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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, ''Nature Nanotech.'' '''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 295: Line 297:
# Z. Yu, M. Centola, J. Valero, M. Matthies, P. Šulc, and M. Famulok, ''J. Am. Chem. Soc.'' '''143''', 13292–13298 (2021)
# Z. Yu, M. Centola, J. Valero, M. Matthies, P. Šulc, and M. Famulok, ''J. Am. Chem. Soc.'' '''143''', 13292–13298 (2021)
#: [https://doi.org/10.1021/jacs.1c06226 A Self-Regulating DNA Rotaxane Linear Actuator Driven by Chemical Energy]
#: [https://doi.org/10.1021/jacs.1c06226 A Self-Regulating DNA Rotaxane Linear Actuator Driven by Chemical Energy]
# T. Lee, S. Do, J.G. Lee, D.-N. Kim and Y. Shin, ''Nanoscale'' '''13''', 17638-17647 (2021)
#: [https://doi.org/10.1039/D1NR03495B The flexibility-based modulation of DNA nanostar phase separation]
# Y. Wang, J. V. Le, K. Crocker, M.A. Darcy, P.D. Halley, D. Zhao, N. Andrioff, C. Croy, M.G Poirier, R. Bundschuh, C.E Castro, ''Nucleic Acids Res.'' '''49''', 8987–8999 (2021)
# Y. Wang, J. V. Le, K. Crocker, M.A. Darcy, P.D. Halley, D. Zhao, N. Andrioff, C. Croy, M.G Poirier, R. Bundschuh, C.E Castro, ''Nucleic Acids Res.'' '''49''', 8987–8999 (2021)
#: [https://doi.org/10.1093/nar/gkab656 A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules]
#: [https://doi.org/10.1093/nar/gkab656 A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules]
Line 355: Line 359:
# E. Benson, R. Carrascosa Marzo, J. Bath and A.J. Turberfield, ''Sci. Robot.'' '''7''', eabn5459 (2022)
# E. Benson, R. Carrascosa Marzo, J. Bath and A.J. Turberfield, ''Sci. Robot.'' '''7''', eabn5459 (2022)
#: [https://doi.org/10.1126/scirobotics.abn5459 A DNA molecular printer capable of programmable positioning and patterning in two dimensions]
#: [https://doi.org/10.1126/scirobotics.abn5459 A DNA molecular printer capable of programmable positioning and patterning in two dimensions]
# A. Dutta, K. Tapio, A. Suma, A. Mostafa, Y. Kanehira, V. Carnevale, G. Bussi and I. Bald, ''Nanoscale'' '''14''', 16467-16478 (2022)
#: [https://doi.org/10.1039/D2NR03664A Molecular states and spin crossover of hemin studied by DNA origami enabled single-molecule surface-enhanced Raman scattering]
# D.J. Hart, J. Jeong, J.C. Gumbart and H.D. Kim,  ''Nucleic Acids Res.'' '''51''', 3030–3040 (2023)
# D.J. Hart, J. Jeong, J.C. Gumbart and H.D. Kim,  ''Nucleic Acids Res.'' '''51''', 3030–3040 (2023)
#: [https://doi.org/10.1093/nar/gkad118 Weak tension accelerates hybridization and dehybridization of short oligonucleotides] ([https://doi.org/10.1101/2022.04.19.488836 bioRxiv])
#: [https://doi.org/10.1093/nar/gkad118 Weak tension accelerates hybridization and dehybridization of short oligonucleotides] ([https://doi.org/10.1101/2022.04.19.488836 bioRxiv])
Line 375: Line 381:
# F. Fontana, T. Bellini and M. Todisco, ''Macromolecules'' '''55''', 5946–5953 (2022)
# F. Fontana, T. Bellini and M. Todisco, ''Macromolecules'' '''55''', 5946–5953 (2022)
#: [https://doi.org/10.1021/acs.macromol.2c00856 Liquid Crystal Ordering in DNA Double Helices with Backbone Discontinuities]
#: [https://doi.org/10.1021/acs.macromol.2c00856 Liquid Crystal Ordering in DNA Double Helices with Backbone Discontinuities]
# Z. Weng, H. Yu, W. Luo, L. Zhang, Z. Zhang, T. Wang, Q. Liu, Y. Guo, Y. Yang, J. Li, L. Yang, L. Dai, Q. Pu, X. Zhou and G. Xie, ''Anal. Chim. Acta'' '''1199''', 339568 (2022)
#: [https://doi.org/10.1016/j.aca.2022.339568 Specific and robust hybridization based on double-stranded nucleic acids with single-base resolution]
# J. Bohlin, A.J. Turberfield, A.A. Louis and P. Šulc, ''ACS Nano'' '''17''', 5387–5398 (2023)
# J. Bohlin, A.J. Turberfield, A.A. Louis and P. Šulc, ''ACS Nano'' '''17''', 5387–5398 (2023)
#: [https://doi.org/10.1021/acsnano.2c09677 Designing the self-assembly of arbitrary shapes using minimal complexity building blocks] ([https://arxiv.org/abs/2207.06954 arXiv])
#: [https://doi.org/10.1021/acsnano.2c09677 Designing the self-assembly of arbitrary shapes using minimal complexity building blocks] ([https://arxiv.org/abs/2207.06954 arXiv])
Line 385: Line 393:
# A. Elonen, A.K. Natarajan, I. Kawamata, L. Oesinghaus, A. Mohammed, J. Seitsonen, Y. Suzuki, F. C. Simmel, A. Kuzyk and P. Orponen, ''ACS Nano'' '''16''', 16608–16616 (2022)
# A. Elonen, A.K. Natarajan, I. Kawamata, L. Oesinghaus, A. Mohammed, J. Seitsonen, Y. Suzuki, F. C. Simmel, A. Kuzyk and P. Orponen, ''ACS Nano'' '''16''', 16608–16616 (2022)
#: [https://doi.org/10.1021/acsnano.2c06035 Algorithmic design of 3D wireframe RNA polyhedra] ([https://doi.org/10.1101/2022.04.27.489653 bioRxiv])
