10166 arXiv])
# Y. Deng, Y. Tan, L. Zhang, C. Zhang, X. Su, submitted.
#: Forecasting the reaction of DNA modifying enzymes on DNA nanostructures by coarse grained model for stimuli-responsive drug delivery ([https://doi.org/10.21203/rs.3.rs-1038517/v1 Research Square])
# D. Smith and G. Tikhomirov, submitted.
#: small: A programmatic nanostructure design and modelling environment ([https://arxiv.org/abs/2111.15184 arXiv])
# S. Assenza and R. Pérez, ''J. Chem. Theory Comput'' '''18''', 3239–3256 (2022)
#: [https://doi.org/10.1021/acs.jctc.2c00138 Accurate sequence-dependent coarse-grained model for conformational and elastic properties of double-stranded DNA] ([https://doi.org/10.1101/2021.12.02.470889  biorXiv])
# D. Kuťák, E. Poppleton, H. Miao, P. Šulc and I. Barišić, ''Molecules'' '''27''', 63 (2022)
#: [https://doi.org/10.3390/molecules27010063 Unified Nanotechnology Format: One Way to Store Them All]
# M. Centola,  E. Poppleton,  M. Centola,  J. Valero,  P. Šulc and  M. Famulok, ''Nat. Nanotechnol.'' '''19''', 226–236 (2024)
#: [https://doi.org/10.1038/s41565-023-01516-x A rhythmically pulsing leaf-spring nanoengine that drives a passive follower] ([https://doi.org/10.1101/2021.12.22.473833 biorXiv])
# C.K. Wong and J.P.K. Doye, ''Appl. Sci.'' '''12''', 5875 (2022)
#: [https://doi.org/10.3390/app12125875 The free-energy landscape of a mechanically bistable DNA origami] ([http://arxiv.org/abs/2201.08920 arXiv])
# L. Zhang, J. Chen, M. He, X. Su, ''Exploration'' '''2''', 20210265 (2022)
#: [https://doi.org/10.1002/EXP.20210265 Molecular dynamics simulation-guided toehold mediated strand displacement probe for single-nucleotide variants detection]
# F. Mambretti, N. Pedrani, L. Casiraghi, E. M. Paraboschi, T. Bellini, S. Suweis, ''Entropy'' '''24''', 458 (2022)
#: [https://doi.org/10.3390/e24040458 OxDNA to study species interactions] ([https://arxiv.org/abs/2202.05653 arXiv])
# Y.A.G. Fosado, ''Soft Matter'' '''19''', 4820-4828 (2023)
#: [https://doi.org/10.1039/D2SM00221C Nanostars planarity modulates the elasticity of DNA hydrogels] ([https://arxiv.org/abs/2202.06331 arXiv])
# X. Hu, L. Tang, M. Zheng, J. Liu, Z. Zhang, Z. Li, Q. Yang, S. Xiang, L. Fang, Q. Ren, X. Liu, C.Z. Huang, C. Mao and H. Zuo, ''J. Am. Chem. Soc.'' '''144''', 4507–4514 (2022)
#: [https://doi.org/10.1021/jacs.1c12593 Structure-guided designing pre-organization in bivalent aptamers]
# L. Liu F. Hong H. Liu X. Zhou S. Jiang P. Šulc J.-H. Jiang and H. Yan, ''Sci. Adv.'' '''8''', eabm9530 (2022)
#: [https://doi.org/10.1126/sciadv.abm9530 A localized DNA finite-state machine with temporal resolution]
# Y. Xin, P. Piskunen, A. Suma, C. Li, H. Ijäs, S. Ojasalo, I. Seitz, M.A. Kostiainen, G. Grundmeier, V. Linko and A. Keller, ''Small'' '''18''', 2107393 (2022)
#: [https://doi.org/10.1002/smll.202107393 Environment-dependent stability and mechanical properties of DNA origami six-helix bundles with different crossover spacings]
# R.L. Bender, H. Ogasawara, A.V. Kellner, A. Velusamy and K. Salaita, submitted
#: Unbreakable DNA tension probes show that cell adhesion receptors detect the molecular force-extension curve of their ligands ([https://doi.org/10.1101/2022.04.04.487040 bioRxiv])
# E. Benson, R. Carrascosa Marzo, J. Bath and A.J. Turberfield, ''Sci. Robot.'' '''7''', eabn5459 (2022)
#: [https://doi.org/10.1126/scirobotics.abn5459 A DNA molecular printer capable of programmable positioning and patterning in two dimensions]
# A. Dutta, K. Tapio, A. Suma, A. Mostafa, Y. Kanehira, V. Carnevale, G. Bussi and I. Bald, ''Nanoscale'' '''14''', 16467-16478 (2022)
#: [https://doi.org/10.1039/D2NR03664A Molecular states and spin crossover of hemin studied by DNA origami enabled single-molecule surface-enhanced Raman scattering]
# D.J. Hart, J. Jeong, J.C. Gumbart and H.D. Kim,  ''Nucleic Acids Res.'' '''51''', 3030–3040 (2023)
#: [https://doi.org/10.1093/nar/gkad118 Weak tension accelerates hybridization and dehybridization of short oligonucleotides] ([https://doi.org/10.1101/2022.04.19.488836 bioRxiv])
# S. Sensale, P. Sharma and G. Arya, ''Phys. Rev. E'' '''105''', 044136 (2022)
#: [https://doi.org/10.1103/PhysRevE.105.044136 Binding kinetics of harmonically confined random walkers]
# S. Dey, A. Dorey, L. Abraham, Y. Xing, I. Zhang, F. Zhang, S. Howorka and H. Yan, ''Nat. Commun.'' '''13''', 2271 (2022)
#: [https://doi.org/10.1038/s41467-022-28522-2 A reversibly gated protein-transporting membrane channel made of DNA]
# D. Luo, A. Kouyoumdjian, O. Strnad, H. Miao, I. Barišić and I. Viola, submitted (2022)
#: SynopSet: Multiscale visual abstraction set for explanatory analysis of DNA nanotechnology simulations ([https://arxiv.org/abs/2205.01628 arXiv])
# L. Rovigatti, J. Russo, F. Romano, M. Matthies, L. Kroc and P. Sulc, ''Nanoscale'' '''14''', 14268-14275 (2022)
#: [https://doi.org/10.1039/D2NR03533B A simple solution to the problem of self-assembling cubic diamond crystals] ([https://arxiv.org/abs/2205.10680 arXIv])
# J. Bohlin, M. Matthies, E. Poppleton, J. Procyk, A. Mallya, H. Yan and P. Šulc, ''Nat. Protoc.'' '''17''', 1762–1788 (2022)
#: [https://doi.org/10.1038/s41596-022-00688-5 Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView]
# C. Zhou, D. Yang, S. Sensale, P. Sharma, D. Wang, L. Yu, G. Arya, Y. Ke and P. Wang, ''Sci. Adv'' '''8''', eade3003 (2022)
#: [https://doi.org/10.1126/sciadv.ade3003 A bistable and reconfigurable molecular system with encodable bonds] ([https://doi.org/10.21203/rs.3.rs-1706596/v1 Research Square])
# R. Li, M. Zheng, A.S. Madhvacharyula, Y. Du, C. Mao and J.H. Choi, ''Biophys. J.'' '''121''', 4078-4090 (2022)
#: [https://doi.org/10.1016/j.bpj.2022.09.036 Mechanical deformation behaviors and structural properties of ligated DNA crystals] ([https://doi.org/10.1101/2022.06.13.495931 bioRxiv])
# C. Xie, Y. Hu, Z. Chen, K. Chen and L. Pan, ''Nanotechnology'' '''33''', 405603 (2022)
#: [https://doi.org/10.1088/1361-6528/ac7d62 Tuning curved DNA origami structures through mechanical design and chemical adducts]
# F. Fontana, T. Bellini and M. Todisco, ''Macromolecules'' '''55''', 5946–5953 (2022)
#: [https://doi.org/10.1021/acs.macromol.2c00856 Liquid Crystal Ordering in DNA Double Helices with Backbone Discontinuities]
# Z. Weng, H. Yu, W. Luo, L. Zhang, Z. Zhang, T. Wang, Q. Liu, Y. Guo, Y. Yang, J. Li, L. Yang, L. Dai, Q. Pu, X. Zhou and G. Xie, ''Anal. Chim. Acta'' '''1199''', 339568 (2022)
#: [https://doi.org/10.1016/j.aca.2022.339568 Specific and robust hybridization based on double-stranded nucleic acids with single-base resolution]
# J. Bohlin, A.J. Turberfield, A.A. Louis and P. Šulc, ''ACS Nano'' '''17''', 5387–5398 (2023)
#: [https://doi.org/10.1021/acsnano.2c09677 Designing the self-assembly of arbitrary shapes using minimal complexity building blocks] ([https://arxiv.org/abs/2207.06954 arXiv])
# Y. Deng, Y. Tan, Y. Zhang, L. Zhang, C. Zhang, Y. Ke and X. Su, ''ACS Appl. Mater. Interfaces'' '''14''', 34470–34479 (2022)
#: [https://doi.org/10.1021/acsami.2c09488 Design of uracil-modified DNA nanotubes for targeted drug release via DNA-modifying enzyme reactions]
# J. G. Lee, K. S. Kim, J. Y. Lee and D.-N. Kim, ''ACS Nano'' '''16''', 4289–4297 (2022)
#: [https://doi.org/10.1021/acsnano.1c10347 Predicting the free-form shape of structured DNA assemblies from their lattice-based design blueprint]
# M. Micheloni, L. Petrolli, G. Lattanzi and R. Potestio, ''Biophys. J.'' '''122''', 3314-3322 (2023)
#: [https://doi.org/10.1016/j.bpj.2023.07.008 Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations] ([https://doi.org/10.1101/2022.07.03.498607 bioRxiv])
# A. Elonen, A.K. Natarajan, I. Kawamata, L. Oesinghaus, A. Mohammed, J. Seitsonen, Y. Suzuki, F. C. Simmel, A. Kuzyk and P. Orponen, ''ACS Nano'' '''16''', 16608–16616 (2022)
#: [https://doi.org/10.1021/acsnano.2c06035 Algorithmic design of 3D wireframe RNA polyhedra] ([https://doi.org/10.1101/2022.04.27.489653 bioRxiv])
# D. Fu, R.P. Narayanan, A. Prasad, F. Zhang, D. Williams, J.S. Schreck, H. Yan and J. Reif, ''Sci. Adv.'' '''8''', ade4455 (2022)
#: [https://doi.org/10.1126/sciadv.ade4455 Automated design of 3D DNA origami with non-rasterized 2D curvature]
# N. Chauhan, Y. Xiong, S. Ren, A. Dwivedy, N. Magazine, L. Zhou, X. Jin, T. Zhang, B.T. Cunningham, S. Yao, W. Huang and X. Wang, ''J. Am. Chem. Soc.'' '''145''', 20214–20228 (2023)
#: [https://doi.org/10.1021/jacs.2c04835 Net-shaped DNA nanostructures designed for rapid/sensitive detection and potential inhibition of the SARS-CoV-2 virus]
# A. Mills, N. Aissaoui, D. Maurel, J. Elezgaray, F. Morvan, J. J. Vasseur, E. Margeat, R.B. Quast, J. Lai Kee-Him, N. Saint, C. Benistant, A. Nord, F. Pedaci and G. Bellot, ''Nat. Commun.'' '''13''', 3182 (2022)
#: [https://doi.org/10.1038/s41467-022-30745-2 A modular spring-loaded actuator for mechanical activation of membrane proteins]
# T. Panczyk, K. Nieszporek and P. Wolski, ''Molecules'' '''27''', 4915 (2022)
#: [https://doi.org/10.3390/molecules27154915 Stability and existence of noncanonical i-motif DNA structures in computer simulations based on atomistic and coarse-grained force fields]
# E.E. Kurisinkal, V. Caroprese, M.M. Koga, D. Morzy and M.M.C. Bastings, ''Molecules'' '''27''' 4968 (2022)
#: [https://doi.org/10.3390/molecules27154968 Selective integrin α5β1 targeting through spatially constrained multivalent DNA-based nanoparticles]
# R.P. Narayanan, J. Procyk, P. Nandi, A. Prasad, Y. Xu, E. Poppleton, D. Williams, F. Zhang, H. Yan, P.-L. Chiu, N. Stephanopoulos and P. Šulc, ''ACS Nano'' '''16''', 14086–14096 (2022)
#: [https://doi.org/10.1021/acsnano.2c04013 Coarse-grained simulations for the characterization and optimization of hybrid protein–DNA nanostructures]
# J. Wang, Y. Wei, P. Zhang, Y. Wang, Q. Xia, X. Liu, S. Luo, J. Shi, J. Hu, C. Fan, B. Li, L. Wang, X. Zhou and J. Li, ''Nano Lett.'' '''22''', 7173–7179 (2022)
#: [https://doi.org/10.1021/acs.nanolett.2c02447 Probing heterogeneous folding pathways of DNA origami self-assembly at the molecular level with atomic force microscopy]
# S. Li, Y. Coffinier, C. Lagadec, F. Cleri, K. Nishiguchi, A. Fujiwara, T. Fujii, S.-H. Kim and N.Clément, ''Biosens. Bioelectron.'' '''216''', 114643 (2022)
#: [https://doi.org/10.1016/j.bios.2022.114643 Redox-labelled electrochemical aptasensors with nanosupported cancer cells]
# S. Bianco, T. Hu, O. Henrich and S. W.Magennis, ''Biophysical Reports'' '''2''', 100070 (2022)
#: [https://doi.org/10.1016/j.bpr.2022.100070 Heterogeneous migration routes of DNA triplet repeat slip-outs]
# Y. Li, C. Maffeo, H. Joshi, A. Aksimentiev, B. Ménard and R. Schulman, ''Sci. Adv.'' '''8''', eabq4834 (2022)
#:[https://doi.org/10.1126/sciadv.abq4834 Leakless end-to-end transport of small molecules through micron-length DNA nanochannels]
# G. Kloes, T.J.D. Bennett, A. Chapet-Batlle, A. Behjatian, A.J. Turberfield and M. Krishnan, ''Nano Lett.''  '''22''', 7834–7840 (2022)
#: [https://doi.org/10.1021/acs.nanolett.2c02485 Far-field electrostatic signatures of macromolecular 3D conformation]
# L. Guo, Y. Zhang, Y. Wang, M. Xie, J. Dai, Z. Qu, M. Zhou, S. Cao, J. Shi, L. Wang, X. Zuo, C. Fan and J. Li, ''Angew. Chem. Int. Ed.'' '''61''', e202117168 (2022)
#: [https://doi.org/10.1002/anie.202117168 Directing multivalent aptamer-receptor binding on the cell surface with programmable atom-like nanoparticles]
# N. Xie, M. Li, Y. Wang, H. Lv, J. Shi, J. Li, Q. Li, F. Wang and C. Fan, ''J. Am. Chem. Soc.'' '''144''', 9479–9488 (2022)
#: [https://doi.org/10.1021/jacs.2c03258 Scaling Up Multi-bit DNA Full Adder Circuits with Minimal Strand Displacement Reactions]
# E. Lattuada, T. Pietrangeli and F. Sciortino, ''J. Chem. Phys.'' '''157''', 135101 (2022)
#: [https://doi.org/10.1063/5.0117047 Interpenetrating gels in binary suspensions of DNA nanostars]
# X. Chen, Y. Wang, X. Dai, L. Ding, J. Chen, G. Yao, X. Liu, S. Luo, J. Shi, L. Wang, R. Nechushtai, E. Pikarsky, I. Willner, C. Fan, and J. Li, ''J. Am. Chem. Soc.'' '''144''', 6311–6320 (2022)
#: [https://doi.org/10.1021/jacs.1c13116 Single-Stranded DNA-Encoded Gold Nanoparticle Clusters as Programmable Enzyme Equivalents]
# Q. Kou, L. Wang, L. Zhang, L. Ma, S. Fu and X. Su, ''Small'' '''18''', 2205191 (2022)
#: [https://doi.org/10.1002/smll.202205191 Simulation-assisted localized DNA logical circuits for cancer biomarkers detection and imaging]
# P. E. Beshay, A. Kucinic, N. Wile, P. Halley, L. Des Rosiers, A. Chowdhury, J. L. Hall, C. E. Castro and M. W. Hudoba, ''The Biophysicist'' '''4''', 68–81 (2023)
#: [https://doi.org/10.35459/tbp.2022.000228 Translating DNA origami nanotechnology to middle school, high school, and undergraduate laboratories] ([https://doi.org/10.1101/2022.09.15.508130 bioRxiv])
