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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]  
Line 135: Line 137:
# E. Locatelli and L. Rovigatti, ''Polymers'' '''10''', 447 (2018)
# E. Locatelli and L. Rovigatti, ''Polymers'' '''10''', 447 (2018)
#: [https://doi.org/10.3390/polym10040447 An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids] ([https://www.preprints.org/manuscript/201803.0203/v1 preprints])
#: [https://doi.org/10.3390/polym10040447 An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids] ([https://www.preprints.org/manuscript/201803.0203/v1 preprints])
# E. Spruijt, S.E. Tusk and H. Bayley, ''Nature Nanotechnology'' '''13''', 739-745 (2018)
# E. Spruijt, S.E. Tusk and H. Bayley, ''Nat. Nanotechnol.'' '''13''', 739-745 (2018)
#: [http://dx.doi.org/10.1038/s41565-018-0139-6 DNA scaffolds support stable and uniform peptide nanopores]
#: [http://dx.doi.org/10.1038/s41565-018-0139-6 DNA scaffolds support stable and uniform peptide nanopores]
# L. Coronel, A. Suma and C. Micheletti, ''Nucleic Acids Res.'' '''46''',7522–7532 (2018)
# L. Coronel, A. Suma and C. Micheletti, ''Nucleic Acids Res.'' '''46''',7522–7532 (2018)
Line 161: Line 163:
# Y. Choi, H. Choi, A.C. Lee, S. Kwon, ''J. Vis. Exp.'', e58364 (2018)
# Y. Choi, H. Choi, A.C. Lee, S. Kwon, ''J. Vis. Exp.'', e58364 (2018)
#: [https://doi.org/10.3791/58364 Design and Synthesis of a Reconfigurable DNA Accordion Rack]
#: [https://doi.org/10.3791/58364 Design and Synthesis of a Reconfigurable DNA Accordion Rack]
# M.M.C. Tortora, G. Mishra, D. Prešern and J.P.K. Doye, ''Sci. Adv.'' '''6''', accepted (2020)
# M.M.C. Tortora, G. Mishra, D. Prešern and J.P.K. Doye, ''Sci. Adv.'' '''6''', eaaw8331 (2020)
#: Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamis ([https://arxiv.org/abs/1811.12331 arXiv])
#: [https://dx.doi.org/10.1126/sciadv.aaw8331 Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamis] ([https://arxiv.org/abs/1811.12331 arXiv])
#  C.-M. Huang,  A. Kucinic, J.V. Le, C.E. Castro and H.-J. Su, ''Nanoscale'' '''11''', 1647-1660 (2019)  
#  C.-M. Huang,  A. Kucinic, J.V. Le, C.E. Castro and H.-J. Su, ''Nanoscale'' '''11''', 1647-1660 (2019)  
#: [https://dx.doi.org/10.1039/C8NR06377J Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis]
#: [https://dx.doi.org/10.1039/C8NR06377J Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis]
Line 185: Line 187:
# J.F. Berengut, J.C. Berengut, J.P.K. Doye, D. Prešern, A. Kawamoto, J. Ruan, M.J. Wainwright and L.K. Lee,, ''Nucleic Acids Res.'' '''47''', 11963–11975(2019)
# J.F. Berengut, J.C. Berengut, J.P.K. Doye, D. Prešern, A. Kawamoto, J. Ruan, M.J. Wainwright and L.K. Lee,, ''Nucleic Acids Res.'' '''47''', 11963–11975(2019)
#: [https://doi.org/10.1093/nar/gkz1056 Design and synthesis of pleated DNA origami nanotubes with adjustable diameters] ([http://dx.doi.org/10.1101/534792 bioRxiv])
#: [https://doi.org/10.1093/nar/gkz1056 Design and synthesis of pleated DNA origami nanotubes with adjustable diameters] ([http://dx.doi.org/10.1101/534792 bioRxiv])
# K.G. Young, B. Najafi, A.A. Louis, J.P.K. Doye, A.J. Turberfield and J. Bath, ''Angew. Chem. Int. Ed.'' '''59''', accepted (2020)
# K.G. Young, B. Najafi, W.M. Sant, S. Contera, A.A. Louis, J.P.K. Doye, A.J. Turberfield and J. Bath, ''Angew. Chem. Int. Ed.'' '''59''', 15942-15946 (2020)
#: [https://doi.org/10.1002/anie.202006281 Reconfigurable T-junction DNA origami]
#: [https://doi.org/10.1002/anie.202006281 Reconfigurable T-junction DNA origami]
# I.D. Stoev, T. Cao, A. Caciagli, J. Yu, C. Ness, R. Liu, R. Ghosh, T. O'Neill, D. Liu and E. Eiser, ''Soft Matter'' '''16''', 990-1001 (2020)
# I.D. Stoev, T. Cao, A. Caciagli, J. Yu, C. Ness, R. Liu, R. Ghosh, T. O'Neill, D. Liu and E. Eiser, ''Soft Matter'' '''16''', 990-1001 (2020)
Line 195: Line 197:
# Z. Shi and G. Arya, ''Nucleic Acids Research'' '''48''', 548-560 (2020)
# Z. Shi and G. Arya, ''Nucleic Acids Research'' '''48''', 548-560 (2020)
#: [https://doi.org/10.1093/nar/gkz1137 Free energy landscape of salt-actuated reconfigurable DNA nanodevices]
#: [https://doi.org/10.1093/nar/gkz1137 Free energy landscape of salt-actuated reconfigurable DNA nanodevices]
# E. Torelli, J.W. Kozyra, B. Shirt-Ediss, L. Piantanida, K. Voïtchovsky, N. Krasnogor, submitted
# E. Torelli, J.W. Kozyra, B. Shirt-Ediss, L. Piantanida, K. Voïtchovsky, N. Krasnogor, ''ACS Synth. Biol.'' '''9''', 1682-1692 (2020)
#: Co-transcriptional folding of a bio-orthogonal fluorescent scaffolded RNA origami ([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).