#: [https://doi.org/10.1021/acsnano.2c06035 Algorithmic design of 3D wireframe RNA polyhedra] ([https://doi.org/10.1101/2022.04.27.489653 bioRxiv])
# D. Fu, R.P. Narayanan, A. Prasad, F. Zhang, D. Williams, J.S. Schreck, H. Yan and J. Reif, ''Sci. Adv.'' '''8''', ade4455 (2022)
#: [https://doi.org/10.1126/sciadv.ade4455 Automated design of 3D DNA origami with non-rasterized 2D curvature]
# N. Chauhan, Y. Xiong, S. Ren, A. Dwivedy, N. Magazine, L. Zhou, X. Jin, T. Zhang, B.T. Cunningham, S. Yao, W. Huang and X. Wang, ''J. Am. Chem. Soc.'' '''144''', accepted (2022)
# N. Chauhan, Y. Xiong, S. Ren, A. Dwivedy, N. Magazine, L. Zhou, X. Jin, T. Zhang, B.T. Cunningham, S. Yao, W. Huang and X. Wang, ''J. Am. Chem. Soc.'' '''144''', accepted (2022)
#: [https://doi.org/10.1021/jacs.2c04835 Net-shaped DNA nanostructures designed for rapid/sensitive detection and potential inhibition of the SARS-CoV-2 virus]
#: [https://doi.org/10.1021/jacs.2c04835 Net-shaped DNA nanostructures designed for rapid/sensitive detection and potential inhibition of the SARS-CoV-2 virus]
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# G. Kloes, T.J.D. Bennett, A. Chapet-Batlle, A. Behjatian, A.J. Turberfield and M. Krishnan, ''Nano Lett.''  '''22''', 7834–7840 (2022)
# G. Kloes, T.J.D. Bennett, A. Chapet-Batlle, A. Behjatian, A.J. Turberfield and M. Krishnan, ''Nano Lett.''  '''22''', 7834–7840 (2022)
#: [https://doi.org/10.1021/acs.nanolett.2c02485 Far-field electrostatic signatures of macromolecular 3D conformation]
#: [https://doi.org/10.1021/acs.nanolett.2c02485 Far-field electrostatic signatures of macromolecular 3D conformation]
# L. Guo, Y. Zhang, Y. Wang, M. Xie, J. Dai, Z. Qu, M. Zhou, S. Cao, J. Shi, L. Wang, X. Zuo, C. Fan and J. Li, ''Angew. Chem. Int. Ed.'' '''61''', e202117168 (2022)
#: [https://doi.org/10.1002/anie.202117168 Directing multivalent aptamer-receptor binding on the cell surface with programmable atom-like nanoparticles]
# N. Xie, M. Li, Y. Wang, H. Lv, J. Shi, J. Li, Q. Li, F. Wang and C. Fan, ''J. Am. Chem. Soc.'' '''144''', 9479–9488 (2022)
#: [https://doi.org/10.1021/jacs.2c03258 Scaling Up Multi-bit DNA Full Adder Circuits with Minimal Strand Displacement Reactions]
# E. Lattuada, T. Pietrangeli and F. Sciortino, ''J. Chem. Phys.'' '''157''', 135101 (2022)
# E. Lattuada, T. Pietrangeli and F. Sciortino, ''J. Chem. Phys.'' '''157''', 135101 (2022)
#: [https://doi.org/10.1063/5.0117047 Interpenetrating gels in binary suspensions of DNA nanostars]
#: [https://doi.org/10.1063/5.0117047 Interpenetrating gels in binary suspensions of DNA nanostars]
# X. Chen, Y. Wang, X. Dai, L. Ding, J. Chen, G. Yao, X. Liu, S. Luo, J. Shi, L. Wang, R. Nechushtai, E. Pikarsky, I. Willner, C. Fan, and J. Li, ''J. Am. Chem. Soc.'' '''144''', 6311–6320 (2022)
#: [https://doi.org/10.1021/jacs.1c13116 Single-Stranded DNA-Encoded Gold Nanoparticle Clusters as Programmable Enzyme Equivalents]
# Q. Kou, L. Wang, L. Zhang, L. Ma, S. Fu and X. Su, ''Small'' '''18''', 2205191 (2022)
# Q. Kou, L. Wang, L. Zhang, L. Ma, S. Fu and X. Su, ''Small'' '''18''', 2205191 (2022)
#: [https://doi.org/10.1002/smll.202205191 Simulation-assisted localized DNA logical circuits for cancer biomarkers detection and imaging]
#: [https://doi.org/10.1002/smll.202205191 Simulation-assisted localized DNA logical circuits for cancer biomarkers detection and imaging]
Line 415: Line 431:
# E. Poppleton, M. Matthies, D. Mandal, F. Romano, P. Šulc and L. Rovigatti,  ''J. Open Source Softw.'' '''8''', 4693 (2023)
# E. Poppleton, M. Matthies, D. Mandal, F. Romano, P. Šulc and L. Rovigatti,  ''J. Open Source Softw.'' '''8''', 4693 (2023)
#: [https://doi.org/10.21105/joss.04693 oxDNA: coarse-grained simulations of nucleic acids made simple]
#: [https://doi.org/10.21105/joss.04693 oxDNA: coarse-grained simulations of nucleic acids made simple]
# A. Suma, V. Carnevale and C. Micheletti, ''Phys. Rev. Lett.'' '''130''', 048101 (2023)
#: [https://doi.org/10.1103/PhysRevLett.130.048101 Nonequilibrium Thermodynamics of DNA Nanopore Unzipping] ([https://doi.org/10.48550/arXiv.2212.05882 arXiv])
# Y. Tang, H. Liu, Q. Wang, X. Qi, L. Yu, P. Šulc, F. Zhang, H. Yan and S. Jiang, ''J. Am. Chem. Soc.'' 145, 25, 13858–13868 (2023)  
# Y. Tang, H. Liu, Q. Wang, X. Qi, L. Yu, P. Šulc, F. Zhang, H. Yan and S. Jiang, ''J. Am. Chem. Soc.'' 145, 25, 13858–13868 (2023)  
#: [https://doi.org/10.1021/jacs.3c03044 DNA Origami Tessellations]
#: [https://doi.org/10.1021/jacs.3c03044 DNA Origami Tessellations]