# A. Büchl, E. Kopperger, M. Vogt, M. Langecker, F.C.Simmel and J. List, ''Biophys. J.'' '''121''', 4849-4859 (2022)
#: [https://doi.org/10.1016/j.bpj.2022.08.046 Energy landscapes of rotary DNA origami devices determined by fluorescence particle tracking]
# E. Poppleton, M. Matthies, D. Mandal, F. Romano, P. Šulc and L. Rovigatti,  ''J. Open Source Softw.'' '''8''', 4693 (2023)
#: [https://doi.org/10.21105/joss.04693 oxDNA: coarse-grained simulations of nucleic acids made simple]
# A. Suma, V. Carnevale and C. Micheletti, ''Phys. Rev. Lett.'' '''130''', 048101 (2023)
#: [https://doi.org/10.1103/PhysRevLett.130.048101 Nonequilibrium Thermodynamics of DNA Nanopore Unzipping] ([https://doi.org/10.48550/arXiv.2212.05882 arXiv])
# Y. Tang, H. Liu, Q. Wang, X. Qi, L. Yu, P. Šulc, F. Zhang, H. Yan and S. Jiang, ''J. Am. Chem. Soc.'' 145, 25, 13858–13868 (2023)
#: [https://doi.org/10.1021/jacs.3c03044 DNA Origami Tessellations]
# M. DeLuca, W.G. Pfeifer, B. Randoing,  C.-M. Huang, M.G. Poirier, C.E. Castro and G. Arya, ''Nanoscale'' '''15''', 8356-8365 (2023)
#: [https://doi.org/10.1039/D2NR05813H Thermally reversible pattern formation in arrays of molecular rotors]
# T. Liang, C. Yang, X. Song, Y. Feng, Y. Liu and H. Chen, ''Phys. Rev. E'' '''108''', 014406 (2023)
#: [https://doi.org/10.1103/PhysRevE.108.014406 Quantification of macromolecule crowding at single-molecule level]
# D. Lysne, T. Hachigian, C. Thachuk, J. Lee and E. Graugnard ''J. Am. Chem. Soc.'' '''145''', 16691–16703 (2023) 
#: [https://doi.org/10.1021/jacs.3c04344 Leveraging Steric Moieties for Kinetic Control of DNA Strand Displacement Reactions]
# A. Kucinic, C.-M. Huang, J. Wang, H.-J. Su and  C.E. Castro, ''Nanoscale'', '''15''' 562-572 (2023)
#: [https://doi.org/10.1039/D2NR05416G DNA origami tubes with reconfigurable cross-sections]
# Y. Zhang, X. Yin, C. Cui, K. He, F. Wang, J. Chao, T. Li, X. Zuo, A. Li, L. Wang, N. Wang, X. Bo and C. Fan, ''Sci. Adv.''  '''9''', adf8263 (2023)
#: [https://doi.org/10.1126/sciadv.adf8263 Prime factorization via localized tile assembly in a DNA origami framework]
# W.G. Pfeifer, C.-M. Huang, M. G. Poirier, G. Arya and C. E. Castro, ''Sci. Adv.'' '''9''', adi0697 (2023)
#: [https://doi.org/10.1126/sciadv.adi0697 Versatile computer-aided design of free-form DNA nanostructures and assemblies] ([https://doi.org/10.1101/2023.03.30.535006 bioRxiv])
# M. Lolaico, S. Blokhuizen, B. Shen, Y. Wang, and B. Högberg, ''ACS Nano'' '''17''', 6565–6574 (2023)
#: [https://doi.org/10.1021/acsnano.2c11982 Computer-Aided Design of A-Trail Routed Wireframe DNA Nanostructures with Square Lattice Edges]
# Y. Wang, A. Kucinic, L. Des Rosiers, P.E. Beshay, N. Wile, M.W. Hudoba and C.E. Castro, ''Appl. Sci.'' '''13''', 3208 (2023)
#: [https://doi.org/10.3390/app13053208 Mechanical Design of DNA Origami in the Classroom]
# D. Morzy, C. Tekin, V. Caroprese, R. Rubio-Sánchez, L. Di Michele and M.M.C. Bastings, ''Nanoscale'' '''15''', 2849-2859 (2023)
#: [https://doi.org/10.1039/D2NR05368C Interplay of the mechanical and structural properties of DNA nanostructures determines their electrostatic interactions with lipid membranes]
# L. Zhang, H. Zhao, H. Yang and X. Su, ''Biosens. Bioelectron.'' '''239''', 115622 (2023)
#:[https://doi.org/10.1016/j.bios.2023.115622 Coarse-grained model simulation-guided localized DNA signal amplification probe for miRNA detection]
# Y.-P. Qiao, C.-L. Ren and Y.-Q. Ma ''J. Phys. Chem. B'' '''127''', 4015–4021 (2023)
#: [https://doi.org/10.1021/acs.jpcb.2c08618 Two Different Ways of Stress Release in Supercoiled DNA Minicircles under DNA Nick]
# K. Cervantes-Salguero, Y.A. Gutiérrez Fosado, W. Megone, J.E. Gautrot and M. Palma, ''Molecules'' '''28''', 3686 (2023)
#: [https://doi.org/10.3390/molecules28093686 Programmed self-assembly of DNA nanosheets with discrete single-molecule thickness and interfacial mechanics: Design, simulation, and characterization]
# H.L. Too and Z. Wang, ''Nanoscale'' '''15''', 11915-11926 (2023)
#: [https://doi.org/10.1039/D3NR01058A Exhaustive classification and systematic free-energy profile study of single-stranded DNA inter-overhang migration]
# D. Saliba, X. Luo, F.J. Rizzuto and H.F. Sleiman, ''Nanoscale'' '''15''', 5403-5413 (2023)
#: [https://doi.org/10.1039/D2NR06185F Programming rigidity into size-defined wireframe DNA nanotubes]
# J. Lee and S. Lee, ''Anal. Chem.'' '''95''', 1856–1866 (2023) 
#: [https://doi.org/10.1021/acs.analchem.2c03378 Non-invasive, reliable, and fast quantification of DNA loading on gold nanoparticles by a one-step optical measurement]
# X. Shen, Q. Ouyang, H. Tan, J. Ouyang and N. Na, ''Anal. Chem.'' '''95''', 5903–5910 (2023)
#: [https://doi.org/10.1021/acs.analchem.2c04916 Computation-assisted design of ssDNA framework nanorobots for cancer logical recognition, toehold disintegration, visual dual-diagnosis, and synergistic therapy]
# L. Tang, M. Huang, M. Zhang, Y. Pei, Y. Liu, Y. Wei, C. Yang, T. Xie, D. Zhang, R. Zhou, Y. Song, J. Song, ''Small Methods'' '''7''', 2300327 (2023)
#: [https://doi.org/10.1002/smtd.202300327 De novo evolution of an antibody-mimicking multivalent aptamer via a DNA framework]
# Z. Zheng, S.H. Kim, A. Chovin, N. Clement and C. Demaille, ''Chem. Sci.'' '''14''', 3652-3660 (2023)
#: [https://doi.org/10.1039/D3SC00320E Electrochemical response of surface-attached redox DNA governed by low activation energy electron transfer kinetics]
# M. Vogt, M. Langecker, M. Gouder, E. Kopperger, F. Rothfischer, F.C. Simmel and J. List, ''Nature Physics'' '''19''', 741–751 (2023)
#: [https://doi.org/10.1038/s41567-023-01938-3 Storage of mechanical energy in DNA nanorobotics using molecular torsion springs]
# C. Xie, Y. Hu, K. Chen, Z. Chen and L. Pan, ''Commun. Comput. Inf. Sci.'', '''1801''', 647–654 (2023)
#: [https://doi.org/10.1007/978-981-99-1549-1_51 Tuning Geometric Conformations of Curved DNA Structures by Controlling Positions of Nicks]
# S. Yu, J. Zhao, R. Chu, X. Li, G. Wu and X. Meng, ''Entropy'' '''25''', 796 (2023) 
#: [https://doi.org/10.3390/e25050796 Anomalous diffusion of polyelectrolyte segments on supported charged lipid bilayers]
# I. Madrid, Z. Zheng, C. Gerbelot, A. Fujiwara, S. Li, S. Grall, K. Nishiguchi, S.H. Kim, A. Chovin, C. Demaille and N. Clement, ''ACS Nano'' '''17''', 17031–17040 (2023)
#: [https://doi.org/10.1021/acsnano.3c04349 Ballistic Brownian Motion of Nanoconfined DNA]
# Y. Ma, W. Guo, Q. Mou, X. Shao, M. Lyu, V. Garcia, L. Kong, W. Lewis, C. Ward, Z. Yang, X. Pan, S.S. Yi and Y. Lu, ''Nat. Biotechnol.'' (2023)
#: [https://doi.org/10.1038/s41587-023-01801-z Spatial imaging of glycoRNA in single cells with ARPLA]
# X. Luo, D. Saliba, T. Yang, S. Gentile, K. Mori, P.I. Garcia, T. Das, N. Bagheri, A. Porchetta, A. Guarne, G. Cosa, H.F. Sleiman, ''Angew. Chem. Int. Ed.'' '''62''' e202309869 (2023)
#: [https://doi.org/10.1002/anie.202309869 Minimalist design of wireframe DNA nanotubes: Tunable geometry, size, chirality, and dynamics]
# Y. Zhao, S. Cao, Y. Wang, F. Li, L. Lin, L. Guo, F. Wang, J. Chao, X. Zuo, Y. Zhu, L. Wang, J. Li and C. Fan, ''Nat. Mach. Intell.'' '''5''', 980–990 (2023)
#: [https://doi.org/10.1038/s42256-023-00707-4 A temporally resolved DNA framework state machine in living cells]
# X.R. Liu, I.Y. Loh, W. Siti, H.L. Too, T. Anderson and Z. Wang, ''Nanoscale Horiz.'', '''8''', 827-841 (2023)
#: [https://doi.org/10.1039/D2NH00565D A light-operated integrated DNA walker–origami system beyond bridge burning]
# H. Lv, N. Xie, M. Li, M. Dong, C. Sun, Q. Zhang, L. Zhao, J. Li, X. Zuo, H. Chen, F. Wang and C. Fan, ''Nature'' '''622''', 292–300(2023). 
#: [https://doi.org/10.1038/s41586-023-06484-9 DNA-based programmable gate arrays for general-purpose DNA computing]
# C. Yang, X. Song, Y. Feng, G. Zhao, and Y. Liu, ''J. Phys.: Condens. Matter'' '''35''', 265101 (2023)
#: [https://doi.org/10.1088/1361-648X/acc7eb Stability of DNA and RNA hairpins: a comparative study based on ox-DNA]
# Xiaoya Song, Chao Yang, Yuyu Feng, Hu Chen, and Yanhui Liu, ''Commun. Theor. Phys.'' '''75''', 055601 (2023)
#: [https://doi.org/10.1088/1572-9494/acc64c A common rule for the intermediate state caused by DNA mismatch in single-molecule experiments]
# W. Siti, H.L. Too, T. Anderson, X.R. Liu, I.Y. Loh and Z. Wang, ''Sci. Adv.'' '''9''', adi8444 (2023)
#: [https://dx.doi.org/10.1126/sciadv.adi8444 Autonomous DNA molecular motor tailor-designed to navigate DNA origami surface for fast complex motion and advanced nanorobotics]
# R. Ma, A. Velusamy, S.A. Rashid, B.R. Deal, W. Chen, B. Petrich, R. Li, K. Salaita, ''Nat. Methods'' '''20''', 1666–1671 (2023)
#: [https://doi.org/10.1038/s41592-023-02030-7 Molecular mechanocytometry using tension-activated cell tagging] ([https://doi.org/10.1101/2023.01.10.523449 bioRxiv])
# D. Karna, E. Mano, J. Ji, I. Kawamata, Y. Suzuki and H. Mao, ''Nat. Commun.'' '''14''', 6459 (2023)
#: [https://doi.org/10.1038/s41467-023-41604-z Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies]
# J. Fu, L. Zhang, Y. Long, Z. Liu, G. Meng, H. Zhao, X. Su and S. Shi, ''Anal. Chem.'' '''95''', 16089–16097 (2023)
#: [https://doi.org/10.1021/acs.analchem.3c01861 Multiplexed CRISPR-based nucleic acid detection using a single Cas protein]
# Y. Yang, Q. Lu, Y. Chen, M. DeLuca, G. Arya, Y. Ke and S. Zauscher, ''Angew. Chem. Int. Ed.'' '''62''', e202311727 (2023)
#: [https://doi.org/10.1002/anie.202311727 Spatiotemporal control over polynucleotide brush growth on DNA origami nanostructures]
# J.Y. Lee, H. Koh and D.-N. Kim, Nat. Commun. '''14''', 7079 (2023)
#: [https://doi.org/10.1038/s41467-023-42873-4 A computational model for structural dynamics and reconfiguration of DNA assemblies]
# M.C. Engel, J.A. Smith and M.P. Brenner, ''Phys. Rev. X'' '''13''', 041032 (2023)
#: [https://doi.org/10.1103/PhysRevX.13.041032 Optimal control of nonequilibrium systems through automatic differentiation]
# L. Yu, Y. Xu, M. Al-Amin, S. Jiang, M. Sample, A. Prasad, N. Stephanopoulos, P. Šulc, and H. Yan, ''J. Am. Chem. Soc.'' '''145''', 27336–27347 (2023)
#: [https://doi.org/10.1021/jacs.3c07491 CytoDirect: A nucleic acid nanodevice for specific and efficient delivery of functional payloads to the cytoplasm]
# Y.-P. Qiao and C.-L. Ren, ''Langmuir'' '''40''', 109–117 (2024)
#: [https://doi.org/10.1021/acs.langmuir.3c02231 Correlated hybrid DNA structures explored by the oxDNA Model]
# L. Kilwing, P. Lill, B. Nathwani, R. Guerra, E. Benson, T. Liedl and W. M. Shih, ''ACS Nano'' '''18''', 885–893 (2024)
#: [https://doi.org/10.1021/acsnano.3c09522 Multilayer DNA origami with terminal interfaces that are flat and wide-area]
# N. Adžić, C. Jochum, C. N. Likos, E. Stiakakis, ''Small'', '''20''', 2308763 (2024)
#: [https://doi.org/10.1002/smll.202308763 Engineering ultrasoft interactions in stiff all-DNA dendrimers by site-specific control of scaffold flexibility]
# A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and  K. Salaita, ''Nat. Commun.'' '''15''', 704 (2024)
#: [https://doi.org/10.1038/s41467-023-44061-w DNA mechanocapsules for programmable piconewton responsive drug delivery]
# Y. Liu, B. Li, F. Wang, Q. Li, S. Jia, X. Liu, and M. Li, ''ACS Appl. Bio Mater.'' '''7''', 1311–1316 (2024)
#: [https://doi.org/10.1021/acsabm.3c01270 Quantitative analysis of resistance to deformation of the DNA origami framework supported by struts]
# S. He, H. Deng, P. Li, Q. Tian, Y. Yang, J. Hu, H. Li, T. Zhao, H. Ling, Y. Liu, S. Liu and Q. Guo, ''J. Nanobiotechnol.'' '''22''', 39 (2024)
#: Bimodal DNA self-origami material with nucleic acid function enhancement
# B. Babatunde, J. Cagan, R.E. Taylor, ''J. Mech. Des.'' '''146''', 051708 (2024)
#: [https://doi.org/10.1115/1.4064242 An improved shape annealing algorithm for the generation of coated deoxyribonucleic acid origami nanostructures]
# A.S.G. Martins, S.D. Reis, E. Benson, M.M. Domingues, J. Cortinhas, J.A. Vidal Silva, S.D. Santos, N.C. Santos, A.P. Pêgo, P.M.D. Moreno, ''Small'' '''20''', 2309140 (2024)
#: [https://doi.org/10.1002/smll.202309140 Enhancing Neuronal Cell Uptake of Therapeutic Nucleic Acids with Tetrahedral DNA Nanostructures]
# S Dey, R. Rivas-Barbosa, F. Sciortino, E. Zaccarelli and P. Zijlstra, ''Nanoscale'' '''16''', 4872-4879 (2024)
#: [https://doi.org/10.1039/D3NR06140J Biomolecular interactions on densely coated nanoparticles: a single-molecule perspective]
# T. Chen, S. Mao, J. Ma, X. Tang, R. Zhu, D. Mao, X. Zhu, Q. Pan, ''Angew. Chem. Int. Ed'' '''63''', e202319117 (2024)
#: [https://doi.org/10.1002/anie.202319117 Proximity-enhanced functional imaging analysis of engineered tumors]
