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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)
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# E. Torelli, J.W. Kozyra, B. Shirt-Ediss, L. Piantanida, K. Voïtchovsky, N. Krasnogor, ''ACS Synth. Biol.'' '''9''', 1682-1692 (2020)
# E. Torelli, J.W. Kozyra, B. Shirt-Ediss, L. Piantanida, K. Voïtchovsky, N. Krasnogor, ''ACS Synth. Biol.'' '''9''', 1682-1692 (2020)
#: [https://doi.org/10.1021/acssynbio.0c00009 Co-transcriptional folding of a bio-orthogonal fluorescent scaffolded RNA origami] ([https://doi.org/10.1101/864678 bioRxiv])
#: [https://doi.org/10.1021/acssynbio.0c00009 Co-transcriptional folding of a bio-orthogonal fluorescent scaffolded RNA origami] ([https://doi.org/10.1101/864678 bioRxiv])
# P.R Desai, S. Brahmachari, J.F. Marko, S. Das, K.C. Neuman, submitted
# 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 ([https://doi.org/10.1101/2019.12.20.885533 bioRxiv])
#: Coarse-Grained Modeling of DNA Plectoneme Formation in the Presence of Base-Pair Mismatches ([https://doi.org/10.1101/2019.12.20.885533 bioRxiv])
# K. Bartnik, A. Barth, M. Pilo-Pais, A.H. Crevenna, T. Liedl and D.C. Lamb, ''J. Am. Chem. Soc'' '''142''', 815-825 (2020).
# K. Bartnik, A. Barth, M. Pilo-Pais, A.H. Crevenna, T. Liedl and D.C. Lamb, ''J. Am. Chem. Soc'' '''142''', 815-825 (2020).
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]
# A.H. Clowsley, W.T. Kaufhold, T. Lutz, A. Meletiou, L. Di Michele, C. Soeller, submitted
# 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 ([https://doi.org/10.1101/2020.04.24.059410 bioRxiv])
#: [https://doi.org/10.1038/s41467-020-20686-z Repeat DNA-PAINT suppresses background and non-specific signals in optical nanoscopy] ([https://doi.org/10.1101/2020.04.24.059410 bioRxiv])
# B. Najafi, K.G. Young, J. Bath, A.A. Louis, J.P.K. Doye and A.J. Turberfield, submitted
# 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 ([https://arxiv.org/abs/2005.11545 arXiv])
#: Characterising DNA T-motifs by simulation and experiment ([https://arxiv.org/abs/2005.11545 arXiv])
# C.M. Huang, A. Kucinic, J.A. Johnson, H.-J. Su, C.E. Castro, submitted
# 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 computer-aided design for DNA assemblies ([https://doi.org/10.1101/2020.05.28.119701 bioRxiv])
#: [https://doi.org/10.1038/s41563-021-00978-5 Integrating computer-aided engineering and design for DNA assemblies] ([https://doi.org/10.1101/2020.05.28.119701 bioRxiv])
# P. Irmisch, T.E. Ouldridge, and R. Seidel, ''J. Am. Chem. Soc'' '''142''', 11451–11463 (2020)
# P. Irmisch, T.E. Ouldridge, and R. Seidel, ''J. Am. Chem. Soc'' '''142''', 11451–11463 (2020)
#: [https://doi.org/10.1021/jacs.0c03105 Modelling DNA-strand displacement reactions in the presence of base-pair mismatches]
#: [https://doi.org/10.1021/jacs.0c03105 Modelling DNA-strand displacement reactions in the presence of base-pair mismatches]
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# 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).