#:[https://doi.org/10.1021/jacs.9b09093 A DNA origami platform for single-pair Förster resonance energy transfer investigation of DNA–DNA interactions and ligation]
#:[https://doi.org/10.1021/jacs.9b09093 A DNA origami platform for single-pair Förster resonance energy transfer investigation of DNA–DNA interactions and ligation]
# E. Poppleton, J. Bohlin, M. Matthies, S. Sharma, F. Zhang and P. Šulc, ''Nucleic Acids Res.'' '''48''', Advance Article (2020)
# E. Poppleton, J. Bohlin, M. Matthies, S. Sharma, F. Zhang and P. Šulc, ''Nucleic Acids Res.'' '''48''', e72 (2020)
#: [https://doi.org/10.1093/nar/gkaa417 Design, optimization, and analysis of large DNA and RNA nanostructures through interactive visualization, editing, and molecular simulation] ([https://doi.org/10.1101/2020.01.24.917419 bioRxiv])
#: [https://doi.org/10.1093/nar/gkaa417 Design, optimization, and analysis of large DNA and RNA nanostructures through interactive visualization, editing, and molecular simulation] ([https://doi.org/10.1101/2020.01.24.917419 bioRxiv])
# M.C. Engel, F. Romano, A.A. Louis and J.P.K. Doye, submitted
# M.C. Engel, F. Romano, A.A. Louis and J.P.K. Doye, ''J. Chem. Theor. Comput.'' '''16''', 7764–7775 (2020).
#: Measuring internal forces in single-stranded DNA: Application to a DNA force clamp
#: [https://doi.org/10.1021/acs.jctc.0c00286 Measuring internal forces in single-stranded DNA: Application to a DNA force clamp] ([http://arxiv.org/abs/arXiv:2007.13865 arXiv])
# C. Bores and B.M. Pettitt, ''Phys. Rev. E'' '''101''', 012406 (2020)
# C. Bores and B.M. Pettitt, ''Phys. Rev. E'' '''101''', 012406 (2020)
#: [https://doi.org/10.1103/PhysRevE.101.012406 Structure and the role of filling rate on model dsDNA packed in a phage capsid]
#: [https://doi.org/10.1103/PhysRevE.101.012406 Structure and the role of filling rate on model dsDNA packed in a phage capsid]
# 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''', accepted (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]
# F. Hong, J.S. Schreck and P. Šulc, submitted
# F. Hong, J.S. Schreck and P. Šulc, ''Nucleic Acids Res.'' '''48''', 10726–10738 (2020).
#: Understanding DNA interactions in crowded environments with a coarse-grained model ([https://doi.org/10.1101/2020.06.08.140434 bioRxiv])
#: [https://doi.org/10.1093/nar/gkaa854 Understanding DNA interactions in crowded environments with a coarse-grained model] ([https://doi.org/10.1101/2020.06.08.140434 bioRxiv])
# 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, ''J. Am. Chem. Soc.'' '''142''', 12069–12078 (2020)
#: Detecting nanoscale distribution of protein pairs by proximity dependent super-resolution microscopy ([https://doi.org/10.1101/591081 bioRxiv])
#: [https://doi.org/10.1021/jacs.9b03418 Detecting nanoscale distribution of protein pairs by proximity dependent super-resolution microscopy] ([https://doi.org/10.1101/591081 bioRxiv])
# 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])
# K. Tapio, A. Mostafa, Y. Kanehira, A. Suma, A. Dutta, I. Bald, ''ACS Nano'' '''15''', 7065–7077 (2021)
#: [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, ''Nature'' 596, 367–371 (2021)
#: [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, ''Soft Matter'' '''17''', 1530-1537 (2021)
#: [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)
#: [https://doi.org/10.1021/acs.langmuir.0c01520 Gelling without structuring: a SAXS study of the interactions among DNA nanostars]
# J. Huang  A. Suma, M. Cui, G. Grundmeier, V. Carnevale, Y. Zhang, C. Kielar and A. Keller, ''Small Str.'' '''1''', 2000038 (2020)
#: [https://doi.org/10.1002/sstr.202000038 Arranging small molecules with sub‐nanometer precision on DNA origami substrates for the single‐molecule investigation of protein‐ligand interactions]
# G. Yao, F. Zhang, F. Wang, T. Peng, H. Liu, E. Poppleton, P. Šulc, S. Jiang, L. Liu, C. Gong, X. Jing, X. Liu, L. Wang, Y. Liu, C. Fan and H. Yan, ''Nat. Chem.'' '''12''', 1067–1075 (2020)
#: [https://doi.org/10.1038/s41557-020-0539-8 Meta-DNA structures]
# 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]
# 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])
# Z. Sierzega, J. Wereszczynski and C. Prior, ''Sci. Rep.'' '''11''', 1527 (2021)
#: [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, ''Phys. Rev. E'' '''103''', 042408 (2021)
#: [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)
#: [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)
#: [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 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]
# 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]
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# Y. Zhang, X. Yin, C. Cui, K. He, F. Wang, J. Chao, T. Li, X. Zuo, A. Li, L. Wang, N. Wang, X. Bo and C. Fan, ''Sci. Adv.''  '''9''', adf8263 (2023)
#: [https://doi.org/10.1126/sciadv.adf8263 Prime factorization via localized tile assembly in a DNA origami framework]
# W.G. Pfeifer, C.-M. Huang, M. G. Poirier, G. Arya and C. E. Castro, ''Sci. Adv.'' '''9''', adi0697 (2023)
#: [https://doi.org/10.1126/sciadv.adi0697 Versatile computer-aided design of free-form DNA nanostructures and assemblies] ([https://doi.org/10.1101/2023.03.30.535006 bioRxiv])