# Y. Liu, Z. Dai, X. Xie, B. Li, S. Jia, Q. Li, M. Li, C. Fan and X. Liu, ''J. Am. Chem. Soc.'' '''146''', 8, 5461–5469 (2024)
#: [https://doi.org/10.1021/jacs.3c13180 Spacer-programmed two-dimensional DNA origami assembly]
# Z. Zheng, S. Grall, S.H. Kim, A. Chovin, N. Clement and C. Demaille, ''J. Am. Chem. Soc.'' '''146''', 9, 6094–6103 (2024)
#: [https://doi.org/10.1021/jacs.3c13532 Activationless electron transfer of redox-DNA in electrochemical nanogaps]
# M. Sample, M. Matthies and P. Šulc, ''ACS Nano'' '''18''', 30004–30016 (2024)
#: [https://doi.org/10.1021/acsnano.4c10796 Hairygami: Analysis of DNA nanostructure's conformational change driven by functionalizable overhangs] ([https://doi.org/10.48550/arXiv.2302.09109 arXiv])
# M. Sample, M. Matthies and P. Šulc, ''2023 Winter Simulation Conference (WSC)'', San Antonio, TX, USA, pp. 91-105 (2023)
#: [https://doi.org/10.1109/WSC60868.2023.10407580 Coarse-grained simulations of DNA and RNA systems with oxDNA and oxRNA models: Introductory tutorial] ([https://doi.org/10.48550/arXiv.2308.01455 arXiv])
# V. Caroprese, C. Tekin, V. Cencen, M. Mosayebi, T.B. Liverpool, D.N. Woolfson, G. Fantner, M.M.C. Bastings, submitted
#: Structural flexibility dominates over binding strength for supramolecular crystallinity ([https://doi.org/10.1101/2023.09.04.556250 bioRxiv])
# C. Shi, D. Yang, X.Ma, L. Pan, Y. Shao, G. Arya, Y. Ke, C. Zhang, F. Wang, X. Zuo, M. Li and P. Wang, ''Angew. Chem. Int. Ed.'' '''63''' e202320179 (2024)
#: [https://doi.org/10.1002/anie.202320179 A programmable DNAzyme for the sensitive detection of nucleic acids] ([https://doi.org/10.1101/2023.08.20.23294196 medRxiv])
# F. Smith, A. Sengar, G.‐B.V. Stan, T.E. Ouldridge, M. Stevens, J. Goertz and W. Bae, submitted
#: Overcoming the speed limit of four‐way DNA branch migration with bulges in toeholds ([https://doi.org/10.1101/2023.05.15.540824 bioRxiv])
# K. Gallagher, J. Yu, D.A. King, R. Liu, E. Eiser, ''APL Mater.'' '''11''', 061129 (2023)
#: [https://doi.org/10.1063/5.0145570 Towards new liquid crystal phases of DNA mesogens] ([https://doi.org/10.48550/arXiv.2302.03501 arXiv])
# G.B.M. Wisna, D. Sukhareva, J. Zhao, D. Satyabola, M. Matthies, S. Roy, P. Šulc, H. Yan and R.F. Hariadia, submitted
#: High-speed 3D DNA-PAINT and unsupervised clustering for unlocking 3D DNA origami cryptography ([https://doi.org/10.1101/2023.08.29.555281 bioRxiv])
# H. Koh, J.Y. Lee, J.G. Lee, submitted
#: Forming superhelix of double stranded DNA from local deformation ([https://doi.org/10.48550/arXiv.2307.04597 arXiv])
# N.P. Agarwal and A. Gopinath, submited
#: DNA origami 2.0 ([https://doi.org/10.1101/2022.12.29.522100 bioRxiv])
# J.M. Weck and A. Heuer-Jungemann, submitted
#: Fully addressable, designer superstructures assembled from a single modular DNA origami ([https://doi.org/10.1101/2023.09.14.557688 bioRxiv])
# Y. Xu, R. Zheng, A. Prasad, M. Liu, Z. Wan, X. Zhou, R.M. Porter, M. Sample, E. Poppleton, J. Procyk, H. Liu, Y. Li,  S. Wang, H. Yan, P. Sulc,  N. Stephanopoulos, submitted
#: High-affinity binding to the SARS-CoV-2 spike trimer by a nanostructured, trivalent protein-DNA synthetic antibody ([https://doi.org/10.1101/2023.09.18.558353 bioRxiv])
# H. Liu, M. Matthies, J. Russo, L. Rovigatti, R.P. Narayanan, T. Diep, D. McKeen, O. Gang, N. Stephanopoulos, F. Sciortino, H. Yan, F. Romano and P. Šulc, ''Science'' '''384''', 776-781 (2024)
#: [https://doi.org/10.1126/science.adl5549 Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments] ([https://doi.org/10.48550/arXiv.2310.10995 arXiv])
# L. Grabenhorst, M. Pfeiffer, T. Schinkel, M. Kümmerlin, J.B. Maglic, G.A. Brüggenthies, F. Selbach, A.T. Murr, P. Tinnefeld, V. Glembockyte, ''Nat. Nanotechnol.'' accepted (2024)
#: [https://doi.org/10.1038/s41565-024-01804-0 Engineering modular and tunable single-molecule sensors by decoupling sensing from signal output] ([https://doi.org/10.1101/2023.11.06.565795 bioRxiv])
# F. Tosti Guerra, E. Poppleton, P. Šulc, L. Rovigatti, submitted
#: nNxB: a new coarse-grained model for RNA and DNA nanotechnology ([https://doi.org/10.48550/arXiv.2311.03317 arXiv])
# E.J. Ratajczyk, P. Šulc, A.J. Turberfield, J.P.K. Doye and A.A. Louis, ''J. Chem. Phys.'' '''160''', 115101 (2024)
#: [https://doi.org/10.1063/5.0199558 Coarse-grained modelling of DNA-RNA hybrids] ([https://doi.org/10.48550/arXiv.2311.07709 arXiv])
# M. DeLuca, D. Duke, T. Ye, M. Poirier, Y. Ke, C. Castro and G. Arya, ''Nat. Commun.'' '''15''', 3015 (2024)
#: [https://doi.org/10.1038/s41467-024-46998-y Mechanism of DNA origami folding elucidated by mesoscopic simulations] ([https://doi.org/10.1101/2023.06.20.545758 bioRxiv])
# S. Cristofaro, L. Querciagrossa, L. Soprani, T.P. Fraccia, T. Bellini, R. Berardi, A. Arcioni, C. Zannoni, L. Muccioli, and S. Orlandi, ''Biomacromolecules'' '''25''', 3920–3929 (2024)
#: [https://doi.org/10.1021/acs.biomac.3c01435 Simulating the lyotropic phase behavior of a partially self-complementary DNA tetramer]
# A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and K. Salaita, ''Nat. Commun.'' '''15''', 704 (2024)
#: [https://doi.org/10.1038/s41467-023-44061-w DNA mechanocapsules for programmable piconewton responsive drug delivery]
# A. Voorspoels, J. Gevers, S. Santermans, N. Akkan, K. Martens, K. Willems, P. Van Dorpe, and A.S. Verhulst, ''J. Phys. Chem. A'' '''128''', 3926–3933 (2024)
#: [https://doi.org/10.1021/acs.jpca.4c01772 Design principles of DNA-barcodes for nanopore-FET readout, based on molecular dynamics and TCAD simulations]
# F. Tosti Guerra, E. Poppletoni, P. Šulc and L. Rovigatti, ''J. Chem. Phys.'' '''160''', 205102 (2024)
#: [https://doi.org/10.1063/5.0202829 ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems] ([https://doi.org/10.48550/arXiv.2311.03317 arXiv])
# Y. Wang, I. Baars, I. Berzina, I. Rocamonde-Lago, B. Shen, Y. Yang, M. Lolaico, J. Waldvogel, I. Smyrlaki, K. Zhu, R.A. Harris and B. Högberg, ''Nat. Nanotechnol.'' '''19''', 1366–137 (2024)
#: [https://doi.org/10.1038/s41565-024-01676-4 A DNA robotic switch with regulated autonomous display of cytotoxic ligand nanopatterns]
# W. Ji, X. Xiong, M. Cao, Y. Zhu, L. Li, F. Wang, C. Fan and H. Pei, ''Nat. Chem.'' '''16''',  1408–1417 (2024)
#: [https://doi.org/10.1038/s41557-024-01565-2 Encoding signal propagation on topology-programmed DNA origami]
# M. van Galen, A. Bok, T. Peshkovsky, J. van der Gucht, B. Albada and J. Sprakel, ''Nat. Chem.'' accepted (2024)
#: [https://doi.org/10.1038/s41557-024-01571-4 De novo DNA-based catch bonds]
# Y. Hu, J. Rogers, Y. Duan, A. Velusamy, S. Narum, S. Al Abdullatif and K. Salaita, ''Nat. Nanotechnol.'' '''19''', 1674–1685 (2024)
#: [https://doi.org/10.1038/s41565-024-01723-0 Quantifying T cell receptor mechanics at membrane junctions using DNA origami tension sensors]
# D. Svenšek, J. Sočan and M. Praprotnik, ''Macromol. Rapid Commun.'' accepted 2400382 (2024)
#: [https://doi.org/10.1002/marc.202400382 Density–nematic coupling in isotropic solution of DNA: Multiscale model]
# M. Mogheiseh and R.H. Ghasemi, ''J. Chem. Phys.'' '''161''', 045101 (2024)
#: [https://doi.org/10.1063/5.0214313 Design and simulation of a wireframe DNA origami nanoactuator]
# S.H. Wong, S.N. Kopf, V. Caroprese, Y. Zosso, D. Morzy, M.M.C. Bastings, ''Nano Lett.'' '''24''', 11210–11216 (2024)
#: [https://doi.org/10.1021/acs.nanolett.4c02564 Modulating the DNA/lipid interface through multivalent hydrophobicity]
# G. Nava, T. Carzaniga, L. Casiraghi, E. Bot, G. Zanchetta, F. Damin, M. Chiari, G. Weber, T. Bellini, L. Mollica and M. Buscaglia, ''Nucl. Acids Res.'' '''52''', 8661–8674 (2024)
#: [https://doi.org/10.1093/nar/gkae576 Weak-cooperative binding of a long single-stranded DNA chain on a surface]
# Y. Du, R. Li, A.S. Madhvacharyula, A.A. Swett, J.H. Choi, submitted
#: DNA nanostar structures with tunable auxetic properties ([https://doi.org/10.1101/2023.12.22.573109  bioRxiv])
# G.M. Roozbahani, P. Colosi, A. Oravecz, E.M. Sorokina, W. Pfeifer, S. Shokri, Y. Wei, P. Didier, M. DeLuca, G. Arya, L. Tora, M. Lakadamyali, M.G. Poirier, C. E. Castro
#: Piggybacking functionalized DNA nanostructures into live cell nuclei ([https://doi.org/10.1101/2023.12.30.573746 bioRxiv])
# A. Walbrun, T. Wang, M. Matthies, P. Šulc, F.C. Simmel, M. Rief, ''Nat. Commun.'' '''15''', 7564 (2024)
#: [https://doi.org/10.1038/s41467-024-51813-9 Single-Molecule Force Spectroscopy of Toehold-Mediated Strand Displacement] ([https://doi.org/10.1101/2024.01.16.575816 bioRxiv])
# S. Chandrasekhar, T.P. Swope, F. Fadaei, D.R. Hollis, R. Bricker, D. Houser, J. Portman, T.L. Schmidt, submitted
#: Bending Unwinds DNA ([https://doi.org/10.1101/2024.02.14.579968 bioRxiv])
# X. Liu, F. Liu, H. Chhabra, C. Maffeo, Q. Huang, A. Aksimentiev, T. Arai, ''Nat. Commun.'' '''15''', 7210 (2024)
#: [https://doi.org/10.1038/s41467-024-51630-0 A lumen-tunable triangular DNA nanopore for molecular sensing and cross-membrane transport] ([https://doi.org/10.21203/rs.3.rs-3878148/v1  ResearchSquare])
# L. Yang, G. Pecastaings, C. Drummond and J. Elezgaray, ''Nano Lett.'' '''24''', 13481–13486 (2024)
#: [https://doi.org/10.1021/acs.nanolett.4c02302 Driving DNA nanopore membrane insertion through dipolar coupling]
# J.-Y. Liou, M. Awan, K. Leyba, P. Šulc, S. Hofmeyr, C.-J. Wu and S. Forrest, ''ACM Trans. Evol. Learn. Optim.'' accepted (2024)
#: [https://doi.org/10.1145/3703920 Evolving to find optimizations humans miss: Using evolutionary computation to improve GPU code for bioinformatics applications]
# C. Karfusehr, M. Eder, F.C. Simmel
#: Self-assembled cell-scale containers made from DNA origami membranes ([https://doi.org/10.1101/2024.02.09.579479 bioRxiv])
# M.T. Luu, J.F. Berengut, J.K.D. Singh, K.C.D. Glieze, M. Turner, K. Skipper, S. Meppat, H. Fowler, W. Close, J.P.K. Doye, A. Abbas, S.F.J. Wickham, submitted
#: Reconfigurable multi-component nanostructures built from DNA origami voxels ([https://doi.org/10.1101/2024.03.10.584331 bioRxiv])
# M.P. Tran,  T. Chakraborty,  E. Poppleton,  L. Monari,  F. Giessler and  K. Göpfrich, submitted
#: Genetic encoding and expression of RNA origami cytoskeletons in synthetic cells ([https://doi.org/10.1101/2024.06.12.598448 bioRxiv])
# V. Bukina and A. Božič,  ''Biophys. J.'' '''123''', 3397-3407 (2024)
#: [https://doi.org/10.1016/j.bpj.2024.08.004 Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA] ([https://doi.org/10.1101/2024.04.17.589867 bioRxiv])
# R. Walker-Gibbons, X. Zhu, A. Behjatian, T.J.D. Bennett and M. Krishnan, Sci. Rep. 14, 20582 (2024)
#: [https://doi.org/10.1038/s41598-024-70641-x Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations]
# E.J. Ratajczyk, J. Bath, P. Sulc, J.P.K. Doye, A.A. Louis, A.J. Turberfield, submitted
#: Controlling DNA-RNA strand displacement kinetics with base distribution ([https://doi.org/10.1101/2024.08.06.606789 bioRxiv])
# A. Suma and C. Micheletti, submitted
#: Unzipping of knotted DNA via nanopore translocation ([https://doi.org/10.48550/arXiv.2407.11567 arXiv])
# G. Mattiotti, M. Micheloni, L. Petrolli, L. Tubiana, S. Pasquali, R. Potestio, submitted.
#: Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model ([https://doi.org/10.48550/arXiv.2408.03662 arXiv])
# S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, submitted.
#: How we simulate DNA origami ([https://doi.org/10.48550/arXiv.2409.13206 arXiv])
# Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted
#: Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells ([https://doi.org/10.21203/rs.3.rs-4897446/v1 ResearchSquare])
# R.K. Krueger, M.C. Engel, R. Hausen, M.P. Brenner, submitted (2024)
#: A Differentiable Model of Nucleic Acid Dynamics ([https://arxiv.org/abs/2411.09216 arXiv])
# Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted
#: Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells ([https://doi.org/10.21203/rs.3.rs-4897446/v1 ResearchSquare])
# K. Zhou, M. Chung, J. Cheng, J.T. Powell, J. Liu, Y. Xiong, M.A. Schwartz and C. Lin, submitted.
#: DNA nanodevice for analysis of force-activated protein extension and interactions ([https://doi.org/10.1101/2024.10.25.620262 bioRxiv])
# W.-S. Wei, T.E. Videbæk, D. Hayakawa, R. Saha, W.B. Rogers, S. Fraden, submitted
#: Economical and versatile subunit design principles for self-assembled DNA origami structures ([https://doi.org/10.48550/arXiv.2411.09801 arXiv])


We are also maintaining a list of all published papers using oxDNA at [https://publons.com/researcher/3051012/oxdna-oxrna/ publons].