# 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).
#: [https://dx.doi.org/10.1021/acs.jctc.0c00661 Computing the elastic mechanical properties of rod-like DNA nanostructures] ([http://arXiv.org arXiv])
#: [https://dx.doi.org/10.1021/acs.jctc.0c00661 Computing the elastic mechanical properties of rod-like DNA nanostructures] ([http://arXiv.org arXiv])
# K. Tapio, A. Mostafa, Y. Kanehira, A. Suma, A. Dutta, I. Bald, submitted
# 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 ([https://doi.org/10.21203/rs.3.rs-47458/v1 Research Square])
#: [https://doi.org/10.1021/acsnano.1c00188 A versatile DNA origami based plasmonic nanoantenna for label-free single-molecule SERS] ([https://doi.org/10.21203/rs.3.rs-47458/v1 Research Square])
# E.G. Noya, C.K. Wong, P. Llombart and J.P.K. Doye, submitted
# 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
#: [https://doi.org/10.1038/s41586-021-03700-2 How to design an icosahedral quasicrystal through directional bonding]
# Y.A.G. Fosado, F. Landuzzi and T. Sakaue, submitted
# 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 ([https://arxiv.org/abs/2008.05686 arXiv])
#: [https://doi.org/10.1039/D0SM01812K Twist dynamics and buckling instability of ring DNA: Effect of groove asymmetry and anisotropic bending] ([https://arxiv.org/abs/2008.05686 arXiv])
# 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)
# 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)
#: [https://doi.org/10.1021/acs.langmuir.0c01520 Gelling without structuring: a SAXS study of the interactions among DNA nanostars]
#: [https://doi.org/10.1021/acs.langmuir.0c01520 Gelling without structuring: a SAXS study of the interactions among DNA nanostars]
Line 241: Line 243:
# 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)
# 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)
#: [http://dx.doi.org/10.1021/acsnano.0c07696 Self-limiting polymerization of DNA origami subunits with strain accumulation]
#: [http://dx.doi.org/10.1021/acsnano.0c07696 Self-limiting polymerization of DNA origami subunits with strain accumulation]
# J. Procyk, E. Poppleton and  P. Šulc, ''Soft Matter'' accepted.
# J. Procyk, E. Poppleton and  P. Šulc, ''Soft Matter'' '''17''', 3586-3593 (2021).
#: [https://doi.org/10.1039/D0SM01639J Coarse-grained nucleic acid-protein model for hybrid nanotechnology] ([https://arxiv.org/abs/2009.09589 arXiv])
#: [https://doi.org/10.1039/D0SM01639J Coarse-grained nucleic acid-protein model for hybrid nanotechnology] ([https://arxiv.org/abs/2009.09589 arXiv])
# Z. Sierzega, J. Wereszczynski and C. Prior, submitted
# 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 ([https://doi.org/10.1101/2020.09.17.301309 bioRXiv])
#: [https://doi.org/10.1038/s41598-020-80851-8 WASP: A software package for correctly characterizing the topological development of ribbon structures] ([https://doi.org/10.1101/2020.09.17.301309 bioRXiv])
# E. Skoruppa, A. Voorspoels, J. Vreede and E. Carlon, submitted
# 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 ([https://arxiv.org/abs/2010.01302 arXiv])
#: [https://doi.org/10.1103/PhysRevE.103.042408 Length scale dependent elasticity in DNA from coarse-grained and all-atom models] ([https://arxiv.org/abs/2010.01302 arXiv])
# C. Bores, M. Woodson, M.C. Morais, and B. Montgomery Pettitt, ''J. Phys. Chem. B'' '''124''', 10337–10344 (2020)
# C. Bores, M. Woodson, M.C. Morais, and B. Montgomery Pettitt, ''J. Phys. Chem. B'' '''124''', 10337–10344 (2020)
#: [https://doi.org/10.1021/acs.jpcb.0c07478 Effects of model shape, volume, and softness of the capsid for DNA packaging of phi29]
#: [https://doi.org/10.1021/acs.jpcb.0c07478 Effects of model shape, volume, and softness of the capsid for DNA packaging of phi29]
# E. Lattuada, D. Caprara, V. Lamberti, F. Sciortino, ''Nanoscale'' '''12''', 23003-23012 (2020)
# E. Lattuada, D. Caprara, V. Lamberti, F. Sciortino, ''Nanoscale'' '''12''', 23003-23012 (2020)
#: [https://ezproxy-prd.bodleian.ox.ac.uk:2102/10.1039/D0NR04840B Hyperbranched DNA clusters] ([https://arxiv.org/abs/2011.07854 arXiv])
#: [https://doi.org/10.1039/D0NR04840B Hyperbranched DNA clusters] ([https://arxiv.org/abs/2011.07854 arXiv])
# B.J.H.M. Rosier, A.J. Markvoort, B. Gumí Audenis, J.A.L. Roodhuizen, A. den Hamer, L. Brunsveld & T.F.A. de Greef, ''Nat. Catal.'' '''3''', 295–306(2020)
# 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)
#: [https://doi.org/10.1038/s41929-019-0403-7 Proximity-induced caspase-9 activation on a DNA origami-based synthetic apoptosome]
#: [https://doi.org/10.1038/s41929-019-0403-7 Proximity-induced caspase-9 activation on a DNA origami-based synthetic apoptosome]