# M. Lolaico, S. Blokhuizen, B. Shen, Y. Wang, and B. Högberg, ''ACS Nano'' '''17''', 6565–6574 (2023)
#: [https://doi.org/10.1021/acsnano.2c11982 Computer-Aided Design of A-Trail Routed Wireframe DNA Nanostructures with Square Lattice Edges]
# Y. Wang, A. Kucinic, L. Des Rosiers, P.E. Beshay, N. Wile, M.W. Hudoba and C.E. Castro, ''Appl. Sci.'' '''13''', 3208 (2023)
#: [https://doi.org/10.3390/app13053208 Mechanical Design of DNA Origami in the Classroom]
# D. Morzy, C. Tekin, V. Caroprese, R. Rubio-Sánchez, L. Di Michele and M.M.C. Bastings, ''Nanoscale'' '''15''', 2849-2859 (2023)
#: [https://doi.org/10.1039/D2NR05368C Interplay of the mechanical and structural properties of DNA nanostructures determines their electrostatic interactions with lipid membranes]
# L. Zhang, H. Zhao, H. Yang and X. Su, ''Biosens. Bioelectron.'' '''239''', 115622 (2023)
#:[https://doi.org/10.1016/j.bios.2023.115622 Coarse-grained model simulation-guided localized DNA signal amplification probe for miRNA detection]
# Y.-P. Qiao, C.-L. Ren and Y.-Q. Ma ''J. Phys. Chem. B'' '''127''', 4015–4021 (2023)
#: [https://doi.org/10.1021/acs.jpcb.2c08618 Two Different Ways of Stress Release in Supercoiled DNA Minicircles under DNA Nick]
# K. Cervantes-Salguero, Y.A. Gutiérrez Fosado, W. Megone, J.E. Gautrot and M. Palma, ''Molecules'' '''28''', 3686 (2023)
#: [https://doi.org/10.3390/molecules28093686 Programmed self-assembly of DNA nanosheets with discrete single-molecule thickness and interfacial mechanics: Design, simulation, and characterization]
# H.L. Too and Z. Wang, ''Nanoscale'' '''15''', 11915-11926 (2023)
#: [https://doi.org/10.1039/D3NR01058A Exhaustive classification and systematic free-energy profile study of single-stranded DNA inter-overhang migration]
# D. Saliba, X. Luo, F.J. Rizzuto and H.F. Sleiman, ''Nanoscale'' '''15''', 5403-5413 (2023)
#: [https://doi.org/10.1039/D2NR06185F Programming rigidity into size-defined wireframe DNA nanotubes]
# J. Lee and S. Lee, ''Anal. Chem.'' '''95''', 1856–1866 (2023) 
#: [https://doi.org/10.1021/acs.analchem.2c03378 Non-invasive, reliable, and fast quantification of DNA loading on gold nanoparticles by a one-step optical measurement]
# X. Shen, Q. Ouyang, H. Tan, J. Ouyang and N. Na, ''Anal. Chem.'' '''95''', 5903–5910 (2023)
#: [https://doi.org/10.1021/acs.analchem.2c04916 Computation-assisted design of ssDNA framework nanorobots for cancer logical recognition, toehold disintegration, visual dual-diagnosis, and synergistic therapy]
# L. Tang, M. Huang, M. Zhang, Y. Pei, Y. Liu, Y. Wei, C. Yang, T. Xie, D. Zhang, R. Zhou, Y. Song, J. Song, ''Small Methods'' '''7''', 2300327 (2023)
#: [https://doi.org/10.1002/smtd.202300327 De novo evolution of an antibody-mimicking multivalent aptamer via a DNA framework]
# Z. Zheng, S.H. Kim, A. Chovin, N. Clement and C. Demaille, ''Chem. Sci.'' '''14''', 3652-3660 (2023)
#: [https://doi.org/10.1039/D3SC00320E Electrochemical response of surface-attached redox DNA governed by low activation energy electron transfer kinetics]
# M. Vogt, M. Langecker, M. Gouder, E. Kopperger, F. Rothfischer, F.C. Simmel and J. List, ''Nature Physics'' '''19''', 741–751 (2023)
#: [https://doi.org/10.1038/s41567-023-01938-3 Storage of mechanical energy in DNA nanorobotics using molecular torsion springs]
# C. Xie, Y. Hu, K. Chen, Z. Chen and L. Pan, ''Commun. Comput. Inf. Sci.'', '''1801''', 647–654 (2023)
#: [https://doi.org/10.1007/978-981-99-1549-1_51 Tuning Geometric Conformations of Curved DNA Structures by Controlling Positions of Nicks]
# S. Yu, J. Zhao, R. Chu, X. Li, G. Wu and X. Meng, ''Entropy'' '''25''', 796 (2023) 
#: [https://doi.org/10.3390/e25050796 Anomalous diffusion of polyelectrolyte segments on supported charged lipid bilayers]
# I. Madrid, Z. Zheng, C. Gerbelot, A. Fujiwara, S. Li, S. Grall, K. Nishiguchi, S.H. Kim, A. Chovin, C. Demaille and N. Clement, ''ACS Nano'' '''17''', 17031–17040 (2023)
#: [https://doi.org/10.1021/acsnano.3c04349 Ballistic Brownian Motion of Nanoconfined DNA]
# Y. Ma, W. Guo, Q. Mou, X. Shao, M. Lyu, V. Garcia, L. Kong, W. Lewis, C. Ward, Z. Yang, X. Pan, S.S. Yi and Y. Lu, ''Nat. Biotechnol.'' (2023)
#: [https://doi.org/10.1038/s41587-023-01801-z Spatial imaging of glycoRNA in single cells with ARPLA]
# X. Luo, D. Saliba, T. Yang, S. Gentile, K. Mori, P.I. Garcia, T. Das, N. Bagheri, A. Porchetta, A. Guarne, G. Cosa, H.F. Sleiman, ''Angew. Chem. Int. Ed.'' '''62''' e202309869 (2023)
#: [https://doi.org/10.1002/anie.202309869 Minimalist design of wireframe DNA nanotubes: Tunable geometry, size, chirality, and dynamics]
# Y. Zhao, S. Cao, Y. Wang, F. Li, L. Lin, L. Guo, F. Wang, J. Chao, X. Zuo, Y. Zhu, L. Wang, J. Li and C. Fan, ''Nat. Mach. Intell.'' '''5''', 980–990 (2023)
#: [https://doi.org/10.1038/s42256-023-00707-4 A temporally resolved DNA framework state machine in living cells]
# X.R. Liu, I.Y. Loh, W. Siti, H.L. Too, T. Anderson and Z. Wang, ''Nanoscale Horiz.'', '''8''', 827-841 (2023)
#: [https://doi.org/10.1039/D2NH00565D A light-operated integrated DNA walker–origami system beyond bridge burning]
# H. Lv, N. Xie, M. Li, M. Dong, C. Sun, Q. Zhang, L. Zhao, J. Li, X. Zuo, H. Chen, F. Wang and C. Fan, ''Nature'' '''622''', 292–300(2023). 