We are also maintaining a list of all published papers using oxDNA at [https://publons.com/researcher/3051012/oxdna-oxrna/ publons].

Latest revision as of 13:12, 23 November 2024

  1. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, Phys. Rev. Lett. 104, 178101 (2010)
    DNA Nanotweezers Studied with a Coarse-Grained Model of DNA (arXiv)
  2. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Phys. Condens. Matter. 22, 104102 (2010)
    Extracting bulk properties of self-assembling systems from small simulations (arXiv)
  3. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Chem. Phys, 134, 085101 (2011)
    Structural, mechanical and thermodynamic properties of a coarse-grained DNA model (arXiv)
  4. T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011.
    Coarse-grained modelling of DNA and DNA self-assembly
  5. F. Romano, A. Hudson, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, J. Chem. Phys. 136, 215102 (2012)
    The effect of topology on the structure and free energy landscape of DNA kissing complexes (arXiv)
  6. C. De Michele, L. Rovigatti, T. Bellini, F. Sciortino, Soft Matter 8, 8388 (2012)
    Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link (arXiv)
  7. C. Matek, T. E. Ouldridge, A. Levy, J. P. K. Doye, A. A. Louis, J. Phys. Chem. B 116, 1161-11625 (2012)
    DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism (arXiv)
  8. P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, J. Chem. Phys. 137, 135101 (2012)
    Sequence-dependent thermodynamics of a coarse-grained DNA model (arxiv)
  9. T.E. Ouldridge, J. Chem. Phys. 137, 144105 (2012)
    Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble (arXiv)
  10. F. Romano, D. Chakraborty, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, J. Chem. Phys. 138, 085101 (2013)
    Coarse-grained simulations of DNA overstretching (arXiv)
  11. T. E. Ouldridge, R. L. Hoare, A. A. Louis, J. P. K. Doye, J. Bath, A. J. Turberfield, ACS Nano 7, 2479-2490 (2013)
    Optimizing DNA nanotechnology through coarse-grained modelling: a two-footed DNA walker
  12. T. E. Ouldridge, P. Šulc, F. Romano, J. P. K. Doye, A. A. Louis, Nucleic Acids Res. 41, 8886-8895 (2013)
    DNA hybridization kinetics: zippering, internal displacement and sequence dependence (arXiv)
  13. J.P.K. Doye, T. E. Ouldridge, A. A. Louis, F. Romano, P. Šulc, C. Matek, B.E.K. Snodin, L. Rovigatti, J. S. Schreck, R.M. Harrison, W.P.J. Smith, Phys. Chem. Chem. Phys 15, 20395-20414 (2013)
    Coarse-graining DNA for simulations of DNA nanotechnology (arXiv)
  14. N. Srinivas, T. E. Ouldridge, P. Šulc, J. M. Schaeffer, B. Yurke, A. A. Louis, J. P. K. Doye, E. Winfree, Nucleic Acids Res. 41, 10641-10658 (2013)
    On the biophysics and kinetics of toehold-mediated DNA strand displacement
  15. P. Šulc, T. E. Ouldridge, F. Romano, J. P. K. Doye, A. A. Louis, Natural Computing 13, 535 (2014)
    Simulating a burnt-bridges DNA motor with a coarse-grained DNA model (arXiv)
  16. L. Rovigatti, F. Bomboi, F. Sciortino, J. Chem. Phys. 140, 154903 (2014)
    Accurate phase diagram of tetravalent DNA nanostars (arXiv)
  17. P. Šulc, F. Romano, T. E. Ouldridge, J. P. K. Doye, A. A. Louis, J. Chem. Phys. 140, 235102 (2014)
    A nucleotide-level coarse-grained model of RNA (arXiv)
  18. L. Rovigatti, F. Smallenburg, F. Romano, F. Sciortino, ACS Nano 8, 3567-3574 (2014)
    Gels of DNA Nanostars Never Crystallise
  19. Q. Wang, B. M. Pettitt, Biophys. J. 106, 1182–1193 (2014)
    Modeling DNA Thermodynamics under Torsional Stress
  20. J. S. Schreck, T. E. Ouldridge, F. Romano, P. Šulc, L. Shaw, A. A. Louis, J.P.K. Doye, Nucleic Acids Res. 43, 6181-6190 (2014)
    DNA hairpins primarily promote duplex melting rather than inhibiting hybridization (arXiv)
  21. R. Machinek, T.E. Ouldridge, N.E.C. Haley, J. Bath, A. J. Turberfield, Nature Comm. 5, 5324 (2014)
    Programmable energy landscapes for kinetic control of DNA strand displacement
  22. M. Mosayebi, F. Romano, T. E. Ouldridge, A. A. Louis, J. P. K. Doye, J. Phys. Chem. B 118, 14326-14335 (2014)
    The role of loop stacking in the dynamics of DNA hairpin formation (arXiv)
  23. I. Y. Loh, J.Cheng, S. R. Tee, A. Efremov, and Z. Wang, ACS Nano 8, 10293–10304 (2014)
    From bistate molecular switches to self-directed track-walking nanomotors
  24. C. Matek, T. E. Ouldridge, J. P. K. Doye, A. A. Louis, Sci. Rep., 5, 7655 (2015)
    Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA (arXiv)
  25. L. Rovigatti, P. Šulc, I. Reguly, F. Romano, J. Comput. Chem., 36, 1-8 (2015)
    A comparison between parallelization approaches in molecular dynamics simulations on GPUs (arXiv)
  26. P. Krstić, B. Ashcroft and S. Lindsay, Nanotechnology, 26, 084001 (2015)
    Physical model for recognition tunneling
  27. F. Romano and F. Sciortino, Phys. Rev. Lett. 114, 078104 (2015)
    Switching Bonds in a DNA Gel: An All-DNA Vitrimer
  28. J. S. Schreck, T. E. Ouldridge, F. Romano, A. A. Louis, J.P.K. Doye, J. Chem. Phys. 142, 165101 (2015)
    Characterizing the bending and flexibility induced by bulges in DNA duplexes (arXiv)
  29. M. Mosayebi, A. A. Louis, J.P.K. Doye, T. E. Ouldridge ACS Nano 9, 11993 (2015)
    Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors (arXiv)
  30. T. E. Ouldridge, Mol. Phys. 113, 1-15 (2015)
    DNA nanotechnology: understanding and optimisation through simulation (arXiv)
  31. P. Šulc, T. E. Ouldridge, F. Romano, J.P.K. Doye, A. A. Louis, Biophys. J. 108, 1238-1247 (2015)
    Modelling toehold-mediated RNA strand displacement (arXiv)
  32. B. E. K. Snodin, F. Randisi, M. Mosayebi, P. Šulc, J. S. Schreck, F. Romano, T. E. Ouldridge, R. Tsukanov, E. Nir, A. A. Louis, J. P. K. Doye, J. Chem. Phys. 142, 234901 (2015)
    Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA (arXiv)
  33. C. Matek, P. Šulc, F. Randisi, J.P.K. Doye, A. A. Louis, J. Chem. Phys. 143, 243122 (2015)
    Coarse-grained modelling of supercoiled RNA (arXiv)
  34. Q. Wang, C.G. Myers, and B.M. Pettitt, J. Phys. Chem. B 119, 4937–4943 (2015)
    Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density
  35. R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye, arXiv (2015)
    Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"
  36. R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye, J. Chem. Theor. Comput. 15 4660-4672 (2019)
    Identifying physical causes of apparent enhanced cyclization of short DNA molecules with a coarse-grained model (arXiv) (data)
  37. J. Y. Lee, T. Terakawa, Z. Qi, J. B. Steinfeld, S. Redding, Y. Kwon, W. A. Gaines, W. Zhao, P. Sung, E. C. Greene, Science 349, 977-981 (2015)
    Base triplet stepping by the Rad51/RecA family of recombinases
  38. B. E. K. Snodin, F. Romano, L. Rovigatti, T. E. Ouldridge, A. A. Louis, J. P. K. Doye, ACS Nano 10, 1724-1737 (2016)
    Direct Simulation of the Self-Assembly of a Small DNA Origami (data)
  39. V. Kočar, J. S. Schreck, S. Čeru, H. Gradišar, N. Bašić, T. Pisanski, J. P. K. Doye, and R. Jerala, Nat. Commun. 7, 10803 (2016)
    Design principles for rapid folding of knotted DNA nanostructures
  40. J. S. Schreck, F. Romano, M.H. Zimmer, A.A. Louis and J.P.K. Doye, ACS Nano, 10, 4236-4247 (2016)
    Characterizing DNA star-tile-based nanostructures using a coarse-grained model
  41. M. Liu, J. Cheng, S.R. Tee, S. Sreelatha, I.Y. Loh, and Z. Wang, ACS Nano, 10, 5882–5890 (2016)
    Biomimetic autonomous enzymatic nanowalker of high fuel efficiency
  42. J. Fernandez-Castanon, F. Bomboi, L. Rovigatti, M. Zanatta, A. Paciaroni, L. Comez, L. Porcar, C.J. Jafta, G.C. Fadda, T. Bellini and F. Sciortino, J. Chem. Phys. 145, 084910 (2016)
    Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars
  43. T. Sutthibutpong, C. Matek, C. Benham, G.G. Slade, A. Noy, C. Laughton, J.P.K. Doye, A.A. Louis and S.A. Harris, Nucleic Acids Res. 44, 9121-9130 (2016)
    Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation
  44. Q. Wang and B.M. Pettitt, J. Phys. Chem. Lett 7, 1042–1046 (2016)
    Sequence affects the cyclization of DNA minicircles
  45. A. Reinhardt, J.S. Schreck, F. Romano and J.P.K. Doye, J. Phys: Condens. Matter 29, 014006 (2017).
    Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal (arXiv) (data)
  46. E. Locatelli, P. H. Handle, C. N. Likos, F. Sciortino and L. Rovigatti, ACS Nano 11, 2094-2102 (2017)
    Condensation and demixing in solutions of DNA nanostars and their mixtures
  47. E. Skoruppa, M. Laleman, S. Nomidis, E. Carlon, J. Chem. Phys 146, 214902 (2017)
    DNA elasticity from coarse-grained simulations: the effect of groove asymmetry (arXiv)
  48. A. Suma and C. Micheletti, Proc. Natl. Acad. Sci. USA 114, E2991–E2997 (2017)
    Pore translocation of knotted DNA rings
  49. Z. Shi, C. E. Castro and G. Arya, ACS Nano 11, 4617–4630 (2017)
    Conformational dynamics of mechanically compliant DNA nanostructures from coarse-grained molecular dynamics simulations
  50. H. Yagyu, J.-Y. Lee, D.-N. Kim, and O. Tabata, J. Phys. Chem. B 121, 5033–5039 (2017)
    Coarse-grained molecular dynamics model of double-stranded DNA for DNA nanostructure design
  51. S. Vangaveti, R. J. D'Esposito, J. L. Lippens, D. Fabris and S. V. Ranganathan, Phys. Chem. Chem. Phys. 19, 14937-14946 (2017)
    A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by ion mobility spectrometry–mass spectrometry
  52. A. Henning-Knechtel, J. Knechtel and M. Magzoub, Nucleic Acids Res. 45, 12057–12068 (2017)
    DNA-assisted oligomerization of pore-forming toxin monomers into precisely-controlled protein channels
  53. R. Sharma, J. S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, ACS Nano 11, 12426–12435 (2017)
    Characterizing the motion of jointed DNA nanostructures using a coarse-grained model
  54. Q.Y. Yeo, I.Y. Loh, S.R. Tee, Y.H. Chiang, J. Cheng, M.H. Liu and Z.S. Wang, Nanoscale 9, 12142-12149 (2017)
    A DNA bipedal nanowalker with a piston-like expulsion stroke
  55. G. Chatterjee, N. Dalchau, R.A. Muscat, A. Phillips and G. Seelig, Nat. Nanotechnol. 12, 920–927 (2017)
    A spatially localized architecture for fast and modular DNA computing
  56. Q. Wang, R.N. Irobalieva, W. Chiu, M.F. Schmid, J.M. Fogg, L. Zechiedrich, B.M. Pettitt, Nucleic Acids Res. 45 7633-7642 (2017)
    Influence of DNA sequence on the structure of minicircles under torsional stress
  57. B. Joffroy, Y.O. Uca, D. Prešern, J.P.K. Doye and T.L. Schmidt, Nucleic Acids Res. 46, 538-545 (2018)
    Rolling circle amplification shows a sinusoidal template length-dependent amplification bias (data)
  58. R.V. Reshetnikov, A.V. Stolyarova, A.O. Zalevsky, D.Y. Panteleev, G.V. Pavlova, D.V. Klinov, A.V. Golovin, A.D. Protopopova, Nucleic Acids Res. 46, 1102–1112 (2018)
    A coarse-grained model for DNA origami
  59. D.C. Khara, J.S. Schreck, T.E. Tomov, Y. Berger, T.E. Ouldridge, J.P.K. Doye and E. Nir, Nucleic Acids Res. 46, 1553-1561 (2018)
    DNA bipedal motor walking dynamics: An experimental and theoretical study of the dependency on step size (data)
  60. P. Fonseca, F. Romano, J. S. Schreck, T.E. Ouldridge, J.P.K. Doye and A.A. Louis, J. Chem. Phys 148, 134910 (2018)
    Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly (arXiv)
  61. T.D. Craggs, M. Sustarsic, A. Plochowietz, M. Mosayebi, H. Kaju, A. Cuthbert, J. Hohlbein, L. Domicevica, P.C. Biggin, J.P.K. Doye and A.N. Kapanidis, Nucleic Acids Res. 47, 10788–10800 (2019)
    Substrate conformational dynamics drive structure-specific recognition of gapped DNA by DNA polymerase (bioRXiv)
  62. S.R. Tee and Z. Wang, ACS Omega, 3, 292-301 (2018)
    How well can DNA rupture DNA? Shearing and unzipping forces inside DNA nanostructures
  63. E. Skoruppa, S.K. Nomidis, J.F. Marko and E. Carlon, Phys. Rev. Lett. 121, 088101 (2018)
    Bend-induced twist waves and the structure of nucleosomal DNA (arXiv)
  64. M.M.C. Tortora and J.P.K. Doye, Mol. Phys. 116, 2773-2791 (2018)
    Incorporating particle flexibility in a density functional description of nematics and cholesterics (arXiv)
  65. O. Henrich, Y.A. Gutierrez-Fosado, T. Curk, T.E. Ouldridge, Eur. Phys. J. E 41, 57 (2018)
    Coarse-Grained Simulation of DNA using LAMMPS (arXiv)
  66. M.C. Engel, D. M. Smith, M.A. Jobst, M. Sajfutdinow, T. Liedl, F. Romano, L. Rovigatti, A.A. Louis and J.P.K. Doye, ACS Nano 12, 6734-6747 (2018)
    Force-induced unravelling of DNA Origami
  67. F. Romano and L. Rovigatti, in Design of Self-Assembling Materials (Springer, ed. I. Coluzza) pp 71-90 (2017)
    A Nucleotide-Level Computational Approach to DNA-Based Materials
  68. S.R. Tee, X. Hu, I.Y. Loh and Z. Wang, Phys. Rev. Applied 9, 034025 (2018)
    Mechanosensing potentials gate fuel consumption in a bipedal DNA nanowalker
  69. E. Locatelli and L. Rovigatti, Polymers 10, 447 (2018)
    An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids (preprints)
  70. E. Spruijt, S.E. Tusk and H. Bayley, Nat. Nanotechnol. 13, 739-745 (2018)
    DNA scaffolds support stable and uniform peptide nanopores
  71. L. Coronel, A. Suma and C. Micheletti, Nucleic Acids Res. 46,7522–7532 (2018)
    Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking (bioRXiv)
  72. E. Torelli, J.W. Kozyra, J.-Y. Gu, U. Stimming, L. Piantanida. K. Voitchovsky and N. Krasnogor, Scientific Reports 8, 6989 (2018)
    Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon
  73. R. Jin and L. Maibaum, J. Chem. Phys. 150, 105103 (2019)
    Mechanisms of DNA hybridization: Transition path analysis of a simulation-informed Markov model(arxiv)
  74. F. Kriegel, C. Matek, T. Dršata, K. Kulenkampff, S. Tschirpke, M. Zacharias, F. Lankas and J. Lipfert, Nucleic Acids Res. 46, 7998–8009 (2018)