# R. Li, H. Chen and J.H. Choi, ''Angew. Chem. Int. Ed.'' '''60''', 7165-7173 (2021)
#: [https://doi.org/10.1002/anie.202014729 Auxetic Two‐Dimensional Nanostructures from DNA] ([https://doi.org/10.1101/2020.08.21.262139 bioRXiv])
# D. Wang, L. Yu, C.-M. Huang, G. Arya, S. Chang, and Y. Ke, ''J. Am. Chem. Soc.'' '''143''', 2256–2263 (2021)
#: [https://doi.org/10.1021/jacs.0c10576 Programmable transformations of DNA origami made of small modular dynamic units]
# R. Li, H. Chen, H. Lee, J. H. Choi, ''Appl. Sci.'' '''11''', 2357 (2021)
#: [https://doi.org/10.3390/app11052357 Elucidating the mechanical energy for cyclization of a DNA origami tile] ([https://doi.org/10.1101/2021.02.07.430115 bioRxiv])
# G. Park, M. K. Cho, and Y. Jung, ''J. Chem. Theory Comput.'', '''17''' 1308-1317 (2021)
#: [https://doi.org/10.1021/acs.jctc.0c01116 Sequence-dependent kink formation in short DNA loops: Theory and molecular dynamics simulations]
# 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)
#:[https://doi.org/10.1021/jacs.0c01978 Duplex DNA Is Weakened in Nanoconfinement]
# R. Li, H. Chen and J. H. Choi, ''Small'' '''17''', 2007069 (2021)
#: [https://doi.org/10.1002/smll.202007069 Topological Assembly of a Deployable Hoberman Flight Ring from DNA]
# S. Naskar, P. K. Maiti, ''J. Mater. Chem. B '' '''9''', 5102-5113
#: [https://doi.org/10.1039/D0TB02970J Mechanical properties of DNA and DNA nanostructures: comparison of atomistic, martini and oxDNA] ([https://arxiv.org/abs/2103.17217 arXiv])
# B. Babatunde, S. Arias, J. Cagan and R.E. Taylor, ''Appl. Sci.'' '''11''', 2950 (2021)
#: [https://doi.org/10.3390/app11072950 Generating DNA origami nanostructures through shape annealing]
# N.M. Gravina, J.C. Gumbart and H.D. Kim, ''J. Phys. Chem. B'' '''125''', 4016–4024 (2021)
#: [https://doi.org/10.1021/acs.jpcb.1c00432 Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding]
# A. Sengar, T.E. Ouldridge, O. Henrich, L. Rovigatti and P. Šulc, ''Front. Mol. Biosci.'' '''8''', 693710 (2021)
#: [https://www.frontiersin.org/articles/10.3389/fmolb.2021.693710/full A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results]  ([https://arxiv.org/abs/2104.11567 arXiv]) ([https://dx.doi.org/10.5281/zenodo.4809769 data])
# E. Poppleton, R. Romero, A. Mallya, L. Rovigatti and P. Šulc, ''Nucl. Acids Res.'' '''49'''  W491–W498 (2021)
#: [https://doi.org/10.1093/nar/gkab324 OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures]
# Y. Yamashita, K. Watanabe, S. Murata and I. Kawamata, ''Chem-Bio Informatics Journal'' '''21''', 28-38 (2021)
#: [https://doi.org/10.1273/cbij.21.28 Web Server with a Simple Interface for Coarse-grained Molecular Dynamics of DNA Nanostructures]
# E. Benson, R. Carrascosa Marzo, J. Bath, A.J. Turberfield, ''Small'' '''17''', 2007704 (2021)
#: [https://doi.org/10.1002/smll.202007704 Strategies for Constructing and Operating DNA Origami Linear Actuators]
# 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)
#: [https://doi.org/10.1002/anie.202106010 DNA framework-engineered long-range electrostatic interactions for DNA hybridization reactions]
# Y. Wang, I. Baars, F. Fördös and B. Högberg, ''ACS Nano'' '''15''' 9614–9626 (2021)
#: [https://doi.org/10.1021/acsnano.0c10104 Clustering of Death Receptor for Apoptosis Using Nanoscale Patterns of Peptides]
# Y. Wang, E. Benson, F. Fördős, M. Lolaico, I. Baars, T. Fang, A.I. Teixeira, B. Högberg, ''Adv. Mater.'' '''33''', 2008457 (2021)
#: [https://doi.org/10.1002/adma.202008457 DNA Origami Penetration in Cell Spheroid Tissue Models is Enhanced by Wireframe Design]
# L. Li, H. Wang, C. Xiong, D. Luo, H. Chen and Y. Liu, ''J. Phys.: Condens. Matter'' '''33''', 185102 (2021)
#: [https://doi.org/10.1088/1361-648X/abee38 Quantify the combined effects of temperature and force on the stability of DNA hairpin]
# J. P. Mahalik and M. Muthukumar, submitted
#: Nucleotide Dynamics During Flossing of Polycation-DNA-Polycation through a Nanopore using Molecular Dynamics ([https://doi.org/10.1101/2021.06.21.449276 bioRxiv])
# 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)
#: [https://doi.org/10.1016/j.nantod.2021.101308 Self-resetting Molecular Probes for Nucleic Acids Enabled by Fuel Dissipative Systems] ([https://doi.org/10.1101/2021.06.01.21257665 medRxiv])
# 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)
#: [https://doi.org/10.1002/anie.202107829 Programmable site-specific functionalization of DNA origami with polynucleotide brushes]
# 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]
# 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)
#: [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)
#: [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, ''J. Phys. Chem. B'' '''126''', 5007–5016 (2022).