#: [https://doi.org/10.1038/s41586-023-06484-9 DNA-based programmable gate arrays for general-purpose DNA computing]
# C. Yang, X. Song, Y. Feng, G. Zhao, and Y. Liu, ''J. Phys.: Condens. Matter'' '''35''', 265101 (2023)
#: [https://doi.org/10.1088/1361-648X/acc7eb Stability of DNA and RNA hairpins: a comparative study based on ox-DNA]
# Xiaoya Song, Chao Yang, Yuyu Feng, Hu Chen, and Yanhui Liu, ''Commun. Theor. Phys.'' '''75''', 055601 (2023)
#: [https://doi.org/10.1088/1572-9494/acc64c A common rule for the intermediate state caused by DNA mismatch in single-molecule experiments]
# W. Siti, H.L. Too, T. Anderson, X.R. Liu, I.Y. Loh and Z. Wang, ''Sci. Adv.'' '''9''', adi8444 (2023)
#: [https://dx.doi.org/10.1126/sciadv.adi8444 Autonomous DNA molecular motor tailor-designed to navigate DNA origami surface for fast complex motion and advanced nanorobotics]
# R. Ma, A. Velusamy, S.A. Rashid, B.R. Deal, W. Chen, B. Petrich, R. Li, K. Salaita, ''Nat. Methods'' '''20''', 1666–1671 (2023)
#: [https://doi.org/10.1038/s41592-023-02030-7 Molecular mechanocytometry using tension-activated cell tagging] ([https://doi.org/10.1101/2023.01.10.523449 bioRxiv])
# D. Karna, E. Mano, J. Ji, I. Kawamata, Y. Suzuki and H. Mao, ''Nat. Commun.'' '''14''', 6459 (2023)
#: [https://doi.org/10.1038/s41467-023-41604-z Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies]
# J. Fu, L. Zhang, Y. Long, Z. Liu, G. Meng, H. Zhao, X. Su and S. Shi, ''Anal. Chem.'' '''95''', 16089–16097 (2023)
#: [https://doi.org/10.1021/acs.analchem.3c01861 Multiplexed CRISPR-based nucleic acid detection using a single Cas protein]
# Y. Yang, Q. Lu, Y. Chen, M. DeLuca, G. Arya, Y. Ke and S. Zauscher, ''Angew. Chem. Int. Ed.'' '''62''', e202311727 (2023)
#: [https://doi.org/10.1002/anie.202311727 Spatiotemporal control over polynucleotide brush growth on DNA origami nanostructures]
# J.Y. Lee, H. Koh and D.-N. Kim, Nat. Commun. '''14''', 7079 (2023)
#: [https://doi.org/10.1038/s41467-023-42873-4 A computational model for structural dynamics and reconfiguration of DNA assemblies]
# M.C. Engel, J.A. Smith and M.P. Brenner, ''Phys. Rev. X'' '''13''', 041032 (2023)
#: [https://doi.org/10.1103/PhysRevX.13.041032 Optimal control of nonequilibrium systems through automatic differentiation]
# L. Yu, Y. Xu, M. Al-Amin, S. Jiang, M. Sample, A. Prasad, N. Stephanopoulos, P. Šulc, and H. Yan, ''J. Am. Chem. Soc.'' '''145''', 27336–27347 (2023)
#: [https://doi.org/10.1021/jacs.3c07491 CytoDirect: A nucleic acid nanodevice for specific and efficient delivery of functional payloads to the cytoplasm]
# Y.-P. Qiao and C.-L. Ren, ''Langmuir'' '''40''', 109–117 (2024)
#: [https://doi.org/10.1021/acs.langmuir.3c02231 Correlated hybrid DNA structures explored by the oxDNA Model]
# L. Kilwing, P. Lill, B. Nathwani, R. Guerra, E. Benson, T. Liedl and W. M. Shih, ''ACS Nano'' '''18''', 885–893 (2024)
#: [https://doi.org/10.1021/acsnano.3c09522 Multilayer DNA origami with terminal interfaces that are flat and wide-area]
# N. Adžić, C. Jochum, C. N. Likos, E. Stiakakis, ''Small'', '''20''', 2308763 (2024)
#: [https://doi.org/10.1002/smll.202308763 Engineering ultrasoft interactions in stiff all-DNA dendrimers by site-specific control of scaffold flexibility]
# A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and  K. Salaita, ''Nat. Commun.'' '''15''', 704 (2024)
#: [https://doi.org/10.1038/s41467-023-44061-w DNA mechanocapsules for programmable piconewton responsive drug delivery]
# Y. Liu, B. Li, F. Wang, Q. Li, S. Jia, X. Liu, and M. Li, ''ACS Appl. Bio Mater.'' '''7''', 1311–1316 (2024)
#: [https://doi.org/10.1021/acsabm.3c01270 Quantitative analysis of resistance to deformation of the DNA origami framework supported by struts]
# S. He, H. Deng, P. Li, Q. Tian, Y. Yang, J. Hu, H. Li, T. Zhao, H. Ling, Y. Liu, S. Liu and Q. Guo, ''J. Nanobiotechnol.'' '''22''', 39 (2024)
#: Bimodal DNA self-origami material with nucleic acid function enhancement
# B. Babatunde, J. Cagan, R.E. Taylor, ''J. Mech. Des.'' '''146''', 051708 (2024)
#: [https://doi.org/10.1115/1.4064242 An improved shape annealing algorithm for the generation of coated deoxyribonucleic acid origami nanostructures]
# A.S.G. Martins, S.D. Reis, E. Benson, M.M. Domingues, J. Cortinhas, J.A. Vidal Silva, S.D. Santos, N.C. Santos, A.P. Pêgo, P.M.D. Moreno, ''Small'' '''20''', 2309140 (2024)
#: [https://doi.org/10.1002/smll.202309140 Enhancing Neuronal Cell Uptake of Therapeutic Nucleic Acids with Tetrahedral DNA Nanostructures]