    The temperature dependence of the helical twist of DNA
  75. E. Benson, A. Mohammed, D. Rayneau-Kirkhope, A. Gådin, P. Orponen, and B. Högberg, ACS Nano 12, 9291-9299 (2018)
    Effects of Design Choices on the Stiffness of Wireframe DNA Origami Structures
  76. S.K. Nomidis, E. Skoruppa, E. Carlon and J.F. Marko, Phys. Rev. E 99 032414 (2019).
    Twist-bend coupling and the statistical mechanics of the twistable worm-like chain model of DNA: Perturbation theory and beyond (bioRXiv,arXiv)
  77. B. E. K. Snodin, J. S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, Nucleic Acids Res. 47, 1585–1597 (2019).
    Coarse-grained modelling of the structural properties of DNA origami (arXiv) (data)
  78. N. E. C. Haley, T. E. Ouldridge, A. Geraldini, A. A. Louis, J. Bath and A. J. Turberfield, Nat. Commun 11, 2562 (2020)
    Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement (bioRXiv)
  79. L. Zhou, A.E. Marras, C.-M. Huang, C.E. Castro and H.-J Su, Small 14, 1802580 (2018)
    Paper origami‐inspired design and actuation of DNA nanomachines with complex motions
  80. R. A. Brady, W.T. Kaufhold, N.J. Brooks, V. Foderà and L. Di Michele, J. Phys. Condens. Matter 31, 074003 (2019)
    Flexibility defines structure in crystals of amphiphilic DNA nanostars (arXiv)
  81. F. Hong, S. Jiang, X. Lan, R.P. Narayanan, P. Šulc, F. Zhang, Y. Liu, and H. Yan, J. Am. Chem. Soc. 140, 14670–14676 (2018)
    Layered-crossover tiles with precisely tunable angles for 2D and 3D DNA crystal engineering
  82. Y. Choi, H. Choi, A.C. Lee, S. Kwon, J. Vis. Exp., e58364 (2018)
    Design and Synthesis of a Reconfigurable DNA Accordion Rack
  83. M.M.C. Tortora, G. Mishra, D. Prešern and J.P.K. Doye, Sci. Adv. 6, eaaw8331 (2020)
    Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamis (arXiv)
  84. C.-M. Huang, A. Kucinic, J.V. Le, C.E. Castro and H.-J. Su, Nanoscale 11, 1647-1660 (2019)
    Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis
  85. I.T. Hoffecker, S. Chen, A. Gådin, A. Bosco, A.I. Teixeira and B. Högberg, Small 15, 1803628 (2019)
    Solution‐controlled conformational switching of an anchored wireframe DNA nanostructure
  86. M. Coraglio, E. Skoruppa and E. Carlon, J. Chem. Phys. 150, 135101 (2019)
    Overtwisting induces polygonal shapes in bent DNA (arXiv)
  87. M. Matthies, N.P. Agarwal, E. Poppleton, F.M. Joshi, P. Šulc, and T.L. Schmidt, ACS Nano 13 1839-1848 (2019)
    Triangulated Wireframe Structures Assembled Using Single-Stranded DNA Tiles
  88. Y.A.G. Fosado, Z. Xing, E. Eiser, M. Hudek, O. Henrich, submitted
    A Numerical Study of Three-Armed DNA Hydrogel Structures (arXiv)
  89. W.T. Kaufhold, R.A. Brady, J.M. Tuffnell, P. Cicuta, and L. Di Michele, Bioconjugate Chem 30, 1850-1859 (2019)
    Membrane scaffolds enhance the responsiveness and stability of DNA-based sensing circuits
  90. S.K. Nomidis, M. Coraglio, M. Laleman, K. Phillips, E. Skoruppa and E. Carlon, Phys. Rev. E 100, 022402 (2019)
    Twist-bend coupling, twist waves and DNA loops (arXiv)
  91. A. Suma, A. Stopar, A.W. Nicholson, M. Castronovo, V. Carnevale, Nucleic Acids Res. 48, 4672–4680 (2020)
    Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure (bioRxiv)
  92. J. Liu, S. Shukor, S. Li, A. Tamayo, L. Tosi, B. Larman, V. Nanda, W.K. Olson and B. Parekkadan, Biomolecules 9, 199 (2019)
    Computational simulation of adapter length-dependent LASSO probe capture efficiency
  93. A. Suma, E. Poppleton, M. Matthies, P. Šulc, F. Romano, A.A. Louis, J.P.K. Doye, C. Micheletti, and L. Rovigatti, J. Comput. Chem. 40, 2586-2595 (2019)
    tacoxDNA: a user-friendly web server for simulations of complex DNA structures, from single strands to origami
  94. J.F. Berengut, J.C. Berengut, J.P.K. Doye, D. Prešern, A. Kawamoto, J. Ruan, M.J. Wainwright and L.K. Lee,, Nucleic Acids Res. 47, 11963–11975(2019)
    Design and synthesis of pleated DNA origami nanotubes with adjustable diameters (bioRxiv)
  95. K.G. Young, B. Najafi, W.M. Sant, S. Contera, A.A. Louis, J.P.K. Doye, A.J. Turberfield and J. Bath, Angew. Chem. Int. Ed. 59, 15942-15946 (2020)
    Reconfigurable T-junction DNA origami
  96. I.D. Stoev, T. Cao, A. Caciagli, J. Yu, C. Ness, R. Liu, R. Ghosh, T. O'Neill, D. Liu and E. Eiser, Soft Matter 16, 990-1001 (2020)
    On the Role of Flexibility in Linker-Mediated DNA Hydrogels (arXiv)
  97. E. Benson, M. Lolaico, Y. Tarasov, A. Gådin and B. Högberg, ACS Nano 13, 12591-12598 (2019)
    Evolutionary Refinement of DNA Nanostructures Using Coarse-Grained Molecular Dynamics Simulations
  98. S.W. Shin, S.Y. Ahn, Y.T. Lim and S.H. Um, Anal. Chem. 91, 14808-14811 (2019)
    Improved Sensitivity of Intramolecular Strand Displacement Based on Localization of Probes
  99. Z. Shi and G. Arya, Nucleic Acids Research 48, 548-560 (2020)
    Free energy landscape of salt-actuated reconfigurable DNA nanodevices
  100. E. Torelli, J.W. Kozyra, B. Shirt-Ediss, L. Piantanida, K. Voïtchovsky, N. Krasnogor, ACS Synth. Biol. 9, 1682-1692 (2020)
    Co-transcriptional folding of a bio-orthogonal fluorescent scaffolded RNA origami (bioRxiv)
  101. P.R Desai, S. Brahmachari, J.F. Marko, S. Das, K.C. Neuman, Nucleic Acids Res. 48, 10713–10725 (2020)
    Coarse-Grained Modeling of DNA Plectoneme Formation in the Presence of Base-Pair Mismatches (bioRxiv)
  102. K. Bartnik, A. Barth, M. Pilo-Pais, A.H. Crevenna, T. Liedl and D.C. Lamb, J. Am. Chem. Soc 142, 815-825 (2020).
    A DNA origami platform for single-pair Förster resonance energy transfer investigation of DNA–DNA interactions and ligation
  103. E. Poppleton, J. Bohlin, M. Matthies, S. Sharma, F. Zhang and P. Šulc, Nucleic Acids Res. 48, e72 (2020)
    Design, optimization, and analysis of large DNA and RNA nanostructures through interactive visualization, editing, and molecular simulation (bioRxiv)
  104. M.C. Engel, F. Romano, A.A. Louis and J.P.K. Doye, J. Chem. Theor. Comput. 16, 7764–7775 (2020).
    Measuring internal forces in single-stranded DNA: Application to a DNA force clamp (arXiv)
  105. C. Bores and B.M. Pettitt, Phys. Rev. E 101, 012406 (2020)
    Structure and the role of filling rate on model dsDNA packed in a phage capsid
  106. A. Bader and S.L. Cockroft, Chem. Commun. 56, 5135-5138 (2020)
    Conformational enhancement of fidelity in toehold-sequestered DNA nanodevices
  107. J.P.K. Doye, H. Fowler, D. Prešern, J. Bohlin, L. Rovigatti, F. Romano, P. Šulc, C.K. Wong, A.A. Louis, J.S. Schreck and M.C. Engel, M. Matthies, E. Benson, E. Poppleton and B.E.K. Snodin, Methods in Molecular Biology 2639, 93-112 (2023).
    The oxDNA coarse-grained model as a tool to simulate DNA origami (arXiv) (data)
  108. J. Lee, J.-H. Huh, S. Lee, Langmuir 36, 5118–5125 (2020)
    DNA Base Pair-Stacking Crystallization of Gold Colloids
  109. A.H. Clowsley, W.T. Kaufhold, T. Lutz, A. Meletiou, L. Di Michele, C. Soeller, Nat. Commun. 12, 501 (2021)
    Repeat DNA-PAINT suppresses background and non-specific signals in optical nanoscopy (bioRxiv)
  110. B. Najafi, K.G. Young, J. Bath, A.A. Louis, J.P.K. Doye and A.J. Turberfield, submitted
    Characterising DNA T-motifs by simulation and experiment (arXiv)
  111. C.M. Huang, A. Kucinic, J.A. Johnson, H.-J. Su, C.E. Castro, Nat. Mater. 20, 1264–1271 (2021)
    Integrating computer-aided engineering and design for DNA assemblies (bioRxiv)
  112. P. Irmisch, T.E. Ouldridge, and R. Seidel, J. Am. Chem. Soc 142, 11451–11463 (2020)
    Modelling DNA-strand displacement reactions in the presence of base-pair mismatches
  113. F. Hong, J.S. Schreck and P. Šulc, Nucleic Acids Res. 48, 10726–10738 (2020).
    Understanding DNA interactions in crowded environments with a coarse-grained model (bioRxiv)
  114. A.H. Clowsley, W.T. Kaufhold, T. Lutz, A. Meletiou, L. Di Michele, C. Soeller, J. Am. Chem. Soc. 142, 12069–12078 (2020)
    Detecting nanoscale distribution of protein pairs by proximity dependent super-resolution microscopy (bioRxiv)
  115. H. Chhabra, G. Mishra, Y. Cao, D. Prešern, E. Skoruppa, M.M.C. Tortora and J.P.K. Doye, J. Chem. Theor. Comput. 16, 7748–7763 (2020).
    Computing the elastic mechanical properties of rod-like DNA nanostructures (arXiv)
  116. K. Tapio, A. Mostafa, Y. Kanehira, A. Suma, A. Dutta, I. Bald, ACS Nano 15, 7065–7077 (2021)
    A versatile DNA origami based plasmonic nanoantenna for label-free single-molecule SERS (Research Square)
  117. E.G. Noya, C.K. Wong, P. Llombart and J.P.K. Doye, Nature 596, 367–371 (2021)
    How to design an icosahedral quasicrystal through directional bonding
  118. Y.A.G. Fosado, F. Landuzzi and T. Sakaue, Soft Matter 17, 1530-1537 (2021)
    Twist dynamics and buckling instability of ring DNA: Effect of groove asymmetry and anisotropic bending (arXiv)
  119. F. Spinozzi, M.G. Ortore, G. Nava, F. Bomboi, F. Carducci, H. Amenitsch, T. Bellini, F. Sciortino, and P. Mariani, Langmuir 36, 10387–10396 (2020)
    Gelling without structuring: a SAXS study of the interactions among DNA nanostars
  120. J. Huang A. Suma, M. Cui, G. Grundmeier, V. Carnevale, Y. Zhang, C. Kielar and A. Keller, Small Str. 1, 2000038 (2020)
    Arranging small molecules with sub‐nanometer precision on DNA origami substrates for the single‐molecule investigation of protein‐ligand interactions
  121. G. Yao, F. Zhang, F. Wang, T. Peng, H. Liu, E. Poppleton, P. Šulc, S. Jiang, L. Liu, C. Gong, X. Jing, X. Liu, L. Wang, Y. Liu, C. Fan and H. Yan, Nat. Chem. 12, 1067–1075 (2020)
