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# L. Kilwing, P. Lill, B. Nathwani, R. Guerra, E. Benson, T. Liedl and W. M. Shih, ''ACS Nano'' '''18''', 885–893 (2024)
# 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]
#: [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'', accepted (2024)
# 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]
#: [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)
# A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and  K. Salaita, ''Nat. Commun.'' '''15''', 704 (2024)
Line 523: Line 523:
# B. Babatunde, J. Cagan, R.E. Taylor, ''J. Mech. Des.'' '''146''', 051708 (2024)
# 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]
#: [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'' accepted (2024)
# 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]
#: [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)
# 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]
#: [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'' accepted
# 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]
#: [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)
# 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)
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# Z. Zheng, S. Grall, S.H. Kim, A. Chovin, N. Clement and C. Demaille, ''J. Am. Chem. Soc.'' '''146''', 9, 6094–6103 (2024)  
# 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]
#: [https://doi.org/10.1021/jacs.3c13532 Activationless electron transfer of redox-DNA in electrochemical nanogaps]
# M. Sample, M. Matthies and P. Šulc, submitted
# M. Sample, M. Matthies and P. Šulc, ''ACS Nano'' accepted (2024)
#: Hairygami: Analysis of DNA nanostructure's conformational change driven by functionalizable overhangs ([https://doi.org/10.48550/arXiv.2302.09109 arXiv])
#: [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)
# 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])
#: [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])
# M. DeLuca, T. Ye, M. Poirier,  Y. Ke,  C. Castro and G. Arya, submitted
#: Mechanism of DNA origami folding elucidated by mesoscopic simulations ([https://doi.org/10.1101/2023.06.20.545758 bioRxiv])
# V. Caroprese, C. Tekin, V. Cencen, M. Mosayebi, T.B. Liverpool, D.N. Woolfson, G. Fantner, M.M.C. Bastings, submitted
# 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])
#: Structural flexibility dominates over binding strength for supramolecular crystallinity ([https://doi.org/10.1101/2023.09.04.556250 bioRxiv])
# C. Shi, P. Wang, submitted
# 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)
#: Allosteric DNAzyme for sensitive detection of nucleic acids for molecular diagnosis ([https://doi.org/10.1101/2023.08.20.23294196 medRxiv])
#: [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
# 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])
#: 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, submitted
# K. Gallagher, J. Yu, D.A. King, R. Liu, E. Eiser, ''APL Mater.'' '''11''', 061129 (2023)
#: Towards New Liquid Crystal Phases of DNA mesogens ([https://doi.org/10.48550/arXiv.2302.03501 arXiv])
#: [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
# 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])
#: High-speed 3D DNA-PAINT and unsupervised clustering for unlocking 3D DNA origami cryptography ([https://doi.org/10.1101/2023.08.29.555281 bioRxiv])
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#: 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])
#: 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)
# 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 ([https://doi.org/10.48550/arXiv.2310.10995 arXiv])
#: [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
# 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])
#: Engineering modular and tunable single Molecule sensors by decoupling sensing from signal output ([https://doi.org/10.1101/2023.11.06.565795 bioRxiv])
Line 566: Line 564:
#: [https://doi.org/10.1063/5.0199558 Coarse-grained modelling of DNA-RNA hybrids] ([https://doi.org/10.48550/arXiv.2311.07709 arXiv])
#: [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)
# 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/10.1038/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)
# 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]
#: [https://doi.org/10.1021/acs.biomac.3c01435 Simulating the lyotropic phase behavior of a partially self-complementary DNA tetramer]
Line 575: Line 573:
# F. Tosti Guerra, E. Poppletoni, P. Šulc and L. Rovigatti, ''J. Chem. Phys.'' '''160''', 205102 (2024)
# 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])
#: [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
# 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])
#: 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
# 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])
#: 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, submitted
# 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 ([https://doi.org/10.1101/2024.01.16.575816 bioRxiv])
#: [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
# 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])
#: 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, submitted
# X. Liu, F. Liu, H. Chhabra, C. Maffeo, Q. Huang, A. Aksimentiev, T. Arai, ''Nat. Commun.'' '''15''', 7210 (2024)
#: A dynamically gated triangular DNA nanopore for molecular sensing and cross-membrane transport ([https://doi.org/10.21203/rs.3.rs-3878148/v1  ResearchSquare])
#: [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
# 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])
#: Self-assembled cell-scale containers made from DNA origami membranes ([https://doi.org/10.1101/2024.02.09.579479 bioRxiv])
Line 591: Line 605:
# M.P. Tran,  T. Chakraborty,  E. Poppleton,  L. Monari,  F. Giessler and  K. Göpfrich, submitted
# 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])
#: 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, submitted
# V. Bukina and A. Božič, ''Biophys. J.'' '''123''', 3397-3407 (2024)
#: Context-dependent structure formation of RNA hairpin motifs ([https://doi.org/10.1101/2024.04.17.589867 bioRxiv])
#: [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
  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)
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    Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA (arXiv)
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    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 accepted (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, 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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