# S Dey, R. Rivas-Barbosa, F. Sciortino, E. Zaccarelli and P. Zijlstra, ''Nanoscale'' '''16''', 4872-4879 (2024)
#: [https://doi.org/10.1039/D3NR06140J Biomolecular interactions on densely coated nanoparticles: a single-molecule perspective]
# T. Chen, S. Mao, J. Ma, X. Tang, R. Zhu, D. Mao, X. Zhu, Q. Pan, ''Angew. Chem. Int. Ed'' '''63''', e202319117 (2024)
#: [https://doi.org/10.1002/anie.202319117 Proximity-enhanced functional imaging analysis of engineered tumors]
# Y. Liu, Z. Dai, X. Xie, B. Li, S. Jia, Q. Li, M. Li, C. Fan and X. Liu, ''J. Am. Chem. Soc.'' '''146''', 8, 5461–5469 (2024)
#: [https://doi.org/10.1021/jacs.3c13180 Spacer-programmed two-dimensional DNA origami assembly]
# Z. Zheng, S. Grall, S.H. Kim, A. Chovin, N. Clement and C. Demaille, ''J. Am. Chem. Soc.'' '''146''', 9, 6094–6103 (2024)
#: [https://doi.org/10.1021/jacs.3c13532 Activationless electron transfer of redox-DNA in electrochemical nanogaps]
# M. Sample, M. Matthies and P. Šulc, 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])
# V. Caroprese, C. Tekin, V. Cencen, M. Mosayebi, T.B. Liverpool, D.N. Woolfson, G. Fantner, M.M.C. Bastings, submitted
#: Structural flexibility dominates over binding strength for supramolecular crystallinity ([https://doi.org/10.1101/2023.09.04.556250 bioRxiv])
# C. Shi, D. Yang, X.Ma, L. Pan, Y. Shao, G. Arya, Y. Ke, C. Zhang, F. Wang, X. Zuo, M. Li and P. Wang, ''Angew. Chem. Int. Ed.'' '''63''' e202320179 (2024)
#: [https://doi.org/10.1002/anie.202320179 A programmable DNAzyme for the sensitive detection of nucleic acids] ([https://doi.org/10.1101/2023.08.20.23294196 medRxiv])
# F. Smith, A. Sengar, G.‐B.V. Stan, T.E. Ouldridge, M. Stevens, J. Goertz and W. Bae, submitted
#: Overcoming the speed limit of four‐way DNA branch migration with bulges in toeholds ([https://doi.org/10.1101/2023.05.15.540824 bioRxiv])
# K. Gallagher, J. Yu, D.A. King, R. Liu, E. Eiser, ''APL Mater.'' '''11''', 061129 (2023)
#: [https://doi.org/10.1063/5.0145570 Towards new liquid crystal phases of DNA mesogens] ([https://doi.org/10.48550/arXiv.2302.03501 arXiv])
# G.B.M. Wisna, D. Sukhareva, J. Zhao, D. Satyabola, M. Matthies, S. Roy, P. Šulc, H. Yan and R.F. Hariadia, submitted
#: High-speed 3D DNA-PAINT and unsupervised clustering for unlocking 3D DNA origami cryptography ([https://doi.org/10.1101/2023.08.29.555281 bioRxiv])
# H. Koh, J.Y. Lee, J.G. Lee, submitted
#: Forming superhelix of double stranded DNA from local deformation ([https://doi.org/10.48550/arXiv.2307.04597 arXiv])
# N.P. Agarwal and A. Gopinath, submited
#: DNA origami 2.0 ([https://doi.org/10.1101/2022.12.29.522100 bioRxiv])
# J.M. Weck and A. Heuer-Jungemann, submitted
#: Fully addressable, designer superstructures assembled from a single modular DNA origami ([https://doi.org/10.1101/2023.09.14.557688 bioRxiv])
# Y. Xu, R. Zheng, A. Prasad, M. Liu, Z. Wan, X. Zhou, R.M. Porter, M. Sample, E. Poppleton, J. Procyk, H. Liu, Y. Li,  S. Wang, H. Yan, P. Sulc,  N. Stephanopoulos, submitted
#: High-affinity binding to the SARS-CoV-2 spike trimer by a nanostructured, trivalent protein-DNA synthetic antibody ([https://doi.org/10.1101/2023.09.18.558353 bioRxiv])
# H. Liu, M. Matthies, J. Russo, L. Rovigatti, R.P. Narayanan, T. Diep, D. McKeen, O. Gang, N. Stephanopoulos, F. Sciortino, H. Yan, F. Romano and P. Šulc, ''Science'' '''384''', 776-781 (2024)
#: [https://doi.org/10.1126/science.adl5549 Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments] ([https://doi.org/10.48550/arXiv.2310.10995 arXiv])
# L. Grabenhorst, M. Pfeiffer, T. Schinkel, M. Kümmerlin, J.B. Maglic, G.A. Brüggenthies, F. Selbach, A.T. Murr, P. Tinnefeld, V. Glembockyte, 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.'' accepted (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.'' accepted (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]
# 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])
# 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, submitted
#: Context-dependent structure formation of RNA hairpin motifs ([https://doi.org/10.1101/2024.04.17.589867 bioRxiv])
# 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])




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].