    Meta-DNA structures
  122. J.F. Berengut, C.K. Wong, J.C. Berengut, J.P.K. Doye, T.E. Ouldridge and L.K. Lee, ACS Nano 14, 17428–17441 (2020)
    Self-limiting polymerization of DNA origami subunits with strain accumulation
  123. J. Procyk, E. Poppleton and P. Šulc, Soft Matter 17, 3586-3593 (2021).
    Coarse-grained nucleic acid-protein model for hybrid nanotechnology (arXiv)
  124. Z. Sierzega, J. Wereszczynski and C. Prior, Sci. Rep. 11, 1527 (2021)
    WASP: A software package for correctly characterizing the topological development of ribbon structures (bioRXiv)
  125. E. Skoruppa, A. Voorspoels, J. Vreede and E. Carlon, Phys. Rev. E 103, 042408 (2021)
    Length scale dependent elasticity in DNA from coarse-grained and all-atom models (arXiv)
  126. C. Bores, M. Woodson, M.C. Morais, and B. Montgomery Pettitt, J. Phys. Chem. B 124, 10337–10344 (2020)
    Effects of model shape, volume, and softness of the capsid for DNA packaging of phi29
  127. E. Lattuada, D. Caprara, V. Lamberti, F. Sciortino, Nanoscale 12, 23003-23012 (2020)
    Hyperbranched DNA clusters (arXiv)
  128. B.J.H.M. Rosier, A.J. Markvoort, B. Gumí Audenis, J.A.L. Roodhuizen, A. den Hamer, L. Brunsveld and T.F.A. de Greef, Nat. Catal. 3, 295–306 (2020)
    Proximity-induced caspase-9 activation on a DNA origami-based synthetic apoptosome
  129. R. Li, H. Chen and J.H. Choi, Angew. Chem. Int. Ed. 60, 7165-7173 (2021)
    Auxetic Two‐Dimensional Nanostructures from DNA (bioRXiv)
  130. D. Wang, L. Yu, C.-M. Huang, G. Arya, S. Chang, and Y. Ke, J. Am. Chem. Soc. 143, 2256–2263 (2021)
    Programmable transformations of DNA origami made of small modular dynamic units
  131. R. Li, H. Chen, H. Lee, J. H. Choi, Appl. Sci. 11, 2357 (2021)
    Elucidating the mechanical energy for cyclization of a DNA origami tile (bioRxiv)
  132. G. Park, M. K. Cho, and Y. Jung, J. Chem. Theory Comput., 17 1308-1317 (2021)
    Sequence-dependent kink formation in short DNA loops: Theory and molecular dynamics simulations
  133. S. Jonchhe, S. Pandey, D. Karna, P. Pokhrel, Y. Cui, S. Mishra, H. Sugiyama, M. Endo and H. Mao, J. Am. Chem. Soc 142, 10042–10049 (2020)
    Duplex DNA Is Weakened in Nanoconfinement
  134. R. Li, H. Chen and J. H. Choi, Small 17, 2007069 (2021)
    Topological Assembly of a Deployable Hoberman Flight Ring from DNA
  135. S. Naskar, P. K. Maiti, J. Mater. Chem. B 9, 5102-5113
    Mechanical properties of DNA and DNA nanostructures: comparison of atomistic, martini and oxDNA (arXiv)
  136. B. Babatunde, S. Arias, J. Cagan and R.E. Taylor, Appl. Sci. 11, 2950 (2021)
    Generating DNA origami nanostructures through shape annealing
  137. N.M. Gravina, J.C. Gumbart and H.D. Kim, J. Phys. Chem. B 125, 4016–4024 (2021)
    Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding
  138. A. Sengar, T.E. Ouldridge, O. Henrich, L. Rovigatti and P. Šulc, Front. Mol. Biosci. 8, 693710 (2021)
    A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results (arXiv) (data)
  139. E. Poppleton, R. Romero, A. Mallya, L. Rovigatti and P. Šulc, Nucl. Acids Res. 49 W491–W498 (2021)
    OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures
  140. Y. Yamashita, K. Watanabe, S. Murata and I. Kawamata, Chem-Bio Informatics Journal 21, 28-38 (2021)
    Web Server with a Simple Interface for Coarse-grained Molecular Dynamics of DNA Nanostructures
  141. E. Benson, R. Carrascosa Marzo, J. Bath, A.J. Turberfield, Small 17, 2007704 (2021)
    Strategies for Constructing and Operating DNA Origami Linear Actuators
  142. Z. Qu, Y.N. Zhang, Z. Dai, Y. Zhang, Y. Hao, J. Shen, F. Wang, Q. Li, C. Fan, X. Liu, Angew. Chem. Int. Ed. 60, 16693-16699 (2021)
    DNA framework-engineered long-range electrostatic interactions for DNA hybridization reactions
  143. Y. Wang, I. Baars, F. Fördös and B. Högberg, ACS Nano 15 9614–9626 (2021)
    Clustering of Death Receptor for Apoptosis Using Nanoscale Patterns of Peptides
  144. Y. Wang, E. Benson, F. Fördős, M. Lolaico, I. Baars, T. Fang, A.I. Teixeira, B. Högberg, Adv. Mater. 33, 2008457 (2021)
    DNA Origami Penetration in Cell Spheroid Tissue Models is Enhanced by Wireframe Design
  145. L. Li, H. Wang, C. Xiong, D. Luo, H. Chen and Y. Liu, J. Phys.: Condens. Matter 33, 185102 (2021)
    Quantify the combined effects of temperature and force on the stability of DNA hairpin
  146. J. P. Mahalik and M. Muthukumar, submitted
    Nucleotide Dynamics During Flossing of Polycation-DNA-Polycation through a Nanopore using Molecular Dynamics (bioRxiv)
  147. N. Li, Y. Liu, Z. Yin, R. Liu, L. Zhang, Y. Zhao, L. Ma, X. Dai, D. Zhou, X. Su, Nano Today 41 101308 (2021)
    Self-resetting Molecular Probes for Nucleic Acids Enabled by Fuel Dissipative Systems (medRxiv)
  148. Y. Yang, Q. Lu, C.-M. Huang, H. Qian, Y. Zhang, S. Deshpande, G. Arya, Y. Ke, S. Zauscher, Angew. Chem. Int. Ed. 60, 3241-23247 (2021)
    Programmable site-specific functionalization of DNA origami with polynucleotide brushes
  149. Z. Yu, M. Centola, J. Valero, M. Matthies, P. Šulc, and M. Famulok, J. Am. Chem. Soc. 143, 13292–13298 (2021)
    A Self-Regulating DNA Rotaxane Linear Actuator Driven by Chemical Energy
  150. T. Lee, S. Do, J.G. Lee, D.-N. Kim and Y. Shin, Nanoscale 13, 17638-17647 (2021)
    The flexibility-based modulation of DNA nanostar phase separation
  151. Y. Wang, J. V. Le, K. Crocker, M.A. Darcy, P.D. Halley, D. Zhao, N. Andrioff, C. Croy, M.G Poirier, R. Bundschuh, C.E Castro, Nucleic Acids Res. 49, 8987–8999 (2021)
    A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules
  152. F. Liu, X. Liu, Q. Shi, C. Maffeo, M. Kojima, L. Dong, A. Aksimentiev, Q. Huang, T. Fukuda and T. Arai, Nanoscale 13, 15552-15559 (2021)
    A tetrahedral DNA nanorobot with conformational change in response to molecular trigger
  153. J. Appeldorn, S. Lemcke, T. Speck and A. Nikoubashman, J. Phys. Chem. B 126, 5007–5016 (2022).
    Employing artificial neural networks to find reaction coordinates and pathways for self-assembly (ChemRxiv)
  154. H. Jun, X. Wang, M.F. Parsons, W.P. Bricker, T. John, S. Li, S. Jackson, W. Chiu, M. Bathe, Nucleic Acids Res. 49, 10265–10274 (2021)
    Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami
  155. C.K. Wong, C. Tang, J.S. Schreck and J.P.K. Doye, Nanoscale 14, 2638–2648 (2022).
    Characterizing the free-energy landscapes of DNA origamis (arXiv)
  156. W. Lim, F. Randisi, J.P.K. Doye and A.A. Louis, Nucleic Acids Res. 50, 2480–2492 (2022).
    The interplay of supercoiling and thymine dimers in DNA (bioRxiv)
  157. W.T. Kaufhold, W. Pfeifer, C.E. Castro and L. Di Michele, ACS Nano 16, 8784–8797 (2022).
    Probing the mechanical properties of DNA nanostructures with metadynamics (arXiv)
  158. H. Su, J.M. Brockman, Y. Duan, N. Sen, H. Chhabra, A. Bazrafshan, A.T. Blanchard, T. Meyer, B. Andrews, J.P.K. Doye, Y. Ke, R.B. Dyer and K. Salaita, J. Am. Chem. Soc. 43, 19466–19473 (2021).
    Massively parallelized molecular force manipulation with on demand thermal and optical control
  159. L. Yang, C. Cullin and J. Elezgaray, ChemPhysChem 23, e202200021 (2022).
    Detection of short DNA sequences with DNA nanopores (arXiv)
  160. Y. Pan, R. Weng, L. Zhang, J. Qiu, X. Wang, G. Liao, Z. Qin, L. Zhang, H. Xiao, Y. Qian, X. Su, Nano Today 46 101573 (2022).
    Simulation guided intramolecular orthogonal reporters for dissecting cellular oxidative stress and response (Research Square)
  161. X. Wang, S. Li, H. Jun, T. John, K. Zhang, H. Fowler, J.P.K. Doye, W. Chiu and M. Bathe, Sci. Adv. 8, eabn0039 (2022).
    Planar 2D wireframe DNA origami
  162. E. Poppleton, A. Mallya, S. Dey, J. Joseph, P. Šulc, Nucleic Acids Res. 50, D246–D252 (2022)
    Nanobase.org: a repository for DNA and RNA nanostructures
  163. R. Foffi, F. Sciortino, J. M. Tavares, P. I. C. Teixeira, Soft Matter 17, 10736-10743 (2021)
    Building up DNA, bit by bit: a simple description of chain assembly (arXiv)
  164. J. Yoo, S. Park, C. Maffeo, T. Ha, A. Aksimentiev, Nucleic Acids Res. 49, 11459–11475 (2021).
    DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles
  165. E. Lin-Shiao, W.G. Pfeifer, B.R. Shy, M. Saffari Doost, E. Chen, V.S. Vykunta, J.R. Hamilton, E.C. Stahl, D.M. Lopez, C.R. Sandoval Espinoza, A.E. Dejanov, R.J. Lew, M.G. Poirer, A. Marson, C.E. Castro, J.A. Doudna, Nucleic Acids Res. 50, 1256–1268 (2022)
    CRISPR-Cas9 mediated nuclear transport and genomic integration of nanostructured genes in human primary cells (bioRxiv)
  166. J.P.K. Doye, A.A. Louis, J.S. Schreck, F. Romano, R.M. Harrison, M. Mosayebi, M.C. Engel, T.E. Ouldridge, in Energy Landscapes of Nanoscale Systems, ed. D.J. Wales, Frontiers of Nanoscience (Elsevier) Vol. 21, Chapter 9, pp 195-210 (2022)
    Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling (arXiv)
  167. Y. Deng, Y. Tan, L. Zhang, C. Zhang, X. Su, submitted.
    Forecasting the reaction of DNA modifying enzymes on DNA nanostructures by coarse grained model for stimuli-responsive drug delivery (Research Square)
  168. D. Smith and G. Tikhomirov, submitted.
    small: A programmatic nanostructure design and modelling environment (arXiv)
  169. S. Assenza and R. Pérez, J. Chem. Theory Comput 18, 3239–3256 (2022)
    Accurate sequence-dependent coarse-grained model for conformational and elastic properties of double-stranded DNA (biorXiv)
  170. D. Kuťák, E. Poppleton, H. Miao, P. Šulc and I. Barišić, Molecules 27, 63 (2022)
    Unified Nanotechnology Format: One Way to Store Them All
  171. M. Centola, E. Poppleton, M. Centola, J. Valero, P. Šulc and M. Famulok, Nat. Nanotechnol. 19, 226–236 (2024)
    A rhythmically pulsing leaf-spring nanoengine that drives a passive follower (biorXiv)
  172. C.K. Wong and J.P.K. Doye, Appl. Sci. 12, 5875 (2022)
    The free-energy landscape of a mechanically bistable DNA origami (arXiv)
  173. L. Zhang, J. Chen, M. He, X. Su, Exploration 2, 20210265 (2022)
    Molecular dynamics simulation-guided toehold mediated strand displacement probe for single-nucleotide variants detection
  174. F. Mambretti, N. Pedrani, L. Casiraghi, E. M. Paraboschi, T. Bellini, S. Suweis, Entropy 24, 458 (2022)
    OxDNA to study species interactions (arXiv)
  175. Y.A.G. Fosado, Soft Matter 19, 4820-4828 (2023)
    Nanostars planarity modulates the elasticity of DNA hydrogels (arXiv)
  176. X. Hu, L. Tang, M. Zheng, J. Liu, Z. Zhang, Z. Li, Q. Yang, S. Xiang, L. Fang, Q. Ren, X. Liu, C.Z. Huang, C. Mao and H. Zuo, J. Am. Chem. Soc. 144, 4507–4514 (2022)
    Structure-guided designing pre-organization in bivalent aptamers
  177. L. Liu F. Hong H. Liu X. Zhou S. Jiang P. Šulc J.-H. Jiang and H. Yan, Sci. Adv. 8, eabm9530 (2022)
    A localized DNA finite-state machine with temporal resolution
  178. Y. Xin, P. Piskunen, A. Suma, C. Li, H. Ijäs, S. Ojasalo, I. Seitz, M.A. Kostiainen, G. Grundmeier, V. Linko and A. Keller, Small 18, 2107393 (2022)
    Environment-dependent stability and mechanical properties of DNA origami six-helix bundles with different crossover spacings
  179. R.L. Bender, H. Ogasawara, A.V. Kellner, A. Velusamy and K. Salaita, submitted
    Unbreakable DNA tension probes show that cell adhesion receptors detect the molecular force-extension curve of their ligands (bioRxiv)
  180. E. Benson, R. Carrascosa Marzo, J. Bath and A.J. Turberfield, Sci. Robot. 7, eabn5459 (2022)
    A DNA molecular printer capable of programmable positioning and patterning in two dimensions
  181. A. Dutta, K. Tapio, A. Suma, A. Mostafa, Y. Kanehira, V. Carnevale, G. Bussi and I. Bald, Nanoscale 14, 16467-16478 (2022)
    Molecular states and spin crossover of hemin studied by DNA origami enabled single-molecule surface-enhanced Raman scattering
  182. D.J. Hart, J. Jeong, J.C. Gumbart and H.D. Kim, Nucleic Acids Res. 51, 3030–3040 (2023)
    Weak tension accelerates hybridization and dehybridization of short oligonucleotides (bioRxiv)
  183. S. Sensale, P. Sharma and G. Arya, Phys. Rev. E 105, 044136 (2022)
    Binding kinetics of harmonically confined random walkers
  184. S. Dey, A. Dorey, L. Abraham, Y. Xing, I. Zhang, F. Zhang, S. Howorka and H. Yan, Nat. Commun. 13, 2271 (2022)
    A reversibly gated protein-transporting membrane channel made of DNA
  185. D. Luo, A. Kouyoumdjian, O. Strnad, H. Miao, I. Barišić and I. Viola, submitted (2022)
    SynopSet: Multiscale visual abstraction set for explanatory analysis of DNA nanotechnology simulations (arXiv)
  186. L. Rovigatti, J. Russo, F. Romano, M. Matthies, L. Kroc and P. Sulc, Nanoscale 14, 14268-14275 (2022)