# M. DeLuca, W.G. Pfeifer, B. Randoing,  C.-M. Huang, M.G. Poirier, C.E. Castro and G. Arya, ''Nanoscale'' '''15''', 8356-8365 (2023)
# M. DeLuca, W.G. Pfeifer, B. Randoing,  C.-M. Huang, M.G. Poirier, C.E. Castro and G. Arya, ''Nanoscale'' '''15''', 8356-8365 (2023)
#: [https://doi.org/10.1039/D2NR05813H Thermally reversible pattern formation in arrays of molecular rotors]
#: [https://doi.org/10.1039/D2NR05813H Thermally reversible pattern formation in arrays of molecular rotors]
# T. Liang, C. Yang, X. Song, Y. Feng, Y. Liu and H. Chen, ''Phys. Rev. E'' '''108''', 014406 (2023)
#: [https://doi.org/10.1103/PhysRevE.108.014406 Quantification of macromolecule crowding at single-molecule level]
# D. Lysne, T. Hachigian, C. Thachuk, J. Lee and E. Graugnard ''J. Am. Chem. Soc.'' '''145''', 16691–16703 (2023)   
# D. Lysne, T. Hachigian, C. Thachuk, J. Lee and E. Graugnard ''J. Am. Chem. Soc.'' '''145''', 16691–16703 (2023)   
#: [https://doi.org/10.1021/jacs.3c04344 Leveraging Steric Moieties for Kinetic Control of DNA Strand Displacement Reactions]
#: [https://doi.org/10.1021/jacs.3c04344 Leveraging Steric Moieties for Kinetic Control of DNA Strand Displacement Reactions]
Line 425: Line 445:
# 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)
# 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]
#: [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, ''Science Advances'' '''9''', adi0697 (2023)
# 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/10.1126/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)
# 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]
#: [https://doi.org/10.1021/acsnano.2c11982 Computer-Aided Design of A-Trail Routed Wireframe DNA Nanostructures with Square Lattice Edges]
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# L. Zhang, H. Zhao, H. Yang and X. Su, ''Biosens. Bioelectron.'' '''239''', 115622 (2023)
# 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]
#:[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)
# 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
#: [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.'' accepted (2023)
# 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.'' accepted (2023)
#: [https://doi.org/10.1002/anie.202309869 Minimalist design of wireframe DNA nanotubes: Tunable geometry, size, chirality, and dynamics]
#: [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.''  (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'' (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]
# R. Ma, A. Velusamy, S.A. Rashid, B.R. Deal, W. Chen, B. Petrich, R. Li, K. Salaita, submitted
#: Molecular Mechanocytometry Using Tension-activated Cell Tagging (TaCT) ([https://doi.org/10.1101/2023.01.10.523449 bioRxiv])
# M. Sample, M. Matthies and P. Šulc, submitted
# 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])
#: 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, submitted
# M. Sample, M. Matthies and P. Šulc, submitted
#: Coarse-grained simulations of DNA and RNA systems with oxDNA and oxRNA models: Introductory tutorial ([https://doi.org/10.48550/arXiv.2308.01455 arXiv])
#: Coarse-grained simulations of DNA and RNA systems with oxDNA and oxRNA models: Introductory tutorial ([https://doi.org/10.48550/arXiv.2308.01455 arXiv])
Line 447: Line 503:
# V. Caroprese, C. Tekin, V. Cencen, M. Mosayebi, T.B. Liverpool, D.N. Woolfson, G. Fantner, M.M.C. Bastings, submitted
# V. Caroprese, C. Tekin, V. Cencen, M. Mosayebi, T.B. Liverpool, D.N. Woolfson, G. Fantner, M.M.C. Bastings, submitted
#: Structural flexibility dominates over binding strength for supramolecular crystallinity ([https://doi.org/10.1101/2023.09.04.556250 bioRxiv])
#: Structural flexibility dominates over binding strength for supramolecular crystallinity ([https://doi.org/10.1101/2023.09.04.556250 bioRxiv])
 
# C. Shi, P. Wang, submitted
#: 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])


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 15:52, 20 September 2023

  1. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, Phys. Rev. Lett. 104, 178101 (2010)
    DNA Nanotweezers Studied with a Coarse-Grained Model of DNA (arXiv)
  2. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Phys. Condens. Matter. 22, 104102 (2010)
    Extracting bulk properties of self-assembling systems from small simulations (arXiv)
  3. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Chem. Phys, 134, 085101 (2011)
    Structural, mechanical and thermodynamic properties of a coarse-grained DNA model (arXiv)