Revision as of 14:08, 4 September 2024

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    Structural, mechanical and thermodynamic properties of a coarse-grained DNA model (arXiv)
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    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)
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    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)
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    Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble (arXiv)
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    Coarse-grained simulations of DNA overstretching (arXiv)
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    Optimizing DNA nanotechnology through coarse-grained modelling: a two-footed DNA walker
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    DNA hybridization kinetics: zippering, internal displacement and sequence dependence (arXiv)
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    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)
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    Accurate phase diagram of tetravalent DNA nanostars (arXiv)
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    A nucleotide-level coarse-grained model of RNA (arXiv)
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    Gels of DNA Nanostars Never Crystallise
  19. Q. Wang, B. M. Pettitt, Biophys. J. 106, 1182–1193 (2014)
    Modeling DNA Thermodynamics under Torsional Stress
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    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
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    The role of loop stacking in the dynamics of DNA hairpin formation (arXiv)
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    From bistate molecular switches to self-directed track-walking nanomotors
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    Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA (arXiv)
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    A comparison between parallelization approaches in molecular dynamics simulations on GPUs (arXiv)
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    Physical model for recognition tunneling
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    Switching Bonds in a DNA Gel: An All-DNA Vitrimer
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    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)
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    DNA nanotechnology: understanding and optimisation through simulation (arXiv)
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    Modelling toehold-mediated RNA strand displacement (arXiv)
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    Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA (arXiv)
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    Coarse-grained modelling of supercoiled RNA (arXiv)
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    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"
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    Identifying physical causes of apparent enhanced cyclization of short DNA molecules with a coarse-grained model (arXiv) (data)
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    Base triplet stepping by the Rad51/RecA family of recombinases
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    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
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    Characterizing DNA star-tile-based nanostructures using a coarse-grained model
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    Biomimetic autonomous enzymatic nanowalker of high fuel efficiency
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    Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars
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    Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation
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    Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal (arXiv) (data)
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    Condensation and demixing in solutions of DNA nanostars and their mixtures
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    DNA elasticity from coarse-grained simulations: the effect of groove asymmetry (arXiv)
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    DNA-assisted oligomerization of pore-forming toxin monomers into precisely-controlled protein channels
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    Characterizing the motion of jointed DNA nanostructures using a coarse-grained model
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  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)
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    A coarse-grained model for DNA origami
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    DNA bipedal motor walking dynamics: An experimental and theoretical study of the dependency on step size (data)
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    Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly (arXiv)
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    Substrate conformational dynamics drive structure-specific recognition of gapped DNA by DNA polymerase (bioRXiv)
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    How well can DNA rupture DNA? Shearing and unzipping forces inside DNA nanostructures
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    Bend-induced twist waves and the structure of nucleosomal DNA (arXiv)
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    Incorporating particle flexibility in a density functional description of nematics and cholesterics (arXiv)
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    Coarse-Grained Simulation of DNA using LAMMPS (arXiv)
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    Force-induced unravelling of DNA Origami
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    Mechanosensing potentials gate fuel consumption in a bipedal DNA nanowalker
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    An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids (preprints)
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    Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking (bioRXiv)
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    Mechanisms of DNA hybridization: Transition path analysis of a simulation-informed Markov model(arxiv)
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    The temperature dependence of the helical twist of DNA
