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# 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]  
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# 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]
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# W. Lim, F. Randisi, J.P.K. Doye and A.A. Louis, ''Nucleic Acids Res.'' '''50''', 2480–2492 (2022).
# W. Lim, F. Randisi, J.P.K. Doye and A.A. Louis, ''Nucleic Acids Res.'' '''50''', 2480–2492 (2022).
#: [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])
#: [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.'' '''43''', 19466–19473 (2021).
# 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, ''ChemPhysChem'' '''23''', e202200021 (2022).
# L. Yang, C. Cullin and J. Elezgaray, ''ChemPhysChem'' '''23''', e202200021 (2022).
#: [https://doi.org/10.1002/cphc.202200021 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.'' '''50''', D246–D252 (2022)
# 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]
Line 325: Line 329:
# 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)
# 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)
#: [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])
#: [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://arxiv.org/abs/2111.10166 arXiv])
#: [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.
# 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])
#: 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.
# D. Smith and G. Tikhomirov, submitted.
#: small: A programmatic nanostructure design and modelling environment ([https://arxiv.org/abs/2111.15184 arXiv])
#: small: A programmatic nanostructure design and modelling environment ([https://arxiv.org/abs/2111.15184 arXiv])
# S. Assenza and R. Pérez, ''J. Chem. Theory Comput'' accepted (2022).
# 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])
#: [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)
# 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]
#: [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, submitted.
# 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 ([https://doi.org/10.1101/2021.12.22.473833 biorXiv])
#: [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, submitted
# C.K. Wong and J.P.K. Doye, ''Appl. Sci.'' '''12''', 5875 (2022)
#: The free-energy landscape of a mechanically bistable DNA origami ([http://arxiv.org/abs/2201.08920 arXiv])
#: [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)
# 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]
#: [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)
# 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])
#: [https://doi.org/10.3390/e24040458 OxDNA to study species interactions] ([https://arxiv.org/abs/2202.05653 arXiv])
# Y.A.G. Fosado, submitted
# Y.A.G. Fosado, ''Soft Matter'' '''19''', 4820-4828 (2023)
#: Nanostars planarity modulates the elasticity of DNA hydrogels ([https://arxiv.org/abs/2202.06331 arXiv])
#: [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)
# 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]
#: [https://doi.org/10.1021/jacs.1c12593 Structure-guided designing pre-organization in bivalent aptamers]
Line 355: Line 359:
# E. Benson, R. Carrascosa Marzo, J. Bath and A.J. Turberfield, ''Sci. Robot.'' '''7''', eabn5459 (2022)
# 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]
#: [https://doi.org/10.1126/scirobotics.abn5459 A DNA molecular printer capable of programmable positioning and patterning in two dimensions]
# D.J. Hart, J. Jeong, J.C. Gumbart and H.D. Kim, submitted
# A. Dutta, K. Tapio, A. Suma, A. Mostafa, Y. Kanehira, V. Carnevale, G. Bussi and I. Bald, ''Nanoscale'' '''14''', 16467-16478 (2022)
#: Weak tension accelerates hybridization and dehybridization of short oligonucleotides ([https://doi.org/10.1101/2022.04.19.488836 bioRxiv])
#: [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)
# 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]
#: [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)
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#: 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, submitted
#: 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.'' accepted (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])
# 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])


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 16:19, 19 October 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
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    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)
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  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, submitted
    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. accepted (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. C. Karfusehr, M. Eder, F.C. Simmel
    Self-assembled cell-scale containers made from DNA origami membranes (bioRxiv)
  302. 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)
  303. 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)
  304. V. Bukina and A. Božič, Biophys. J. 123, 3397-3407 (2024)
    Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA (bioRxiv)
  305. 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
  306. 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)
  307. A. Suma and C. Micheletti, submitted
    Unzipping of knotted DNA via nanopore translocation (arXiv)
  308. 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)
  309. S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, submitted.
    How we simulate DNA origami (arXiv)
  310. 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)


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

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