  4. T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011.
    Coarse-grained modelling of DNA and DNA self-assembly
  5. F. Romano, A. Hudson, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, J. Chem. Phys. 136, 215102 (2012)
    The effect of topology on the structure and free energy landscape of DNA kissing complexes (arXiv)
  6. C. De Michele, L. Rovigatti, T. Bellini, F. Sciortino, Soft Matter 8, 8388 (2012)
    Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link (arXiv)
  7. C. Matek, T. E. Ouldridge, A. Levy, J. P. K. Doye, A. A. Louis, J. Phys. Chem. B 116, 1161-11625 (2012)
    DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism (arXiv)
  8. P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, J. Chem. Phys. 137, 135101 (2012)
    Sequence-dependent thermodynamics of a coarse-grained DNA model (arxiv)
  9. T.E. Ouldridge, J. Chem. Phys. 137, 144105 (2012)
    Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble (arXiv)
  10. F. Romano, D. Chakraborty, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, J. Chem. Phys. 138, 085101 (2013)
    Coarse-grained simulations of DNA overstretching (arXiv)
  11. T. E. Ouldridge, R. L. Hoare, A. A. Louis, J. P. K. Doye, J. Bath, A. J. Turberfield, ACS Nano 7, 2479-2490 (2013)
    Optimizing DNA nanotechnology through coarse-grained modelling: a two-footed DNA walker
  12. T. E. Ouldridge, P. Šulc, F. Romano, J. P. K. Doye, A. A. Louis, Nucleic Acids Res. 41, 8886-8895 (2013)
    DNA hybridization kinetics: zippering, internal displacement and sequence dependence (arXiv)
  13. J.P.K. Doye, T. E. Ouldridge, A. A. Louis, F. Romano, P. Šulc, C. Matek, B.E.K. Snodin, L. Rovigatti, J. S. Schreck, R.M. Harrison, W.P.J. Smith, Phys. Chem. Chem. Phys 15, 20395-20414 (2013)
    Coarse-graining DNA for simulations of DNA nanotechnology (arXiv)
  14. N. Srinivas, T. E. Ouldridge, P. Šulc, J. M. Schaeffer, B. Yurke, A. A. Louis, J. P. K. Doye, E. Winfree, Nucleic Acids Res. 41, 10641-10658 (2013)
    On the biophysics and kinetics of toehold-mediated DNA strand displacement
  15. P. Šulc, T. E. Ouldridge, F. Romano, J. P. K. Doye, A. A. Louis, Natural Computing 13, 535 (2014)
    Simulating a burnt-bridges DNA motor with a coarse-grained DNA model (arXiv)
  16. L. Rovigatti, F. Bomboi, F. Sciortino, J. Chem. Phys. 140, 154903 (2014)
    Accurate phase diagram of tetravalent DNA nanostars (arXiv)
  17. P. Šulc, F. Romano, T. E. Ouldridge, J. P. K. Doye, A. A. Louis, J. Chem. Phys. 140, 235102 (2014)
    A nucleotide-level coarse-grained model of RNA (arXiv)
  18. L. Rovigatti, F. Smallenburg, F. Romano, F. Sciortino, ACS Nano 8, 3567-3574 (2014)
    Gels of DNA Nanostars Never Crystallise
  19. Q. Wang, B. M. Pettitt, Biophys. J. 106, 1182–1193 (2014)
    Modeling DNA Thermodynamics under Torsional Stress
  20. J. S. Schreck, T. E. Ouldridge, F. Romano, P. Šulc, L. Shaw, A. A. Louis, J.P.K. Doye, Nucleic Acids Res. 43, 6181-6190 (2014)
    DNA hairpins primarily promote duplex melting rather than inhibiting hybridization (arXiv)
  21. R. Machinek, T.E. Ouldridge, N.E.C. Haley, J. Bath, A. J. Turberfield, Nature Comm. 5, 5324 (2014)
    Programmable energy landscapes for kinetic control of DNA strand displacement
  22. M. Mosayebi, F. Romano, T. E. Ouldridge, A. A. Louis, J. P. K. Doye, J. Phys. Chem. B 118, 14326-14335 (2014)
    The role of loop stacking in the dynamics of DNA hairpin formation (arXiv)
  23. I. Y. Loh, J.Cheng, S. R. Tee, A. Efremov, and Z. Wang, ACS Nano 8, 10293–10304 (2014)
    From bistate molecular switches to self-directed track-walking nanomotors
  24. C. Matek, T. E. Ouldridge, J. P. K. Doye, A. A. Louis, Sci. Rep., 5, 7655 (2015)
    Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA (arXiv)
  25. L. Rovigatti, P. Šulc, I. Reguly, F. Romano, J. Comput. Chem., 36, 1-8 (2015)
    A comparison between parallelization approaches in molecular dynamics simulations on GPUs (arXiv)
  26. P. Krstić, B. Ashcroft and S. Lindsay, Nanotechnology, 26, 084001 (2015)
    Physical model for recognition tunneling
  27. F. Romano and F. Sciortino, Phys. Rev. Lett. 114, 078104 (2015)
    Switching Bonds in a DNA Gel: An All-DNA Vitrimer
  28. J. S. Schreck, T. E. Ouldridge, F. Romano, A. A. Louis, J.P.K. Doye, J. Chem. Phys. 142, 165101 (2015)
    Characterizing the bending and flexibility induced by bulges in DNA duplexes (arXiv)
  29. M. Mosayebi, A. A. Louis, J.P.K. Doye, T. E. Ouldridge ACS Nano 9, 11993 (2015)
    Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors (arXiv)
  30. T. E. Ouldridge, Mol. Phys. 113, 1-15 (2015)
    DNA nanotechnology: understanding and optimisation through simulation (arXiv)
  31. P. Šulc, T. E. Ouldridge, F. Romano, J.P.K. Doye, A. A. Louis, Biophys. J. 108, 1238-1247 (2015)
    Modelling toehold-mediated RNA strand displacement (arXiv)
  32. B. E. K. Snodin, F. Randisi, M. Mosayebi, P. Šulc, J. S. Schreck, F. Romano, T. E. Ouldridge, R. Tsukanov, E. Nir, A. A. Louis, J. P. K. Doye, J. Chem. Phys. 142, 234901 (2015)
    Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA (arXiv)
  33. C. Matek, P. Šulc, F. Randisi, J.P.K. Doye, A. A. Louis, J. Chem. Phys. 143, 243122 (2015)
    Coarse-grained modelling of supercoiled RNA (arXiv)
  34. Q. Wang, C.G. Myers, and B.M. Pettitt, J. Phys. Chem. B 119, 4937–4943 (2015)
    Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density
  35. R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye, arXiv (2015)
    Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"
  36. R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye, J. Chem. Theor. Comput. 15 4660-4672 (2019)
    Identifying physical causes of apparent enhanced cyclization of short DNA molecules with a coarse-grained model (arXiv) (data)
  37. J. Y. Lee, T. Terakawa, Z. Qi, J. B. Steinfeld, S. Redding, Y. Kwon, W. A. Gaines, W. Zhao, P. Sung, E. C. Greene, Science 349, 977-981 (2015)
    Base triplet stepping by the Rad51/RecA family of recombinases
  38. B. E. K. Snodin, F. Romano, L. Rovigatti, T. E. Ouldridge, A. A. Louis, J. P. K. Doye, ACS Nano 10, 1724-1737 (2016)
    Direct Simulation of the Self-Assembly of a Small DNA Origami (data)
  39. V. Kočar, J. S. Schreck, S. Čeru, H. Gradišar, N. Bašić, T. Pisanski, J. P. K. Doye, and R. Jerala, Nat. Commun. 7, 10803 (2016)
    Design principles for rapid folding of knotted DNA nanostructures
  40. J. S. Schreck, F. Romano, M.H. Zimmer, A.A. Louis and J.P.K. Doye, ACS Nano, 10, 4236-4247 (2016)
    Characterizing DNA star-tile-based nanostructures using a coarse-grained model
  41. M. Liu, J. Cheng, S.R. Tee, S. Sreelatha, I.Y. Loh, and Z. Wang, ACS Nano, 10, 5882–5890 (2016)
    Biomimetic autonomous enzymatic nanowalker of high fuel efficiency
  42. J. Fernandez-Castanon, F. Bomboi, L. Rovigatti, M. Zanatta, A. Paciaroni, L. Comez, L. Porcar, C.J. Jafta, G.C. Fadda, T. Bellini and F. Sciortino, J. Chem. Phys. 145, 084910 (2016)
    Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars
  43. T. Sutthibutpong, C. Matek, C. Benham, G.G. Slade, A. Noy, C. Laughton, J.P.K. Doye, A.A. Louis and S.A. Harris, Nucleic Acids Res. 44, 9121-9130 (2016)
    Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation
  44. Q. Wang and B.M. Pettitt, J. Phys. Chem. Lett 7, 1042–1046 (2016)
    Sequence affects the cyclization of DNA minicircles
  45. A. Reinhardt, J.S. Schreck, F. Romano and J.P.K. Doye, J. Phys: Condens. Matter 29, 014006 (2017).
    Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal (arXiv) (data)
  46. E. Locatelli, P. H. Handle, C. N. Likos, F. Sciortino and L. Rovigatti, ACS Nano 11, 2094-2102 (2017)
    Condensation and demixing in solutions of DNA nanostars and their mixtures
  47. E. Skoruppa, M. Laleman, S. Nomidis, E. Carlon, J. Chem. Phys 146, 214902 (2017)
    DNA elasticity from coarse-grained simulations: the effect of groove asymmetry (arXiv)
  48. A. Suma and C. Micheletti, Proc. Natl. Acad. Sci. USA 114, E2991–E2997 (2017)
    Pore translocation of knotted DNA rings
  49. Z. Shi, C. E. Castro and G. Arya, ACS Nano 11, 4617–4630 (2017)
    Conformational dynamics of mechanically compliant DNA nanostructures from coarse-grained molecular dynamics simulations
  50. H. Yagyu, J.-Y. Lee, D.-N. Kim, and O. Tabata, J. Phys. Chem. B 121, 5033–5039 (2017)
    Coarse-grained molecular dynamics model of double-stranded DNA for DNA nanostructure design
  51. S. Vangaveti, R. J. D'Esposito, J. L. Lippens, D. Fabris and S. V. Ranganathan, Phys. Chem. Chem. Phys. 19, 14937-14946 (2017)
    A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by ion mobility spectrometry–mass spectrometry
  52. A. Henning-Knechtel, J. Knechtel and M. Magzoub, Nucleic Acids Res. 45, 12057–12068 (2017)
    DNA-assisted oligomerization of pore-forming toxin monomers into precisely-controlled protein channels
  53. R. Sharma, J. S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, ACS Nano 11, 12426–12435 (2017)
    Characterizing the motion of jointed DNA nanostructures using a coarse-grained model
  54. Q.Y. Yeo, I.Y. Loh, S.R. Tee, Y.H. Chiang, J. Cheng, M.H. Liu and Z.S. Wang, Nanoscale 9, 12142-12149 (2017)
    A DNA bipedal nanowalker with a piston-like expulsion stroke
  55. G. Chatterjee, N. Dalchau, R.A. Muscat, A. Phillips and G. Seelig, Nature Nanotech. 12, 920–927 (2017)
    A spatially localized architecture for fast and modular DNA computing
  56. Q. Wang, R.N. Irobalieva, W. Chiu, M.F. Schmid, J.M. Fogg, L. Zechiedrich, B.M. Pettitt, Nucleic Acids Res. 45 7633-7642 (2017)
    Influence of DNA sequence on the structure of minicircles under torsional stress
  57. B. Joffroy, Y.O. Uca, D. Prešern, J.P.K. Doye and T.L. Schmidt, Nucleic Acids Res. 46, 538-545 (2018)
    Rolling circle amplification shows a sinusoidal template length-dependent amplification bias (data)
  58. R.V. Reshetnikov, A.V. Stolyarova, A.O. Zalevsky, D.Y. Panteleev, G.V. Pavlova, D.V. Klinov, A.V. Golovin, A.D. Protopopova, Nucleic Acids Res. 46, 1102–1112 (2018)
    A coarse-grained model for DNA origami
  59. D.C. Khara, J.S. Schreck, T.E. Tomov, Y. Berger, T.E. Ouldridge, J.P.K. Doye and E. Nir, Nucleic Acids Res. 46, 1553-1561 (2018)
    DNA bipedal motor walking dynamics: An experimental and theoretical study of the dependency on step size (data)
  60. P. Fonseca, F. Romano, J. S. Schreck, T.E. Ouldridge, J.P.K. Doye and A.A. Louis, J. Chem. Phys 148, 134910 (2018)
    Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly (arXiv)
  61. T.D. Craggs, M. Sustarsic, A. Plochowietz, M. Mosayebi, H. Kaju, A. Cuthbert, J. Hohlbein, L. Domicevica, P.C. Biggin, J.P.K. Doye and A.N. Kapanidis, Nucleic Acids Res. 47, 10788–10800 (2019)
    Substrate conformational dynamics drive structure-specific recognition of gapped DNA by DNA polymerase (bioRXiv)
  62. S.R. Tee and Z. Wang, ACS Omega, 3, 292-301 (2018)
    How well can DNA rupture DNA? Shearing and unzipping forces inside DNA nanostructures
  63. E. Skoruppa, S.K. Nomidis, J.F. Marko and E. Carlon, Phys. Rev. Lett. 121, 088101 (2018)
    Bend-induced twist waves and the structure of nucleosomal DNA (arXiv)
  64. M.M.C. Tortora and J.P.K. Doye, Mol. Phys. 116, 2773-2791 (2018)
    Incorporating particle flexibility in a density functional description of nematics and cholesterics (arXiv)
  65. O. Henrich, Y.A. Gutierrez-Fosado, T. Curk, T.E. Ouldridge, Eur. Phys. J. E 41, 57 (2018)
    Coarse-Grained Simulation of DNA using LAMMPS (arXiv)
  66. M.C. Engel, D. M. Smith, M.A. Jobst, M. Sajfutdinow, T. Liedl, F. Romano, L. Rovigatti, A.A. Louis and J.P.K. Doye, ACS Nano 12, 6734-6747 (2018)
    Force-induced unravelling of DNA Origami
  67. F. Romano and L. Rovigatti, in Design of Self-Assembling Materials (Springer, ed. I. Coluzza) pp 71-90 (2017)
    A Nucleotide-Level Computational Approach to DNA-Based Materials
  68. S.R. Tee, X. Hu, I.Y. Loh and Z. Wang, Phys. Rev. Applied 9, 034025 (2018)
    Mechanosensing potentials gate fuel consumption in a bipedal DNA nanowalker
