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# D. Kuťák, E. Poppleton, H. Miao, P. Šulc and I. Barišić, ''Molecules'' '''27''', 63 (2022) | # D. Kuťák, E. Poppleton, H. Miao, P. Šulc and I. Barišić, ''Molecules'' '''27''', 63 (2022) | ||
#: [https://doi.org/10.3390/molecules27010063 Unified Nanotechnology Format: One Way to Store Them All] | #: [https://doi.org/10.3390/molecules27010063 Unified Nanotechnology Format: One Way to Store Them All] | ||
# M. Centola, E. Poppleton, M. Centola, J. Valero, P. Šulc and M. Famulok, ''Nat. Nanotechnol.'' | # M. Centola, E. Poppleton, M. Centola, J. Valero, P. Šulc and M. Famulok, ''Nat. Nanotechnol.'' '''19''', 226–236 (2024) | ||
#: [https://doi.org/10.1038/s41565-023-01516-x A rhythmically pulsing leaf-spring nanoengine that drives a passive follower] ([https://doi.org/10.1101/2021.12.22.473833 biorXiv]) | #: [https://doi.org/10.1038/s41565-023-01516-x A rhythmically pulsing leaf-spring nanoengine that drives a passive follower] ([https://doi.org/10.1101/2021.12.22.473833 biorXiv]) | ||
# C.K. Wong and J.P.K. Doye, ''Appl. Sci.'' '''12''', 5875 (2022) | # C.K. Wong and J.P.K. Doye, ''Appl. Sci.'' '''12''', 5875 (2022) | ||
Line 425: | Line 425: | ||
# 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] | ||
# 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''', | # 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''', 68–81 (2023) | ||
#: [https://doi.org/10.35459/tbp.2022.000228 Translating DNA origami nanotechnology to middle school, high school, and undergraduate laboratories] ([https://doi.org/10.1101/2022.09.15.508130 bioRxiv]) | #: [https://doi.org/10.35459/tbp.2022.000228 Translating DNA origami nanotechnology to middle school, high school, and undergraduate laboratories] ([https://doi.org/10.1101/2022.09.15.508130 bioRxiv]) | ||
# A. Büchl, E. Kopperger, M. Vogt, M. Langecker, F.C.Simmel and J. List, ''Biophys. J.'' '''121''', 4849-4859 (2022) | # A. Büchl, E. Kopperger, M. Vogt, M. Langecker, F.C.Simmel and J. List, ''Biophys. J.'' '''121''', 4849-4859 (2022) | ||
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# 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) | # 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] | #: [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.'' | # 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] | #: [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) | # X.R. Liu, I.Y. Loh, W. Siti, H.L. Too, T. Anderson and Z. Wang, ''Nanoscale Horiz.'', '''8''', 827-841 (2023) | ||
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# J. Fu, L. Zhang, Y. Long, Z. Liu, G. Meng, H. Zhao, X. Su and S. Shi, ''Anal. Chem.'' '''95''', 16089–16097 (2023) | # 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] | #: [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. | # 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] | #: [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) | # 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] | #: [https://doi.org/10.1038/s41467-023-42873-4 A computational model for structural dynamics and reconfiguration of DNA assemblies] | ||
# M. Sample, M. Matthies and P. Šulc, | # M.C. Engel, J.A. Smith and M.P. Brenner, ''Phys. Rev. X'' '''13''', 041032 (2023) | ||
#: Hairygami: Analysis of DNA nanostructure's conformational change driven by functionalizable overhangs ([https://doi.org/10.48550/arXiv.2302.09109 arXiv]) | #: [https://doi.org/10.1103/PhysRevX.13.041032 Optimal control of nonequilibrium systems through automatic differentiation] | ||