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    Twist-bend coupling and the statistical mechanics of the twistable worm-like chain model of DNA: Perturbation theory and beyond (bioRXiv,arXiv)
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    Coarse-grained modelling of the structural properties of DNA origami (arXiv) (data)
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    Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement (bioRXiv)
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    Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis
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    Computational simulation of adapter length-dependent LASSO probe capture efficiency
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    tacoxDNA: a user-friendly web server for simulations of complex DNA structures, from single strands to origami
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    Design and synthesis of pleated DNA origami nanotubes with adjustable diameters (bioRxiv)
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    Reconfigurable T-junction DNA origami
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    On the Role of Flexibility in Linker-Mediated DNA Hydrogels (arXiv)
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    Evolutionary Refinement of DNA Nanostructures Using Coarse-Grained Molecular Dynamics Simulations
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    Design, optimization, and analysis of large DNA and RNA nanostructures through interactive visualization, editing, and molecular simulation (bioRxiv)
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  222. A. Kucinic, C.-M. Huang, J. Wang, H.-J. Su and C.E. Castro, Nanoscale, 15 562-572 (2023)
    DNA origami tubes with reconfigurable cross-sections
  223. Y. Zhang, X. Yin, C. Cui, K. He, F. Wang, J. Chao, T. Li, X. Zuo, A. Li, L. Wang, N. Wang, X. Bo and C. Fan, Sci. Adv. 9, adf8263 (2023)
    Prime factorization via localized tile assembly in a DNA origami framework
  224. W.G. Pfeifer, C.-M. Huang, M. G. Poirier, G. Arya and C. E. Castro, Sci. Adv. 9, adi0697 (2023)
    Versatile computer-aided design of free-form DNA nanostructures and assemblies (bioRxiv)
  225. M. Lolaico, S. Blokhuizen, B. Shen, Y. Wang, and B. Högberg, ACS Nano 17, 6565–6574 (2023)
    Computer-Aided Design of A-Trail Routed Wireframe DNA Nanostructures with Square Lattice Edges
  226. Y. Wang, A. Kucinic, L. Des Rosiers, P.E. Beshay, N. Wile, M.W. Hudoba and C.E. Castro, Appl. Sci. 13, 3208 (2023)
    Mechanical Design of DNA Origami in the Classroom
  227. D. Morzy, C. Tekin, V. Caroprese, R. Rubio-Sánchez, L. Di Michele and M.M.C. Bastings, Nanoscale 15, 2849-2859 (2023)
    Interplay of the mechanical and structural properties of DNA nanostructures determines their electrostatic interactions with lipid membranes
  228. L. Zhang, H. Zhao, H. Yang and X. Su, Biosens. Bioelectron. 239, 115622 (2023)
    Coarse-grained model simulation-guided localized DNA signal amplification probe for miRNA detection
  229. Y.-P. Qiao, C.-L. Ren and Y.-Q. Ma J. Phys. Chem. B 127, 4015–4021 (2023)
    Two Different Ways of Stress Release in Supercoiled DNA Minicircles under DNA Nick
  230. K. Cervantes-Salguero, Y.A. Gutiérrez Fosado, W. Megone, J.E. Gautrot and M. Palma, Molecules 28, 3686 (2023)
    Programmed self-assembly of DNA nanosheets with discrete single-molecule thickness and interfacial mechanics: Design, simulation, and characterization
  231. H.L. Too and Z. Wang, Nanoscale 15, 11915-11926 (2023)
    Exhaustive classification and systematic free-energy profile study of single-stranded DNA inter-overhang migration
  232. D. Saliba, X. Luo, F.J. Rizzuto and H.F. Sleiman, Nanoscale 15, 5403-5413 (2023)
    Programming rigidity into size-defined wireframe DNA nanotubes
  233. J. Lee and S. Lee, Anal. Chem. 95, 1856–1866 (2023)
    Non-invasive, reliable, and fast quantification of DNA loading on gold nanoparticles by a one-step optical measurement
  234. X. Shen, Q. Ouyang, H. Tan, J. Ouyang and N. Na, Anal. Chem. 95, 5903–5910 (2023)
    Computation-assisted design of ssDNA framework nanorobots for cancer logical recognition, toehold disintegration, visual dual-diagnosis, and synergistic therapy
  235. L. Tang, M. Huang, M. Zhang, Y. Pei, Y. Liu, Y. Wei, C. Yang, T. Xie, D. Zhang, R. Zhou, Y. Song, J. Song, Small Methods 7, 2300327 (2023)
    De novo evolution of an antibody-mimicking multivalent aptamer via a DNA framework
  236. Z. Zheng, S.H. Kim, A. Chovin, N. Clement and C. Demaille, Chem. Sci. 14, 3652-3660 (2023)
    Electrochemical response of surface-attached redox DNA governed by low activation energy electron transfer kinetics
  237. M. Vogt, M. Langecker, M. Gouder, E. Kopperger, F. Rothfischer, F.C. Simmel and J. List, Nature Physics 19, 741–751 (2023)
    Storage of mechanical energy in DNA nanorobotics using molecular torsion springs
  238. C. Xie, Y. Hu, K. Chen, Z. Chen and L. Pan, Commun. Comput. Inf. Sci., 1801, 647–654 (2023)
    Tuning Geometric Conformations of Curved DNA Structures by Controlling Positions of Nicks
  239. S. Yu, J. Zhao, R. Chu, X. Li, G. Wu and X. Meng, Entropy 25, 796 (2023)
    Anomalous diffusion of polyelectrolyte segments on supported charged lipid bilayers
  240. I. Madrid, Z. Zheng, C. Gerbelot, A. Fujiwara, S. Li, S. Grall, K. Nishiguchi, S.H. Kim, A. Chovin, C. Demaille and N. Clement, ACS Nano 17, 17031–17040 (2023)
    Ballistic Brownian Motion of Nanoconfined DNA
  241. Y. Ma, W. Guo, Q. Mou, X. Shao, M. Lyu, V. Garcia, L. Kong, W. Lewis, C. Ward, Z. Yang, X. Pan, S.S. Yi and Y. Lu, Nat. Biotechnol. (2023)
    Spatial imaging of glycoRNA in single cells with ARPLA
  242. X. Luo, D. Saliba, T. Yang, S. Gentile, K. Mori, P.I. Garcia, T. Das, N. Bagheri, A. Porchetta, A. Guarne, G. Cosa, H.F. Sleiman, Angew. Chem. Int. Ed. 62 e202309869 (2023)
    Minimalist design of wireframe DNA nanotubes: Tunable geometry, size, chirality, and dynamics
  243. Y. Zhao, S. Cao, Y. Wang, F. Li, L. Lin, L. Guo, F. Wang, J. Chao, X. Zuo, Y. Zhu, L. Wang, J. Li and C. Fan, Nat. Mach. Intell. 5, 980–990 (2023)
    A temporally resolved DNA framework state machine in living cells
  244. X.R. Liu, I.Y. Loh, W. Siti, H.L. Too, T. Anderson and Z. Wang, Nanoscale Horiz., 8, 827-841 (2023)
    A light-operated integrated DNA walker–origami system beyond bridge burning
  245. H. Lv, N. Xie, M. Li, M. Dong, C. Sun, Q. Zhang, L. Zhao, J. Li, X. Zuo, H. Chen, F. Wang and C. Fan, Nature 622, 292–300(2023).