  69. E. Locatelli and L. Rovigatti, Polymers 10, 447 (2018)
    An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids (preprints)
  70. E. Spruijt, S.E. Tusk and H. Bayley, Nature Nanotechnology 13, 739-745 (2018)
    DNA scaffolds support stable and uniform peptide nanopores
  71. L. Coronel, A. Suma and C. Micheletti, Nucleic Acids Res. 46,7522–7532 (2018)
    Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking (bioRXiv)
  72. E. Torelli, J.W. Kozyra, J.-Y. Gu, U. Stimming, L. Piantanida. K. Voitchovsky and N. Krasnogor, Scientific Reports 8, 6989 (2018)
    Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon
  73. R. Jin and L. Maibaum, J. Chem. Phys. 150, 105103 (2019)
    Mechanisms of DNA hybridization: Transition path analysis of a simulation-informed Markov model(arxiv)
  74. F. Kriegel, C. Matek, T. Dršata, K. Kulenkampff, S. Tschirpke, M. Zacharias, F. Lankas and J. Lipfert, Nucleic Acids Res. 46, 7998–8009 (2018)
    The temperature dependence of the helical twist of DNA
  75. E. Benson, A. Mohammed, D. Rayneau-Kirkhope, A. Gådin, P. Orponen, and B. Högberg, ACS Nano 12, 9291-9299 (2018)
    Effects of Design Choices on the Stiffness of Wireframe DNA Origami Structures
  76. S.K. Nomidis, E. Skoruppa, E. Carlon and J.F. Marko, Phys. Rev. E 99 032414 (2019).
    Twist-bend coupling and the statistical mechanics of the twistable worm-like chain model of DNA: Perturbation theory and beyond (bioRXiv,arXiv)
  77. B. E. K. Snodin, J. S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, Nucleic Acids Res. 47, 1585–1597 (2019).
    Coarse-grained modelling of the structural properties of DNA origami (arXiv) (data)
  78. N. E. C. Haley, T. E. Ouldridge, A. Geraldini, A. A. Louis, J. Bath and A. J. Turberfield, Nat. Commun 11, 2562 (2020)
    Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement (bioRXiv)
  79. L. Zhou, A.E. Marras, C.-M. Huang, C.E. Castro and H.-J Su, Small 14, 1802580 (2018)
    Paper origami‐inspired design and actuation of DNA nanomachines with complex motions
  80. R. A. Brady, W.T. Kaufhold, N.J. Brooks, V. Foderà and L. Di Michele, J. Phys. Condens. Matter 31, 074003 (2019)
    Flexibility defines structure in crystals of amphiphilic DNA nanostars (arXiv)
  81. F. Hong, S. Jiang, X. Lan, R.P. Narayanan, P. Šulc, F. Zhang, Y. Liu, and H. Yan, J. Am. Chem. Soc. 140, 14670–14676 (2018)
    Layered-crossover tiles with precisely tunable angles for 2D and 3D DNA crystal engineering
  82. Y. Choi, H. Choi, A.C. Lee, S. Kwon, J. Vis. Exp., e58364 (2018)
    Design and Synthesis of a Reconfigurable DNA Accordion Rack
  83. M.M.C. Tortora, G. Mishra, D. Prešern and J.P.K. Doye, Sci. Adv. 6, eaaw8331 (2020)
    Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamis (arXiv)
  84. C.-M. Huang, A. Kucinic, J.V. Le, C.E. Castro and H.-J. Su, Nanoscale 11, 1647-1660 (2019)
    Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis
  85. I.T. Hoffecker, S. Chen, A. Gådin, A. Bosco, A.I. Teixeira and B. Högberg, Small 15, 1803628 (2019)
    Solution‐controlled conformational switching of an anchored wireframe DNA nanostructure
  86. M. Coraglio, E. Skoruppa and E. Carlon, J. Chem. Phys. 150, 135101 (2019)
    Overtwisting induces polygonal shapes in bent DNA (arXiv)
  87. M. Matthies, N.P. Agarwal, E. Poppleton, F.M. Joshi, P. Šulc, and T.L. Schmidt, ACS Nano 13 1839-1848 (2019)
    Triangulated Wireframe Structures Assembled Using Single-Stranded DNA Tiles
  88. Y.A.G. Fosado, Z. Xing, E. Eiser, M. Hudek, O. Henrich, submitted
    A Numerical Study of Three-Armed DNA Hydrogel Structures (arXiv)
  89. W.T. Kaufhold, R.A. Brady, J.M. Tuffnell, P. Cicuta, and L. Di Michele, Bioconjugate Chem 30, 1850-1859 (2019)
    Membrane scaffolds enhance the responsiveness and stability of DNA-based sensing circuits
  90. S.K. Nomidis, M. Coraglio, M. Laleman, K. Phillips, E. Skoruppa and E. Carlon, Phys. Rev. E 100, 022402 (2019)
    Twist-bend coupling, twist waves and DNA loops (arXiv)
  91. A. Suma, A. Stopar, A.W. Nicholson, M. Castronovo, V. Carnevale, Nucleic Acids Res. 48, 4672–4680 (2020)
    Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure (bioRxiv)
  92. J. Liu, S. Shukor, S. Li, A. Tamayo, L. Tosi, B. Larman, V. Nanda, W.K. Olson and B. Parekkadan, Biomolecules 9, 199 (2019)
    Computational simulation of adapter length-dependent LASSO probe capture efficiency
  93. A. Suma, E. Poppleton, M. Matthies, P. Šulc, F. Romano, A.A. Louis, J.P.K. Doye, C. Micheletti, and L. Rovigatti, J. Comput. Chem. 40, 2586-2595 (2019)
    tacoxDNA: a user-friendly web server for simulations of complex DNA structures, from single strands to origami
  94. J.F. Berengut, J.C. Berengut, J.P.K. Doye, D. Prešern, A. Kawamoto, J. Ruan, M.J. Wainwright and L.K. Lee,, Nucleic Acids Res. 47, 11963–11975(2019)