# M. Sample, M. Matthies and P. Šulc, | # 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) | ||
#: Coarse-grained simulations of DNA and RNA systems with oxDNA and oxRNA models: Introductory tutorial ([https://doi.org/10.48550/arXiv.2308.01455 arXiv | #: [https://doi.org/10.1021/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, ''ACS Nano'' '''18''', 30004–30016 (2024) | |||
#: [https://doi.org/10.1021/acsnano.4c10796 Hairygami: Analysis of DNA nanostructure's conformational change driven by functionalizable overhangs] ([https://doi.org/10.48550/arXiv.2302.09109 arXiv]) | |||
# M. Sample, M. Matthies and P. Šulc, ''2023 Winter Simulation Conference (WSC)'', San Antonio, TX, USA, pp. 91-105 (2023) | |||
#: [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 | # 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, | # 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 | # F. Smith, A. Sengar, G.‐B.V. Stan, T.E. Ouldridge, M. Stevens, J. Goertz and W. Bae, submitted | ||
#: Overcoming the speed limit of four‐way DNA branch migration with bulges in toeholds ([https://doi.org/10.1101/2023.05.15.540824 bioRxiv]) | #: Overcoming the speed limit of four‐way DNA branch migration with bulges in toeholds ([https://doi.org/10.1101/2023.05.15.540824 bioRxiv]) | ||
# K. Gallagher, J. Yu, D.A. King, R. Liu, E. Eiser, | # K. Gallagher, J. Yu, D.A. King, R. Liu, E. Eiser, ''APL Mater.'' '''11''', 061129 (2023) | ||
#: Towards | #: [https://doi.org/10.1063/5.0145570 Towards new liquid crystal phases of DNA mesogens] ([https://doi.org/10.48550/arXiv.2302.03501 arXiv]) | ||
# G.B.M. Wisna, D. Sukhareva, J. Zhao, D. Satyabola, M. Matthies, S. Roy, P. Šulc, H. Yan and R.F. Hariadia, submitted | # G.B.M. Wisna, D. Sukhareva, J. Zhao, D. Satyabola, M. Matthies, S. Roy, P. Šulc, H. Yan and R.F. Hariadia, submitted | ||
#: High-speed 3D DNA-PAINT and unsupervised clustering for unlocking 3D DNA origami cryptography ([https://doi.org/10.1101/2023.08.29.555281 bioRxiv]) | #: High-speed 3D DNA-PAINT and unsupervised clustering for unlocking 3D DNA origami cryptography ([https://doi.org/10.1101/2023.08.29.555281 bioRxiv]) | ||
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# 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 | # 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]) | #: 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, | # H. Liu, M. Matthies, J. Russo, L. Rovigatti, R.P. Narayanan, T. Diep, D. McKeen, O. Gang, N. Stephanopoulos, F. Sciortino, H. Yan, F. Romano and P. Šulc, ''Science'' '''384''', 776-781 (2024) | ||
#: Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments ([https://doi.org/10.48550/arXiv.2310.10995 arXiv]) | #: [https://doi.org/10.1126/science.adl5549 Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments] ([https://doi.org/10.48550/arXiv.2310.10995 arXiv]) | ||
# L. Grabenhorst, M. Pfeiffer, T. Schinkel, M. Kümmerlin, J.B. Maglic, G.A. Brüggenthies, F. Selbach, A.T. Murr, P. Tinnefeld, V. Glembockyte, | # L. Grabenhorst, M. Pfeiffer, T. Schinkel, M. Kümmerlin, J.B. Maglic, G.A. Brüggenthies, F. Selbach, A.T. Murr, P. Tinnefeld, V. Glembockyte, ''Nat. Nanotechnol.'' accepted (2024) | ||
#: Engineering modular and tunable single | #: [https://doi.org/10.1038/s41565-024-01804-0 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 | # 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]) | #: nNxB: a new coarse-grained model for RNA and DNA nanotechnology ([https://doi.org/10.48550/arXiv.2311.03317 arXiv]) | ||
# E.J. Ratajczyk, P. Šulc, A.J. Turberfield, J.P.K. Doye and A.A. Louis, ''J. Chem. Phys.'' '''160''', 115101 (2024) | |||
#: [https://doi.org/10.1063/5.0199558 Coarse-grained modelling of DNA-RNA hybrids] ([https://doi.org/10.48550/arXiv.2311.07709 arXiv]) | |||
# M. DeLuca, D. Duke, T. Ye, M. Poirier, Y. Ke, C. Castro and G. Arya, ''Nat. Commun.'' '''15''', 3015 (2024) | |||
#: [https://doi.org/10.1038/s41467-024-46998-y Mechanism of DNA origami folding elucidated by mesoscopic simulations] ([https://doi.org/10.1101/2023.06.20.545758 bioRxiv]) | |||