    A simple solution to the problem of self-assembling cubic diamond crystals (arXIv)
  187. J. Bohlin, M. Matthies, E. Poppleton, J. Procyk, A. Mallya, H. Yan and P. Šulc, Nat. Protoc. 17, 1762–1788 (2022)
    Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView
  188. C. Zhou, D. Yang, S. Sensale, P. Sharma, D. Wang, L. Yu, G. Arya, Y. Ke and P. Wang, Sci. Adv 8, eade3003 (2022)
    A bistable and reconfigurable molecular system with encodable bonds (Research Square)
  189. R. Li, M. Zheng, A.S. Madhvacharyula, Y. Du, C. Mao and J.H. Choi, Biophys. J. 121, 4078-4090 (2022)
    Mechanical deformation behaviors and structural properties of ligated DNA crystals (bioRxiv)
  190. C. Xie, Y. Hu, Z. Chen, K. Chen and L. Pan, Nanotechnology 33, 405603 (2022)
    Tuning curved DNA origami structures through mechanical design and chemical adducts
  191. F. Fontana, T. Bellini and M. Todisco, Macromolecules 55, 5946–5953 (2022)
    Liquid Crystal Ordering in DNA Double Helices with Backbone Discontinuities
  192. Z. Weng, H. Yu, W. Luo, L. Zhang, Z. Zhang, T. Wang, Q. Liu, Y. Guo, Y. Yang, J. Li, L. Yang, L. Dai, Q. Pu, X. Zhou and G. Xie, Anal. Chim. Acta 1199, 339568 (2022)
    Specific and robust hybridization based on double-stranded nucleic acids with single-base resolution
  193. J. Bohlin, A.J. Turberfield, A.A. Louis and P. Šulc, ACS Nano 17, 5387–5398 (2023)
    Designing the self-assembly of arbitrary shapes using minimal complexity building blocks (arXiv)
  194. Y. Deng, Y. Tan, Y. Zhang, L. Zhang, C. Zhang, Y. Ke and X. Su, ACS Appl. Mater. Interfaces 14, 34470–34479 (2022)
    Design of uracil-modified DNA nanotubes for targeted drug release via DNA-modifying enzyme reactions
  195. J. G. Lee, K. S. Kim, J. Y. Lee and D.-N. Kim, ACS Nano 16, 4289–4297 (2022)
    Predicting the free-form shape of structured DNA assemblies from their lattice-based design blueprint
  196. M. Micheloni, L. Petrolli, G. Lattanzi and R. Potestio, Biophys. J. 122, 3314-3322 (2023)
    Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations (bioRxiv)
  197. A. Elonen, A.K. Natarajan, I. Kawamata, L. Oesinghaus, A. Mohammed, J. Seitsonen, Y. Suzuki, F. C. Simmel, A. Kuzyk and P. Orponen, ACS Nano 16, 16608–16616 (2022)
    Algorithmic design of 3D wireframe RNA polyhedra (bioRxiv)
  198. D. Fu, R.P. Narayanan, A. Prasad, F. Zhang, D. Williams, J.S. Schreck, H. Yan and J. Reif, Sci. Adv. 8, ade4455 (2022)
    Automated design of 3D DNA origami with non-rasterized 2D curvature
  199. N. Chauhan, Y. Xiong, S. Ren, A. Dwivedy, N. Magazine, L. Zhou, X. Jin, T. Zhang, B.T. Cunningham, S. Yao, W. Huang and X. Wang, J. Am. Chem. Soc. 145, 20214–20228 (2023)
    Net-shaped DNA nanostructures designed for rapid/sensitive detection and potential inhibition of the SARS-CoV-2 virus
  200. A. Mills, N. Aissaoui, D. Maurel, J. Elezgaray, F. Morvan, J. J. Vasseur, E. Margeat, R.B. Quast, J. Lai Kee-Him, N. Saint, C. Benistant, A. Nord, F. Pedaci and G. Bellot, Nat. Commun. 13, 3182 (2022)
    A modular spring-loaded actuator for mechanical activation of membrane proteins
  201. T. Panczyk, K. Nieszporek and P. Wolski, Molecules 27, 4915 (2022)
    Stability and existence of noncanonical i-motif DNA structures in computer simulations based on atomistic and coarse-grained force fields
  202. E.E. Kurisinkal, V. Caroprese, M.M. Koga, D. Morzy and M.M.C. Bastings, Molecules 27 4968 (2022)
    Selective integrin α5β1 targeting through spatially constrained multivalent DNA-based nanoparticles
  203. R.P. Narayanan, J. Procyk, P. Nandi, A. Prasad, Y. Xu, E. Poppleton, D. Williams, F. Zhang, H. Yan, P.-L. Chiu, N. Stephanopoulos and P. Šulc, ACS Nano 16, 14086–14096 (2022)
    Coarse-grained simulations for the characterization and optimization of hybrid protein–DNA nanostructures
  204. J. Wang, Y. Wei, P. Zhang, Y. Wang, Q. Xia, X. Liu, S. Luo, J. Shi, J. Hu, C. Fan, B. Li, L. Wang, X. Zhou and J. Li, Nano Lett. 22, 7173–7179 (2022)
    Probing heterogeneous folding pathways of DNA origami self-assembly at the molecular level with atomic force microscopy
  205. S. Li, Y. Coffinier, C. Lagadec, F. Cleri, K. Nishiguchi, A. Fujiwara, T. Fujii, S.-H. Kim and N.Clément, Biosens. Bioelectron. 216, 114643 (2022)
    Redox-labelled electrochemical aptasensors with nanosupported cancer cells
  206. S. Bianco, T. Hu, O. Henrich and S. W.Magennis, Biophysical Reports 2, 100070 (2022)
    Heterogeneous migration routes of DNA triplet repeat slip-outs
  207. Y. Li, C. Maffeo, H. Joshi, A. Aksimentiev, B. Ménard and R. Schulman, Sci. Adv. 8, eabq4834 (2022)
    Leakless end-to-end transport of small molecules through micron-length DNA nanochannels
  208. G. Kloes, T.J.D. Bennett, A. Chapet-Batlle, A. Behjatian, A.J. Turberfield and M. Krishnan, Nano Lett. 22, 7834–7840 (2022)
    Far-field electrostatic signatures of macromolecular 3D conformation
  209. L. Guo, Y. Zhang, Y. Wang, M. Xie, J. Dai, Z. Qu, M. Zhou, S. Cao, J. Shi, L. Wang, X. Zuo, C. Fan and J. Li, Angew. Chem. Int. Ed. 61, e202117168 (2022)
    Directing multivalent aptamer-receptor binding on the cell surface with programmable atom-like nanoparticles
  210. N. Xie, M. Li, Y. Wang, H. Lv, J. Shi, J. Li, Q. Li, F. Wang and C. Fan, J. Am. Chem. Soc. 144, 9479–9488 (2022)
    Scaling Up Multi-bit DNA Full Adder Circuits with Minimal Strand Displacement Reactions
  211. E. Lattuada, T. Pietrangeli and F. Sciortino, J. Chem. Phys. 157, 135101 (2022)
    Interpenetrating gels in binary suspensions of DNA nanostars
  212. X. Chen, Y. Wang, X. Dai, L. Ding, J. Chen, G. Yao, X. Liu, S. Luo, J. Shi, L. Wang, R. Nechushtai, E. Pikarsky, I. Willner, C. Fan, and J. Li, J. Am. Chem. Soc. 144, 6311–6320 (2022)
    Single-Stranded DNA-Encoded Gold Nanoparticle Clusters as Programmable Enzyme Equivalents
  213. Q. Kou, L. Wang, L. Zhang, L. Ma, S. Fu and X. Su, Small 18, 2205191 (2022)
    Simulation-assisted localized DNA logical circuits for cancer biomarkers detection and imaging
  214. P. E. Beshay, A. Kucinic, N. Wile, P. Halley, L. Des Rosiers, A. Chowdhury, J. L. Hall, C. E. Castro and M. W. Hudoba, The Biophysicist 4, 68–81 (2023)
    Translating DNA origami nanotechnology to middle school, high school, and undergraduate laboratories (bioRxiv)
  215. A. Büchl, E. Kopperger, M. Vogt, M. Langecker, F.C.Simmel and J. List, Biophys. J. 121, 4849-4859 (2022)
    Energy landscapes of rotary DNA origami devices determined by fluorescence particle tracking
  216. E. Poppleton, M. Matthies, D. Mandal, F. Romano, P. Šulc and L. Rovigatti, J. Open Source Softw. 8, 4693 (2023)
    oxDNA: coarse-grained simulations of nucleic acids made simple
  217. A. Suma, V. Carnevale and C. Micheletti, Phys. Rev. Lett. 130, 048101 (2023)
    Nonequilibrium Thermodynamics of DNA Nanopore Unzipping (arXiv)
  218. Y. Tang, H. Liu, Q. Wang, X. Qi, L. Yu, P. Šulc, F. Zhang, H. Yan and S. Jiang, J. Am. Chem. Soc. 145, 25, 13858–13868 (2023)
    DNA Origami Tessellations
  219. M. DeLuca, W.G. Pfeifer, B. Randoing, C.-M. Huang, M.G. Poirier, C.E. Castro and G. Arya, Nanoscale 15, 8356-8365 (2023)
    Thermally reversible pattern formation in arrays of molecular rotors
  220. T. Liang, C. Yang, X. Song, Y. Feng, Y. Liu and H. Chen, Phys. Rev. E 108, 014406 (2023)
    Quantification of macromolecule crowding at single-molecule level
  221. D. Lysne, T. Hachigian, C. Thachuk, J. Lee and E. Graugnard J. Am. Chem. Soc. 145, 16691–16703 (2023)
    Leveraging Steric Moieties for Kinetic Control of DNA Strand Displacement Reactions
  222. A. Kucinic, C.-M. Huang, J. Wang, H.-J. Su and C.E. Castro, Nanoscale, 15 562-572 (2023)
    DNA origami tubes with reconfigurable cross-sections
  223. Y. Zhang, X. Yin, C. Cui, K. He, F. Wang, J. Chao, T. Li, X. Zuo, A. Li, L. Wang, N. Wang, X. Bo and C. Fan, Sci. Adv. 9, adf8263 (2023)
    Prime factorization via localized tile assembly in a DNA origami framework
  224. W.G. Pfeifer, C.-M. Huang, M. G. Poirier, G. Arya and C. E. Castro, Sci. Adv. 9, adi0697 (2023)
    Versatile computer-aided design of free-form DNA nanostructures and assemblies (bioRxiv)
  225. M. Lolaico, S. Blokhuizen, B. Shen, Y. Wang, and B. Högberg, ACS Nano 17, 6565–6574 (2023)
    Computer-Aided Design of A-Trail Routed Wireframe DNA Nanostructures with Square Lattice Edges
  226. Y. Wang, A. Kucinic, L. Des Rosiers, P.E. Beshay, N. Wile, M.W. Hudoba and C.E. Castro, Appl. Sci. 13, 3208 (2023)
    Mechanical Design of DNA Origami in the Classroom
  227. D. Morzy, C. Tekin, V. Caroprese, R. Rubio-Sánchez, L. Di Michele and M.M.C. Bastings, Nanoscale 15, 2849-2859 (2023)
    Interplay of the mechanical and structural properties of DNA nanostructures determines their electrostatic interactions with lipid membranes
  228. L. Zhang, H. Zhao, H. Yang and X. Su, Biosens. Bioelectron. 239, 115622 (2023)
    Coarse-grained model simulation-guided localized DNA signal amplification probe for miRNA detection
  229. Y.-P. Qiao, C.-L. Ren and Y.-Q. Ma J. Phys. Chem. B 127, 4015–4021 (2023)
    Two Different Ways of Stress Release in Supercoiled DNA Minicircles under DNA Nick
  230. K. Cervantes-Salguero, Y.A. Gutiérrez Fosado, W. Megone, J.E. Gautrot and M. Palma, Molecules 28, 3686 (2023)
    Programmed self-assembly of DNA nanosheets with discrete single-molecule thickness and interfacial mechanics: Design, simulation, and characterization
  231. H.L. Too and Z. Wang, Nanoscale 15, 11915-11926 (2023)
    Exhaustive classification and systematic free-energy profile study of single-stranded DNA inter-overhang migration
  232. D. Saliba, X. Luo, F.J. Rizzuto and H.F. Sleiman, Nanoscale 15, 5403-5413 (2023)
    Programming rigidity into size-defined wireframe DNA nanotubes
  233. J. Lee and S. Lee, Anal. Chem. 95, 1856–1866 (2023)
    Non-invasive, reliable, and fast quantification of DNA loading on gold nanoparticles by a one-step optical measurement
  234. X. Shen, Q. Ouyang, H. Tan, J. Ouyang and N. Na, Anal. Chem. 95, 5903–5910 (2023)
    Computation-assisted design of ssDNA framework nanorobots for cancer logical recognition, toehold disintegration, visual dual-diagnosis, and synergistic therapy
  235. L. Tang, M. Huang, M. Zhang, Y. Pei, Y. Liu, Y. Wei, C. Yang, T. Xie, D. Zhang, R. Zhou, Y. Song, J. Song, Small Methods 7, 2300327 (2023)
    De novo evolution of an antibody-mimicking multivalent aptamer via a DNA framework
  236. Z. Zheng, S.H. Kim, A. Chovin, N. Clement and C. Demaille, Chem. Sci. 14, 3652-3660 (2023)
    Electrochemical response of surface-attached redox DNA governed by low activation energy electron transfer kinetics
  237. M. Vogt, M. Langecker, M. Gouder, E. Kopperger, F. Rothfischer, F.C. Simmel and J. List, Nature Physics 19, 741–751 (2023)
    Storage of mechanical energy in DNA nanorobotics using molecular torsion springs
  238. C. Xie, Y. Hu, K. Chen, Z. Chen and L. Pan, Commun. Comput. Inf. Sci., 1801, 647–654 (2023)
    Tuning Geometric Conformations of Curved DNA Structures by Controlling Positions of Nicks
  239. S. Yu, J. Zhao, R. Chu, X. Li, G. Wu and X. Meng, Entropy 25, 796 (2023)
    Anomalous diffusion of polyelectrolyte segments on supported charged lipid bilayers
  240. I. Madrid, Z. Zheng, C. Gerbelot, A. Fujiwara, S. Li, S. Grall, K. Nishiguchi, S.H. Kim, A. Chovin, C. Demaille and N. Clement, ACS Nano 17, 17031–17040 (2023)
    Ballistic Brownian Motion of Nanoconfined DNA
  241. Y. Ma, W. Guo, Q. Mou, X. Shao, M. Lyu, V. Garcia, L. Kong, W. Lewis, C. Ward, Z. Yang, X. Pan, S.S. Yi and Y. Lu, Nat. Biotechnol. (2023)
    Spatial imaging of glycoRNA in single cells with ARPLA
  242. X. Luo, D. Saliba, T. Yang, S. Gentile, K. Mori, P.I. Garcia, T. Das, N. Bagheri, A. Porchetta, A. Guarne, G. Cosa, H.F. Sleiman, Angew. Chem. Int. Ed. 62 e202309869 (2023)
    Minimalist design of wireframe DNA nanotubes: Tunable geometry, size, chirality, and dynamics
  243. Y. Zhao, S. Cao, Y. Wang, F. Li, L. Lin, L. Guo, F. Wang, J. Chao, X. Zuo, Y. Zhu, L. Wang, J. Li and C. Fan, Nat. Mach. Intell. 5, 980–990 (2023)
    A temporally resolved DNA framework state machine in living cells
  244. X.R. Liu, I.Y. Loh, W. Siti, H.L. Too, T. Anderson and Z. Wang, Nanoscale Horiz., 8, 827-841 (2023)
    A light-operated integrated DNA walker–origami system beyond bridge burning
  245. H. Lv, N. Xie, M. Li, M. Dong, C. Sun, Q. Zhang, L. Zhao, J. Li, X. Zuo, H. Chen, F. Wang and C. Fan, Nature 622, 292–300(2023).