    DNA-based programmable gate arrays for general-purpose DNA computing
  246. C. Yang, X. Song, Y. Feng, G. Zhao, and Y. Liu, J. Phys.: Condens. Matter 35, 265101 (2023)
    Stability of DNA and RNA hairpins: a comparative study based on ox-DNA
  247. Xiaoya Song, Chao Yang, Yuyu Feng, Hu Chen, and Yanhui Liu, Commun. Theor. Phys. 75, 055601 (2023)
    A common rule for the intermediate state caused by DNA mismatch in single-molecule experiments
  248. W. Siti, H.L. Too, T. Anderson, X.R. Liu, I.Y. Loh and Z. Wang, Sci. Adv. 9, adi8444 (2023)
    Autonomous DNA molecular motor tailor-designed to navigate DNA origami surface for fast complex motion and advanced nanorobotics
  249. R. Ma, A. Velusamy, S.A. Rashid, B.R. Deal, W. Chen, B. Petrich, R. Li, K. Salaita, Nat. Methods 20, 1666–1671 (2023)
    Molecular mechanocytometry using tension-activated cell tagging (bioRxiv)
  250. D. Karna, E. Mano, J. Ji, I. Kawamata, Y. Suzuki and H. Mao, Nat. Commun. 14, 6459 (2023)
    Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies
  251. J. Fu, L. Zhang, Y. Long, Z. Liu, G. Meng, H. Zhao, X. Su and S. Shi, Anal. Chem. 95, 16089–16097 (2023)
    Multiplexed CRISPR-based nucleic acid detection using a single Cas protein
  252. Y. Yang, Q. Lu, Y. Chen, M. DeLuca, G. Arya, Y. Ke and S. Zauscher, Angew. Chem. Int. Ed. 62, e202311727 (2023)
    Spatiotemporal control over polynucleotide brush growth on DNA origami nanostructures
  253. J.Y. Lee, H. Koh and D.-N. Kim, Nat. Commun. 14, 7079 (2023)
    A computational model for structural dynamics and reconfiguration of DNA assemblies
  254. M.C. Engel, J.A. Smith and M.P. Brenner, Phys. Rev. X 13, 041032 (2023)
    Optimal control of nonequilibrium systems through automatic differentiation
  255. L. Yu, Y. Xu, M. Al-Amin, S. Jiang, M. Sample, A. Prasad, N. Stephanopoulos, P. Šulc, and H. Yan, J. Am. Chem. Soc. 145, 27336–27347 (2023)
    CytoDirect: A nucleic acid nanodevice for specific and efficient delivery of functional payloads to the cytoplasm
  256. Y.-P. Qiao and C.-L. Ren, Langmuir 40, 109–117 (2024)
    Correlated hybrid DNA structures explored by the oxDNA Model
  257. L. Kilwing, P. Lill, B. Nathwani, R. Guerra, E. Benson, T. Liedl and W. M. Shih, ACS Nano 18, 885–893 (2024)
    Multilayer DNA origami with terminal interfaces that are flat and wide-area
  258. N. Adžić, C. Jochum, C. N. Likos, E. Stiakakis, Small, 20, 2308763 (2024)
    Engineering ultrasoft interactions in stiff all-DNA dendrimers by site-specific control of scaffold flexibility
  259. A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and K. Salaita, Nat. Commun. 15, 704 (2024)
    DNA mechanocapsules for programmable piconewton responsive drug delivery
  260. Y. Liu, B. Li, F. Wang, Q. Li, S. Jia, X. Liu, and M. Li, ACS Appl. Bio Mater. 7, 1311–1316 (2024)
    Quantitative analysis of resistance to deformation of the DNA origami framework supported by struts
  261. S. He, H. Deng, P. Li, Q. Tian, Y. Yang, J. Hu, H. Li, T. Zhao, H. Ling, Y. Liu, S. Liu and Q. Guo, J. Nanobiotechnol. 22, 39 (2024)
    Bimodal DNA self-origami material with nucleic acid function enhancement
  262. B. Babatunde, J. Cagan, R.E. Taylor, J. Mech. Des. 146, 051708 (2024)
    An improved shape annealing algorithm for the generation of coated deoxyribonucleic acid origami nanostructures
  263. A.S.G. Martins, S.D. Reis, E. Benson, M.M. Domingues, J. Cortinhas, J.A. Vidal Silva, S.D. Santos, N.C. Santos, A.P. Pêgo, P.M.D. Moreno, Small 20, 2309140 (2024)
    Enhancing Neuronal Cell Uptake of Therapeutic Nucleic Acids with Tetrahedral DNA Nanostructures
  264. S Dey, R. Rivas-Barbosa, F. Sciortino, E. Zaccarelli and P. Zijlstra, Nanoscale 16, 4872-4879 (2024)
    Biomolecular interactions on densely coated nanoparticles: a single-molecule perspective
  265. T. Chen, S. Mao, J. Ma, X. Tang, R. Zhu, D. Mao, X. Zhu, Q. Pan, Angew. Chem. Int. Ed 63, e202319117 (2024)
    Proximity-enhanced functional imaging analysis of engineered tumors
  266. Y. Liu, Z. Dai, X. Xie, B. Li, S. Jia, Q. Li, M. Li, C. Fan and X. Liu, J. Am. Chem. Soc. 146, 8, 5461–5469 (2024)
    Spacer-programmed two-dimensional DNA origami assembly
  267. Z. Zheng, S. Grall, S.H. Kim, A. Chovin, N. Clement and C. Demaille, J. Am. Chem. Soc. 146, 9, 6094–6103 (2024)
    Activationless electron transfer of redox-DNA in electrochemical nanogaps
  268. M. Sample, M. Matthies and P. Šulc, 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. 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. accepted (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. accepted (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. Y. Du, R. Li, A.S. Madhvacharyula, A.A. Swett, J.H. Choi, submitted
    DNA nanostar structures with tunable auxetic properties (bioRxiv)
  294. 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)
  295. A. Walbrun, T. Wang, M. Matthies, P. Šulc, F.C. Simmel, M. Rief, submitted
    Single-Molecule Force Spectroscopy of Toehold-Mediated Strand Displacement (bioRxiv)
  296. S. Chandrasekhar, T.P. Swope, F. Fadaei, D.R. Hollis, R. Bricker, D. Houser, J. Portman, T.L. Schmidt, submitted
    Bending Unwinds DNA (bioRxiv)
  297. 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)
  298. C. Karfusehr, M. Eder, F.C. Simmel
    Self-assembled cell-scale containers made from DNA origami membranes (bioRxiv)
  299. 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)
  300. 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)
  301. V. Bukina and A. Božič, submitted
    Context-dependent structure formation of RNA hairpin motifs (bioRxiv)
  302. 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)
  303. A. Suma and C. Micheletti, submitted
    Unzipping of knotted DNA via nanopore translocation (arXiv)
  304. 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)


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

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