# S. Cristofaro, L. Querciagrossa, L. Soprani, T.P. Fraccia, T. Bellini, R. Berardi, A. Arcioni, C. Zannoni, L. Muccioli, and S. Orlandi, ''Biomacromolecules'' '''25''', 3920–3929 (2024) | |||
#: [https://doi.org/10.1021/acs.biomac.3c01435 Simulating the lyotropic phase behavior of a partially self-complementary DNA tetramer] | |||
# A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and K. Salaita, ''Nat. Commun.'' '''15''', 704 (2024) | |||
#: [https://doi.org/10.1038/s41467-023-44061-w DNA mechanocapsules for programmable piconewton responsive drug delivery] | |||
# A. Voorspoels, J. Gevers, S. Santermans, N. Akkan, K. Martens, K. Willems, P. Van Dorpe, and A.S. Verhulst, ''J. Phys. Chem. A'' '''128''', 3926–3933 (2024) | |||
#: [https://doi.org/10.1021/acs.jpca.4c01772 Design principles of DNA-barcodes for nanopore-FET readout, based on molecular dynamics and TCAD simulations] | |||
# F. Tosti Guerra, E. Poppletoni, P. Šulc and L. Rovigatti, ''J. Chem. Phys.'' '''160''', 205102 (2024) | |||
#: [https://doi.org/10.1063/5.0202829 ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems] ([https://doi.org/10.48550/arXiv.2311.03317 arXiv]) | |||
# Y. Wang, I. Baars, I. Berzina, I. Rocamonde-Lago, B. Shen, Y. Yang, M. Lolaico, J. Waldvogel, I. Smyrlaki, K. Zhu, R.A. Harris and B. Högberg, ''Nat. Nanotechnol.'' '''19''', 1366–137 (2024) | |||
#: [https://doi.org/10.1038/s41565-024-01676-4 A DNA robotic switch with regulated autonomous display of cytotoxic ligand nanopatterns] | |||
# W. Ji, X. Xiong, M. Cao, Y. Zhu, L. Li, F. Wang, C. Fan and H. Pei, ''Nat. Chem.'' '''16''', 1408–1417 (2024) | |||
#: [https://doi.org/10.1038/s41557-024-01565-2 Encoding signal propagation on topology-programmed DNA origami] | |||
# M. van Galen, A. Bok, T. Peshkovsky, J. van der Gucht, B. Albada and J. Sprakel, ''Nat. Chem.'' accepted (2024) | |||
#: [https://doi.org/10.1038/s41557-024-01571-4 De novo DNA-based catch bonds] | |||
# Y. Hu, J. Rogers, Y. Duan, A. Velusamy, S. Narum, S. Al Abdullatif and K. Salaita, ''Nat. Nanotechnol.'' '''19''', 1674–1685 (2024) | |||
#: [https://doi.org/10.1038/s41565-024-01723-0 Quantifying T cell receptor mechanics at membrane junctions using DNA origami tension sensors] | |||
# D. Svenšek, J. Sočan and M. Praprotnik, ''Macromol. Rapid Commun.'' accepted 2400382 (2024) | |||
#: [https://doi.org/10.1002/marc.202400382 Density–nematic coupling in isotropic solution of DNA: Multiscale model] | |||
# M. Mogheiseh and R.H. Ghasemi, ''J. Chem. Phys.'' '''161''', 045101 (2024) | |||
#: [https://doi.org/10.1063/5.0214313 Design and simulation of a wireframe DNA origami nanoactuator] | |||
# S.H. Wong, S.N. Kopf, V. Caroprese, Y. Zosso, D. Morzy, M.M.C. Bastings, ''Nano Lett.'' '''24''', 11210–11216 (2024) | |||
#: [https://doi.org/10.1021/acs.nanolett.4c02564 Modulating the DNA/lipid interface through multivalent hydrophobicity] | |||
# G. Nava, T. Carzaniga, L. Casiraghi, E. Bot, G. Zanchetta, F. Damin, M. Chiari, G. Weber, T. Bellini, L. Mollica and M. Buscaglia, ''Nucl. Acids Res.'' '''52''', 8661–8674 (2024) | |||
#: [https://doi.org/10.1093/nar/gkae576 Weak-cooperative binding of a long single-stranded DNA chain on a surface] | |||
# Y. Du, R. Li, A.S. Madhvacharyula, A.A. Swett, J.H. Choi, submitted | |||
#: DNA nanostar structures with tunable auxetic properties ([https://doi.org/10.1101/2023.12.22.573109 bioRxiv]) | |||
# G.M. Roozbahani, P. Colosi, A. Oravecz, E.M. Sorokina, W. Pfeifer, S. Shokri, Y. Wei, P. Didier, M. DeLuca, G. Arya, L. Tora, M. Lakadamyali, M.G. Poirier, C. E. Castro | |||
#: Piggybacking functionalized DNA nanostructures into live cell nuclei ([https://doi.org/10.1101/2023.12.30.573746 bioRxiv]) | |||