    DNA-based programmable gate arrays for general-purpose DNA computing
  246. C. Yang, X. Song, Y. Feng, G. Zhao, and Y. Liu, J. Phys.: Condens. Matter 35, 265101 (2023)
    Stability of DNA and RNA hairpins: a comparative study based on ox-DNA
  247. Xiaoya Song, Chao Yang, Yuyu Feng, Hu Chen, and Yanhui Liu, Commun. Theor. Phys. 75, 055601 (2023)
    A common rule for the intermediate state caused by DNA mismatch in single-molecule experiments
  248. W. Siti, H.L. Too, T. Anderson, X.R. Liu, I.Y. Loh and Z. Wang, Sci. Adv. 9, adi8444 (2023)
    Autonomous DNA molecular motor tailor-designed to navigate DNA origami surface for fast complex motion and advanced nanorobotics
  249. R. Ma, A. Velusamy, S.A. Rashid, B.R. Deal, W. Chen, B. Petrich, R. Li, K. Salaita, Nat. Methods 20, 1666–1671 (2023)
    Molecular mechanocytometry using tension-activated cell tagging (bioRxiv)
  250. D. Karna, E. Mano, J. Ji, I. Kawamata, Y. Suzuki and H. Mao, Nat. Commun. 14, 6459 (2023)
    Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies
  251. J. Fu, L. Zhang, Y. Long, Z. Liu, G. Meng, H. Zhao, X. Su and S. Shi, Anal. Chem. 95, 16089–16097 (2023)
    Multiplexed CRISPR-based nucleic acid detection using a single Cas protein
  252. Y. Yang, Q. Lu, Y. Chen, M. DeLuca, G. Arya, Y. Ke and S. Zauscher, Angew. Chem. Int. Ed. 62, e202311727 (2023)
    Spatiotemporal control over polynucleotide brush growth on DNA origami nanostructures
  253. J.Y. Lee, H. Koh and D.-N. Kim, Nat. Commun. 14, 7079 (2023)
    A computational model for structural dynamics and reconfiguration of DNA assemblies
  254. M.C. Engel, J.A. Smith and M.P. Brenner, Phys. Rev. X 13, 041032 (2023)
    Optimal control of nonequilibrium systems through automatic differentiation
  255. L. Yu, Y. Xu, M. Al-Amin, S. Jiang, M. Sample, A. Prasad, N. Stephanopoulos, P. Šulc, and H. Yan, J. Am. Chem. Soc. 145, 27336–27347 (2023)
    CytoDirect: A nucleic acid nanodevice for specific and efficient delivery of functional payloads to the cytoplasm
  256. Y.-P. Qiao and C.-L. Ren, Langmuir 40, 109–117 (2024)
    Correlated hybrid DNA structures explored by the oxDNA Model
  257. L. Kilwing, P. Lill, B. Nathwani, R. Guerra, E. Benson, T. Liedl and W. M. Shih, ACS Nano 18, 885–893 (2024)
    Multilayer DNA origami with terminal interfaces that are flat and wide-area
  258. N. Adžić, C. Jochum, C. N. Likos, E. Stiakakis, Small, 20, 2308763 (2024)
    Engineering ultrasoft interactions in stiff all-DNA dendrimers by site-specific control of scaffold flexibility
  259. A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and K. Salaita, Nat. Commun. 15, 704 (2024)
    DNA mechanocapsules for programmable piconewton responsive drug delivery
  260. Y. Liu, B. Li, F. Wang, Q. Li, S. Jia, X. Liu, and M. Li, ACS Appl. Bio Mater. 7, 1311–1316 (2024)
    Quantitative analysis of resistance to deformation of the DNA origami framework supported by struts
  261. S. He, H. Deng, P. Li, Q. Tian, Y. Yang, J. Hu, H. Li, T. Zhao, H. Ling, Y. Liu, S. Liu and Q. Guo, J. Nanobiotechnol. 22, 39 (2024)
    Bimodal DNA self-origami material with nucleic acid function enhancement
  262. B. Babatunde, J. Cagan, R.E. Taylor, J. Mech. Des. 146, 051708 (2024)
    An improved shape annealing algorithm for the generation of coated deoxyribonucleic acid origami nanostructures
  263. A.S.G. Martins, S.D. Reis, E. Benson, M.M. Domingues, J. Cortinhas, J.A. Vidal Silva, S.D. Santos, N.C. Santos, A.P. Pêgo, P.M.D. Moreno, Small 20, 2309140 (2024)
    Enhancing Neuronal Cell Uptake of Therapeutic Nucleic Acids with Tetrahedral DNA Nanostructures
  264. S Dey, R. Rivas-Barbosa, F. Sciortino, E. Zaccarelli and P. Zijlstra, Nanoscale 16, 4872-4879 (2024)
    Biomolecular interactions on densely coated nanoparticles: a single-molecule perspective
  265. T. Chen, S. Mao, J. Ma, X. Tang, R. Zhu, D. Mao, X. Zhu, Q. Pan, Angew. Chem. Int. Ed 63, e202319117 (2024)
    Proximity-enhanced functional imaging analysis of engineered tumors
  266. Y. Liu, Z. Dai, X. Xie, B. Li, S. Jia, Q. Li, M. Li, C. Fan and X. Liu, J. Am. Chem. Soc. 146, 8, 5461–5469 (2024)
    Spacer-programmed two-dimensional DNA origami assembly
  267. Z. Zheng, S. Grall, S.H. Kim, A. Chovin, N. Clement and C. Demaille, J. Am. Chem. Soc. 146, 9, 6094–6103 (2024)
    Activationless electron transfer of redox-DNA in electrochemical nanogaps
  268. M. Sample, M. Matthies and P. Šulc, ACS Nano 18, 30004–30016 (2024)
    Hairygami: Analysis of DNA nanostructure's conformational change driven by functionalizable overhangs (arXiv)
  269. M. Sample, M. Matthies and P. Šulc, 2023 Winter Simulation Conference (WSC), San Antonio, TX, USA, pp. 91-105 (2023)
    Coarse-grained simulations of DNA and RNA systems with oxDNA and oxRNA models: Introductory tutorial (arXiv)
  270. V. Caroprese, C. Tekin, V. Cencen, M. Mosayebi, T.B. Liverpool, D.N. Woolfson, G. Fantner, M.M.C. Bastings, submitted
    Structural flexibility dominates over binding strength for supramolecular crystallinity (bioRxiv)
  271. C. Shi, D. Yang, X.Ma, L. Pan, Y. Shao, G. Arya, Y. Ke, C. Zhang, F. Wang, X. Zuo, M. Li and P. Wang, Angew. Chem. Int. Ed. 63 e202320179 (2024)
    A programmable DNAzyme for the sensitive detection of nucleic acids (medRxiv)
  272. F. Smith, A. Sengar, G.‐B.V. Stan, T.E. Ouldridge, M. Stevens, J. Goertz and W. Bae, submitted
    Overcoming the speed limit of four‐way DNA branch migration with bulges in toeholds (bioRxiv)
  273. K. Gallagher, J. Yu, D.A. King, R. Liu, E. Eiser, APL Mater. 11, 061129 (2023)
    Towards new liquid crystal phases of DNA mesogens (arXiv)
  274. G.B.M. Wisna, D. Sukhareva, J. Zhao, D. Satyabola, M. Matthies, S. Roy, P. Šulc, H. Yan and R.F. Hariadia, submitted
    High-speed 3D DNA-PAINT and unsupervised clustering for unlocking 3D DNA origami cryptography (bioRxiv)
  275. H. Koh, J.Y. Lee, J.G. Lee, submitted
    Forming superhelix of double stranded DNA from local deformation (arXiv)
  276. N.P. Agarwal and A. Gopinath, submited
    DNA origami 2.0 (bioRxiv)
  277. J.M. Weck and A. Heuer-Jungemann, submitted
    Fully addressable, designer superstructures assembled from a single modular DNA origami (bioRxiv)
  278. Y. Xu, R. Zheng, A. Prasad, M. Liu, Z. Wan, X. Zhou, R.M. Porter, M. Sample, E. Poppleton, J. Procyk, H. Liu, Y. Li, S. Wang, H. Yan, P. Sulc, N. Stephanopoulos, submitted
    High-affinity binding to the SARS-CoV-2 spike trimer by a nanostructured, trivalent protein-DNA synthetic antibody (bioRxiv)
  279. H. Liu, M. Matthies, J. Russo, L. Rovigatti, R.P. Narayanan, T. Diep, D. McKeen, O. Gang, N. Stephanopoulos, F. Sciortino, H. Yan, F. Romano and P. Šulc, Science 384, 776-781 (2024)
    Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments (arXiv)
  280. L. Grabenhorst, M. Pfeiffer, T. Schinkel, M. Kümmerlin, J.B. Maglic, G.A. Brüggenthies, F. Selbach, A.T. Murr, P. Tinnefeld, V. Glembockyte, Nat. Nanotechnol. accepted (2024)
    Engineering modular and tunable single-molecule sensors by decoupling sensing from signal output (bioRxiv)
  281. F. Tosti Guerra, E. Poppleton, P. Šulc, L. Rovigatti, submitted
    nNxB: a new coarse-grained model for RNA and DNA nanotechnology (arXiv)
  282. E.J. Ratajczyk, P. Šulc, A.J. Turberfield, J.P.K. Doye and A.A. Louis, J. Chem. Phys. 160, 115101 (2024)
    Coarse-grained modelling of DNA-RNA hybrids (arXiv)
  283. M. DeLuca, D. Duke, T. Ye, M. Poirier, Y. Ke, C. Castro and G. Arya, Nat. Commun. 15, 3015 (2024)
    Mechanism of DNA origami folding elucidated by mesoscopic simulations (bioRxiv)
  284. S. Cristofaro, L. Querciagrossa, L. Soprani, T.P. Fraccia, T. Bellini, R. Berardi, A. Arcioni, C. Zannoni, L. Muccioli, and S. Orlandi, Biomacromolecules 25, 3920–3929 (2024)
    Simulating the lyotropic phase behavior of a partially self-complementary DNA tetramer
  285. A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and K. Salaita, Nat. Commun. 15, 704 (2024)
    DNA mechanocapsules for programmable piconewton responsive drug delivery
  286. A. Voorspoels, J. Gevers, S. Santermans, N. Akkan, K. Martens, K. Willems, P. Van Dorpe, and A.S. Verhulst, J. Phys. Chem. A 128, 3926–3933 (2024)
    Design principles of DNA-barcodes for nanopore-FET readout, based on molecular dynamics and TCAD simulations
  287. F. Tosti Guerra, E. Poppletoni, P. Šulc and L. Rovigatti, J. Chem. Phys. 160, 205102 (2024)
    ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems (arXiv)
  288. Y. Wang, I. Baars, I. Berzina, I. Rocamonde-Lago, B. Shen, Y. Yang, M. Lolaico, J. Waldvogel, I. Smyrlaki, K. Zhu, R.A. Harris and B. Högberg, Nat. Nanotechnol. 19, 1366–137 (2024)
    A DNA robotic switch with regulated autonomous display of cytotoxic ligand nanopatterns
  289. W. Ji, X. Xiong, M. Cao, Y. Zhu, L. Li, F. Wang, C. Fan and H. Pei, Nat. Chem. 16, 1408–1417 (2024)
    Encoding signal propagation on topology-programmed DNA origami
  290. M. van Galen, A. Bok, T. Peshkovsky, J. van der Gucht, B. Albada and J. Sprakel, Nat. Chem. accepted (2024)
    De novo DNA-based catch bonds
  291. Y. Hu, J. Rogers, Y. Duan, A. Velusamy, S. Narum, S. Al Abdullatif and K. Salaita, Nat. Nanotechnol. 19, 1674–1685 (2024)
    Quantifying T cell receptor mechanics at membrane junctions using DNA origami tension sensors
  292. D. Svenšek, J. Sočan and M. Praprotnik, Macromol. Rapid Commun. accepted 2400382 (2024)
    Density–nematic coupling in isotropic solution of DNA: Multiscale model
  293. M. Mogheiseh and R.H. Ghasemi, J. Chem. Phys. 161, 045101 (2024)
    Design and simulation of a wireframe DNA origami nanoactuator
  294. S.H. Wong, S.N. Kopf, V. Caroprese, Y. Zosso, D. Morzy, M.M.C. Bastings, Nano Lett. 24, 11210–11216 (2024)
    Modulating the DNA/lipid interface through multivalent hydrophobicity
  295. G. Nava, T. Carzaniga, L. Casiraghi, E. Bot, G. Zanchetta, F. Damin, M. Chiari, G. Weber, T. Bellini, L. Mollica and M. Buscaglia, Nucl. Acids Res. 52, 8661–8674 (2024)
    Weak-cooperative binding of a long single-stranded DNA chain on a surface
  296. Y. Du, R. Li, A.S. Madhvacharyula, A.A. Swett, J.H. Choi, submitted
    DNA nanostar structures with tunable auxetic properties (bioRxiv)
  297. G.M. Roozbahani, P. Colosi, A. Oravecz, E.M. Sorokina, W. Pfeifer, S. Shokri, Y. Wei, P. Didier, M. DeLuca, G. Arya, L. Tora, M. Lakadamyali, M.G. Poirier, C. E. Castro
    Piggybacking functionalized DNA nanostructures into live cell nuclei (bioRxiv)
  298. A. Walbrun, T. Wang, M. Matthies, P. Šulc, F.C. Simmel, M. Rief, Nat. Commun. 15, 7564 (2024)
    Single-Molecule Force Spectroscopy of Toehold-Mediated Strand Displacement (bioRxiv)
  299. S. Chandrasekhar, T.P. Swope, F. Fadaei, D.R. Hollis, R. Bricker, D. Houser, J. Portman, T.L. Schmidt, submitted
    Bending Unwinds DNA (bioRxiv)
  300. X. Liu, F. Liu, H. Chhabra, C. Maffeo, Q. Huang, A. Aksimentiev, T. Arai, Nat. Commun. 15, 7210 (2024)
    A lumen-tunable triangular DNA nanopore for molecular sensing and cross-membrane transport (ResearchSquare)
  301. L. Yang, G. Pecastaings, C. Drummond and J. Elezgaray, Nano Lett. 24, 13481–13486 (2024)
    Driving DNA nanopore membrane insertion through dipolar coupling
  302. J.-Y. Liou, M. Awan, K. Leyba, P. Šulc, S. Hofmeyr, C.-J. Wu and S. Forrest, ACM Trans. Evol. Learn. Optim. accepted (2024)
    Evolving to find optimizations humans miss: Using evolutionary computation to improve GPU code for bioinformatics applications
  303. C. Karfusehr, M. Eder, F.C. Simmel
    Self-assembled cell-scale containers made from DNA origami membranes (bioRxiv)
  304. M.T. Luu, J.F. Berengut, J.K.D. Singh, K.C.D. Glieze, M. Turner, K. Skipper, S. Meppat, H. Fowler, W. Close, J.P.K. Doye, A. Abbas, S.F.J. Wickham, submitted
    Reconfigurable multi-component nanostructures built from DNA origami voxels (bioRxiv)
  305. M.P. Tran, T. Chakraborty, E. Poppleton, L. Monari, F. Giessler and K. Göpfrich, submitted
    Genetic encoding and expression of RNA origami cytoskeletons in synthetic cells (bioRxiv)
  306. V. Bukina and A. Božič, Biophys. J. 123, 3397-3407 (2024)
    Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA (bioRxiv)
  307. R. Walker-Gibbons, X. Zhu, A. Behjatian, T.J.D. Bennett and M. Krishnan, Sci. Rep. 14, 20582 (2024)
    Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations
  308. E.J. Ratajczyk, J. Bath, P. Sulc, J.P.K. Doye, A.A. Louis, A.J. Turberfield, submitted
    Controlling DNA-RNA strand displacement kinetics with base distribution (bioRxiv)
  309. A. Suma and C. Micheletti, submitted
    Unzipping of knotted DNA via nanopore translocation (arXiv)
  310. G. Mattiotti, M. Micheloni, L. Petrolli, L. Tubiana, S. Pasquali, R. Potestio, submitted.
    Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model (arXiv)
  311. S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, submitted.
    How we simulate DNA origami (arXiv)
  312. Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted
    Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells (ResearchSquare)
  313. R.K. Krueger, M.C. Engel, R. Hausen, M.P. Brenner, submitted (2024)
    A Differentiable Model of Nucleic Acid Dynamics (arXiv)
  314. Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted
    Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells (ResearchSquare)
  315. K. Zhou, M. Chung, J. Cheng, J.T. Powell, J. Liu, Y. Xiong, M.A. Schwartz and C. Lin, submitted.
    DNA nanodevice for analysis of force-activated protein extension and interactions (bioRxiv)
  316. W.-S. Wei, T.E. Videbæk, D. Hayakawa, R. Saha, W.B. Rogers, S. Fraden, submitted
    Economical and versatile subunit design principles for self-assembled DNA origami structures (arXiv)

We are also maintaining a list of all published papers using oxDNA at publons.

Retrieved from "https://dna.physics.ox.ac.uk/index.php?title=Publications&oldid=1870"