#: [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)
#:[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'' '''14''', 2638–2648 (2022).
#: [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.'' '''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])
# W.T. Kaufhold, W. Pfeifer, C.E. Castro and L. Di Michele, ''ACS Nano'' '''16''', 8784–8797 (2022).
#: [https://doi.org/10.1021/acsnano.1c08999 Probing the mechanical properties of DNA nanostructures with metadynamics] ([https://arxiv.org/abs/2110.01477 arXiv])
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# 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'', accepted (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'' accepted (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'' accepted
#: [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, submitted
#: 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])
# 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
#: Structural flexibility dominates over binding strength for supramolecular crystallinity ([https://doi.org/10.1101/2023.09.04.556250 bioRxiv])
# C. Shi, P. Wang, submitted
#: Allosteric DNAzyme for sensitive detection of nucleic acids for molecular diagnosis ([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, submitted
#: 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, submitted
#: 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)
#: Coarse-grained modelling of DNA-RNA hybrids ([https://doi.org/10.48550/arXiv.2311.07709 arXiv])
# 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, submitted
#: 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, submitted
#: A dynamically gated 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])


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 23:14, 18 March 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
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    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)
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    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
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    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 accepted (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 accepted
    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, submitted
    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. M. DeLuca, T. Ye, M. Poirier, Y. Ke, C. Castro and G. Arya, submitted
    Mechanism of DNA origami folding elucidated by mesoscopic simulations (bioRxiv)
  271. 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)
  272. C. Shi, P. Wang, submitted
    Allosteric DNAzyme for sensitive detection of nucleic acids for molecular diagnosis (medRxiv)
  273. 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)
  274. K. Gallagher, J. Yu, D.A. King, R. Liu, E. Eiser, submitted
    Towards New Liquid Crystal Phases of DNA mesogens (arXiv)
  275. 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)
  276. H. Koh, J.Y. Lee, J.G. Lee, submitted
    Forming superhelix of double stranded DNA from local deformation (arXiv)
  277. N.P. Agarwal and A. Gopinath, submited
    DNA origami 2.0 (bioRxiv)
  278. J.M. Weck and A. Heuer-Jungemann, submitted
    Fully addressable, designer superstructures assembled from a single modular DNA origami (bioRxiv)
  279. 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)
  280. 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, submitted
    Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments (arXiv)
  281. 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)
  282. F. Tosti Guerra, E. Poppleton, P. Šulc, L. Rovigatti, submitted
    nNxB: a new coarse-grained model for RNA and DNA nanotechnology (arXiv)
  283. 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)
  284. Y. Du, R. Li, A.S. Madhvacharyula, A.A. Swett, J.H. Choi, submitted
    DNA nanostar structures with tunable auxetic properties (bioRxiv)
  285. 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)
  286. A. Walbrun, T. Wang, M. Matthies, P. Šulc, F.C. Simmel, M. Rief, submitted
    Single-Molecule Force Spectroscopy of Toehold-Mediated Strand Displacement (bioRxiv)
  287. S. Chandrasekhar, T.P. Swope, F. Fadaei, D.R. Hollis, R. Bricker, D. Houser, J. Portman, T.L. Schmidt, submitted
    Bending Unwinds DNA (bioRxiv)
  288. X. Liu, F. Liu, H. Chhabra, C. Maffeo, Q. Huang, A. Aksimentiev, T. Arai, submitted
    A dynamically gated triangular DNA nanopore for molecular sensing and cross-membrane transport (ResearchSquare)
  289. C. Karfusehr, M. Eder, F.C. Simmel
    Self-assembled cell-scale containers made from DNA origami membranes (bioRxiv)
  290. 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)

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