    Design and synthesis of pleated DNA origami nanotubes with adjustable diameters (bioRxiv)
  95. K.G. Young, B. Najafi, W.M. Sant, S. Contera, A.A. Louis, J.P.K. Doye, A.J. Turberfield and J. Bath, Angew. Chem. Int. Ed. 59, 15942-15946 (2020)
    Reconfigurable T-junction DNA origami
  96. I.D. Stoev, T. Cao, A. Caciagli, J. Yu, C. Ness, R. Liu, R. Ghosh, T. O'Neill, D. Liu and E. Eiser, Soft Matter 16, 990-1001 (2020)
    On the Role of Flexibility in Linker-Mediated DNA Hydrogels (arXiv)
  97. E. Benson, M. Lolaico, Y. Tarasov, A. Gådin and B. Högberg, ACS Nano 13, 12591-12598 (2019)
    Evolutionary Refinement of DNA Nanostructures Using Coarse-Grained Molecular Dynamics Simulations
  98. S.W. Shin, S.Y. Ahn, Y.T. Lim and S.H. Um, Anal. Chem. 91, 14808-14811 (2019)
    Improved Sensitivity of Intramolecular Strand Displacement Based on Localization of Probes
  99. Z. Shi and G. Arya, Nucleic Acids Research 48, 548-560 (2020)
    Free energy landscape of salt-actuated reconfigurable DNA nanodevices
  100. E. Torelli, J.W. Kozyra, B. Shirt-Ediss, L. Piantanida, K. Voïtchovsky, N. Krasnogor, ACS Synth. Biol. 9, 1682-1692 (2020)
    Co-transcriptional folding of a bio-orthogonal fluorescent scaffolded RNA origami (bioRxiv)
  101. P.R Desai, S. Brahmachari, J.F. Marko, S. Das, K.C. Neuman, Nucleic Acids Res. 48, 10713–10725 (2020)
    Coarse-Grained Modeling of DNA Plectoneme Formation in the Presence of Base-Pair Mismatches (bioRxiv)
  102. K. Bartnik, A. Barth, M. Pilo-Pais, A.H. Crevenna, T. Liedl and D.C. Lamb, J. Am. Chem. Soc 142, 815-825 (2020).
    A DNA origami platform for single-pair Förster resonance energy transfer investigation of DNA–DNA interactions and ligation
  103. E. Poppleton, J. Bohlin, M. Matthies, S. Sharma, F. Zhang and P. Šulc, Nucleic Acids Res. 48, e72 (2020)
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  213. Q. Kou, L. Wang, L. Zhang, L. Ma, S. Fu and X. Su, Small 18, 2205191 (2022)
    Simulation-assisted localized DNA logical circuits for cancer biomarkers detection and imaging
  214. P. E. Beshay, A. Kucinic, N. Wile, P. Halley, L. Des Rosiers, A. Chowdhury, J. L. Hall, C. E. Castro and M. W. Hudoba, The Biophysicist 4, accepted (2023)
    Translating DNA origami nanotechnology to middle school, high school, and undergraduate laboratories (bioRxiv)
  215. A. Büchl, E. Kopperger, M. Vogt, M. Langecker, F.C.Simmel and J. List, Biophys. J. 121, 4849-4859 (2022)
    Energy landscapes of rotary DNA origami devices determined by fluorescence particle tracking
  216. E. Poppleton, M. Matthies, D. Mandal, F. Romano, P. Šulc and L. Rovigatti, J. Open Source Softw. 8, 4693 (2023)
    oxDNA: coarse-grained simulations of nucleic acids made simple
  217. A. Suma, V. Carnevale and C. Micheletti, Phys. Rev. Lett. 130, 048101 (2023)
    Nonequilibrium Thermodynamics of DNA Nanopore Unzipping (arXiv)
  218. Y. Tang, H. Liu, Q. Wang, X. Qi, L. Yu, P. Šulc, F. Zhang, H. Yan and S. Jiang, J. Am. Chem. Soc. 145, 25, 13858–13868 (2023)
    DNA Origami Tessellations
  219. M. DeLuca, W.G. Pfeifer, B. Randoing, C.-M. Huang, M.G. Poirier, C.E. Castro and G. Arya, Nanoscale 15, 8356-8365 (2023)
    Thermally reversible pattern formation in arrays of molecular rotors
  220. T. Liang, C. Yang, X. Song, Y. Feng, Y. Liu and H. Chen, Phys. Rev. E 108, 014406 (2023)
    Quantification of macromolecule crowding at single-molecule level
  221. D. Lysne, T. Hachigian, C. Thachuk, J. Lee and E. Graugnard J. Am. Chem. Soc. 145, 16691–16703 (2023)
    Leveraging Steric Moieties for Kinetic Control of DNA Strand Displacement Reactions
  222. A. Kucinic, C.-M. Huang, J. Wang, H.-J. Su and C.E. Castro, Nanoscale, 15 562-572 (2023)
    DNA origami tubes with reconfigurable cross-sections
  223. Y. Zhang, X. Yin, C. Cui, K. He, F. Wang, J. Chao, T. Li, X. Zuo, A. Li, L. Wang, N. Wang, X. Bo and C. Fan, Sci. Adv. 9, adf8263 (2023)
    Prime factorization via localized tile assembly in a DNA origami framework
  224. W.G. Pfeifer, C.-M. Huang, M. G. Poirier, G. Arya and C. E. Castro, Sci. Adv. 9, adi0697 (2023)
    Versatile computer-aided design of free-form DNA nanostructures and assemblies (bioRxiv)
  225. M. Lolaico, S. Blokhuizen, B. Shen, Y. Wang, and B. Högberg, ACS Nano 17, 6565–6574 (2023)
    Computer-Aided Design of A-Trail Routed Wireframe DNA Nanostructures with Square Lattice Edges
  226. Y. Wang, A. Kucinic, L. Des Rosiers, P.E. Beshay, N. Wile, M.W. Hudoba and C.E. Castro, Appl. Sci. 13, 3208 (2023)
    Mechanical Design of DNA Origami in the Classroom
  227. D. Morzy, C. Tekin, V. Caroprese, R. Rubio-Sánchez, L. Di Michele and M.M.C. Bastings, Nanoscale 15, 2849-2859 (2023)
    Interplay of the mechanical and structural properties of DNA nanostructures determines their electrostatic interactions with lipid membranes
  228. L. Zhang, H. Zhao, H. Yang and X. Su, Biosens. Bioelectron. 239, 115622 (2023)
    Coarse-grained model simulation-guided localized DNA signal amplification probe for miRNA detection
  229. Y.-P. Qiao, C.-L. Ren and Y.-Q. Ma J. Phys. Chem. B 127, 4015–4021 (2023)
    Two Different Ways of Stress Release in Supercoiled DNA Minicircles under DNA Nick
  230. K. Cervantes-Salguero, Y.A. Gutiérrez Fosado, W. Megone, J.E. Gautrot and M. Palma, Molecules 28, 3686 (2023)
    Programmed self-assembly of DNA nanosheets with discrete single-molecule thickness and interfacial mechanics: Design, simulation, and characterization
  231. H.L. Too and Z. Wang, Nanoscale 15, 11915-11926 (2023)
    Exhaustive classification and systematic free-energy profile study of single-stranded DNA inter-overhang migration
  232. D. Saliba, X. Luo, F.J. Rizzuto and H.F. Sleiman, Nanoscale 15, 5403-5413 (2023)
    Programming rigidity into size-defined wireframe DNA nanotubes
  233. J. Lee and S. Lee, Anal. Chem. 95, 1856–1866 (2023)
    Non-invasive, reliable, and fast quantification of DNA loading on gold nanoparticles by a one-step optical measurement
  234. X. Shen, Q. Ouyang, H. Tan, J. Ouyang and N. Na, Anal. Chem. 95, 5903–5910 (2023)
    Computation-assisted design of ssDNA framework nanorobots for cancer logical recognition, toehold disintegration, visual dual-diagnosis, and synergistic therapy
  235. L. Tang, M. Huang, M. Zhang, Y. Pei, Y. Liu, Y. Wei, C. Yang, T. Xie, D. Zhang, R. Zhou, Y. Song, J. Song, Small Methods 7, 2300327 (2023)
    De novo evolution of an antibody-mimicking multivalent aptamer via a DNA framework
  236. Z. Zheng, S.H. Kim, A. Chovin, N. Clement and C. Demaille, Chem. Sci. 14, 3652-3660 (2023)
    Electrochemical response of surface-attached redox DNA governed by low activation energy electron transfer kinetics
  237. M. Vogt, M. Langecker, M. Gouder, E. Kopperger, F. Rothfischer, F.C. Simmel and J. List, Nature Physics 19, 741–751 (2023)
    Storage of mechanical energy in DNA nanorobotics using molecular torsion springs
  238. C. Xie, Y. Hu, K. Chen, Z. Chen and L. Pan, Commun. Comput. Inf. Sci., 1801, 647–654 (2023)
    Tuning Geometric Conformations of Curved DNA Structures by Controlling Positions of Nicks
  239. S. Yu, J. Zhao, R. Chu, X. Li, G. Wu and X. Meng, Entropy 25, 796 (2023)
    Anomalous diffusion of polyelectrolyte segments on supported charged lipid bilayers
  240. I. Madrid, Z. Zheng, C. Gerbelot, A. Fujiwara, S. Li, S. Grall, K. Nishiguchi, S.H. Kim, A. Chovin, C. Demaille and N. Clement, ACS Nano 17, 17031–17040 (2023)
    Ballistic Brownian Motion of Nanoconfined DNA
  241. Y. Ma, W. Guo, Q. Mou, X. Shao, M. Lyu, V. Garcia, L. Kong, W. Lewis, C. Ward, Z. Yang, X. Pan, S.S. Yi and Y. Lu, Nat. Biotechnol. (2023)
    Spatial imaging of glycoRNA in single cells with ARPLA
  242. X. Luo, D. Saliba, T. Yang, S. Gentile, K. Mori, P.I. Garcia, T. Das, N. Bagheri, A. Porchetta, A. Guarne, G. Cosa, H.F. Sleiman, Angew. Chem. Int. Ed. accepted (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. (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 (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. R. Ma, A. Velusamy, S.A. Rashid, B.R. Deal, W. Chen, B. Petrich, R. Li, K. Salaita, submitted
    Molecular Mechanocytometry Using Tension-activated Cell Tagging (TaCT) (bioRxiv)
  249. M. Sample, M. Matthies and P. Šulc, submitted
    Hairygami: Analysis of DNA nanostructure's conformational change driven by functionalizable overhangs (arXiv)
  250. M. Sample, M. Matthies and P. Šulc, submitted
    Coarse-grained simulations of DNA and RNA systems with oxDNA and oxRNA models: Introductory tutorial (arXiv)
  251. M. DeLuca, T. Ye, M. Poirier, Y. Ke, C. Castro and G. Arya, submitted
    Mechanism of DNA origami folding elucidated by mesoscopic simulations (bioRxiv)
  252. 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)
  253. C. Shi, P. Wang, submitted
    Allosteric DNAzyme for sensitive detection of nucleic acids for molecular diagnosis (medRxiv)
  254. 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)
  255. K. Gallagher, J. Yu, D.A. King, R. Liu, E. Eiser, submitted
    Towards New Liquid Crystal Phases of DNA mesogens (arXiv)
  256. 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)
  257. H. Koh, J.Y. Lee, J.G. Lee, submitted
    Forming superhelix of double stranded DNA from local deformation (arXiv)
  258. N.P. Agarwal and A. Gopinath, submited
    DNA origami 2.0 (bioRxiv)
  259. J.M. Weck and A. Heuer-Jungemann, submitted
    Fully addressable, designer superstructures assembled from a single modular DNA origami (bioRxiv)
  260. 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)

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

Retrieved from "https://dna.physics.ox.ac.uk/index.php?title=Publications&oldid=1761"