# A. Walbrun, T. Wang, M. Matthies, P. Šulc, F.C. Simmel, M. Rief, ''Nat. Commun.'' '''15''', 7564 (2024) | |||
#: [https://doi.org/10.1038/s41467-024-51813-9 Single-Molecule Force Spectroscopy of Toehold-Mediated Strand Displacement] ([https://doi.org/10.1101/2024.01.16.575816 bioRxiv]) | |||
# S. Chandrasekhar, T.P. Swope, F. Fadaei, D.R. Hollis, R. Bricker, D. Houser, J. Portman, T.L. Schmidt, submitted | |||
#: Bending Unwinds DNA ([https://doi.org/10.1101/2024.02.14.579968 bioRxiv]) | |||
# X. Liu, F. Liu, H. Chhabra, C. Maffeo, Q. Huang, A. Aksimentiev, T. Arai, ''Nat. Commun.'' '''15''', 7210 (2024) | |||
#: [https://doi.org/10.1038/s41467-024-51630-0 A lumen-tunable triangular DNA nanopore for molecular sensing and cross-membrane transport] ([https://doi.org/10.21203/rs.3.rs-3878148/v1 ResearchSquare]) | |||
# L. Yang, G. Pecastaings, C. Drummond and J. Elezgaray, ''Nano Lett.'' '''24''', 13481–13486 (2024) | |||
#: [https://doi.org/10.1021/acs.nanolett.4c02302 Driving DNA nanopore membrane insertion through dipolar coupling] | |||
# J.-Y. Liou, M. Awan, K. Leyba, P. Šulc, S. Hofmeyr, C.-J. Wu and S. Forrest, ''ACM Trans. Evol. Learn. Optim.'' accepted (2024) | |||
#: [https://doi.org/10.1145/3703920 Evolving to find optimizations humans miss: Using evolutionary computation to improve GPU code for bioinformatics applications] | |||
# C. Karfusehr, M. Eder, F.C. Simmel | |||
#: Self-assembled cell-scale containers made from DNA origami membranes ([https://doi.org/10.1101/2024.02.09.579479 bioRxiv]) | |||
# M.T. Luu, J.F. Berengut, J.K.D. Singh, K.C.D. Glieze, M. Turner, K. Skipper, S. Meppat, H. Fowler, W. Close, J.P.K. Doye, A. Abbas, S.F.J. Wickham, submitted | |||
#: Reconfigurable multi-component nanostructures built from DNA origami voxels ([https://doi.org/10.1101/2024.03.10.584331 bioRxiv]) | |||
# M.P. Tran, T. Chakraborty, E. Poppleton, L. Monari, F. Giessler and K. Göpfrich, submitted | |||
#: Genetic encoding and expression of RNA origami cytoskeletons in synthetic cells ([https://doi.org/10.1101/2024.06.12.598448 bioRxiv]) | |||
# V. Bukina and A. Božič, ''Biophys. J.'' '''123''', 3397-3407 (2024) | |||
#: [https://doi.org/10.1016/j.bpj.2024.08.004 Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA] ([https://doi.org/10.1101/2024.04.17.589867 bioRxiv]) | |||
# R. Walker-Gibbons, X. Zhu, A. Behjatian, T.J.D. Bennett and M. Krishnan, Sci. Rep. 14, 20582 (2024) | |||
#: [https://doi.org/10.1038/s41598-024-70641-x Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations] | |||
# E.J. Ratajczyk, J. Bath, P. Sulc, J.P.K. Doye, A.A. Louis, A.J. Turberfield, submitted | |||
#: Controlling DNA-RNA strand displacement kinetics with base distribution ([https://doi.org/10.1101/2024.08.06.606789 bioRxiv]) | |||
# A. Suma and C. Micheletti, submitted | |||
#: Unzipping of knotted DNA via nanopore translocation ([https://doi.org/10.48550/arXiv.2407.11567 arXiv]) | |||
# G. Mattiotti, M. Micheloni, L. Petrolli, L. Tubiana, S. Pasquali, R. Potestio, submitted. | |||
#: Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model ([https://doi.org/10.48550/arXiv.2408.03662 arXiv]) | |||
# S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, submitted. | |||
#: How we simulate DNA origami ([https://doi.org/10.48550/arXiv.2409.13206 arXiv]) | |||
# Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted | |||
#: Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells ([https://doi.org/10.21203/rs.3.rs-4897446/v1 ResearchSquare]) | |||
# R.K. Krueger, M.C. Engel, R. Hausen, M.P. Brenner, submitted (2024) | |||
#: A Differentiable Model of Nucleic Acid Dynamics ([https://arxiv.org/abs/2411.09216 arXiv]) | |||
# Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted | |||
#: Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells ([https://doi.org/10.21203/rs.3.rs-4897446/v1 ResearchSquare]) | |||
# K. Zhou, M. Chung, J. Cheng, J.T. Powell, J. Liu, Y. Xiong, M.A. Schwartz and C. Lin, submitted. | |||
#: DNA nanodevice for analysis of force-activated protein extension and interactions ([https://doi.org/10.1101/2024.10.25.620262 bioRxiv]) | |||
# W.-S. Wei, T.E. Videbæk, D. Hayakawa, R. Saha, W.B. Rogers, S. Fraden, submitted | |||
#: Economical and versatile subunit design principles for self-assembled DNA origami structures ([https://doi.org/10.48550/arXiv.2411.09801 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]. |
Latest revision as of 13:12, 23 November 2024
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- 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)
- A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and K. Salaita, Nat. Commun. 15, 704 (2024)
- 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)
- F. Tosti Guerra, E. Poppletoni, P. Šulc and L. Rovigatti, J. Chem. Phys. 160, 205102 (2024)
- Y. Wang, I. Baars, I. Berzina, I. Rocamonde-Lago, B. Shen, Y. Yang, M. Lolaico, J. Waldvogel, I. Smyrlaki, K. Zhu, R.A. Harris and B. Högberg, Nat. Nanotechnol. 19, 1366–137 (2024)
- W. Ji, X. Xiong, M. Cao, Y. Zhu, L. Li, F. Wang, C. Fan and H. Pei, Nat. Chem. 16, 1408–1417 (2024)
- M. van Galen, A. Bok, T. Peshkovsky, J. van der Gucht, B. Albada and J. Sprakel, Nat. Chem. accepted (2024)
- Y. Hu, J. Rogers, Y. Duan, A. Velusamy, S. Narum, S. Al Abdullatif and K. Salaita, Nat. Nanotechnol. 19, 1674–1685 (2024)
- D. Svenšek, J. Sočan and M. Praprotnik, Macromol. Rapid Commun. accepted 2400382 (2024)
- M. Mogheiseh and R.H. Ghasemi, J. Chem. Phys. 161, 045101 (2024)
- S.H. Wong, S.N. Kopf, V. Caroprese, Y. Zosso, D. Morzy, M.M.C. Bastings, Nano Lett. 24, 11210–11216 (2024)
- G. Nava, T. Carzaniga, L. Casiraghi, E. Bot, G. Zanchetta, F. Damin, M. Chiari, G. Weber, T. Bellini, L. Mollica and M. Buscaglia, Nucl. Acids Res. 52, 8661–8674 (2024)
- Y. Du, R. Li, A.S. Madhvacharyula, A.A. Swett, J.H. Choi, submitted
- DNA nanostar structures with tunable auxetic properties (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 (bioRxiv)
- A. Walbrun, T. Wang, M. Matthies, P. Šulc, F.C. Simmel, M. Rief, Nat. Commun. 15, 7564 (2024)
- S. Chandrasekhar, T.P. Swope, F. Fadaei, D.R. Hollis, R. Bricker, D. Houser, J. Portman, T.L. Schmidt, submitted
- Bending Unwinds DNA (bioRxiv)
- X. Liu, F. Liu, H. Chhabra, C. Maffeo, Q. Huang, A. Aksimentiev, T. Arai, Nat. Commun. 15, 7210 (2024)
- L. Yang, G. Pecastaings, C. Drummond and J. Elezgaray, Nano Lett. 24, 13481–13486 (2024)
- J.-Y. Liou, M. Awan, K. Leyba, P. Šulc, S. Hofmeyr, C.-J. Wu and S. Forrest, ACM Trans. Evol. Learn. Optim. accepted (2024)
- C. Karfusehr, M. Eder, F.C. Simmel
- Self-assembled cell-scale containers made from DNA origami membranes (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 (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 (bioRxiv)
- V. Bukina and A. Božič, Biophys. J. 123, 3397-3407 (2024)
- R. Walker-Gibbons, X. Zhu, A. Behjatian, T.J.D. Bennett and M. Krishnan, Sci. Rep. 14, 20582 (2024)
- 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)
- A. Suma and C. Micheletti, submitted
- Unzipping of knotted DNA via nanopore translocation (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 (arXiv)
- S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, submitted.
- How we simulate DNA origami (arXiv)
- Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted
- Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells (ResearchSquare)
- R.K. Krueger, M.C. Engel, R. Hausen, M.P. Brenner, submitted (2024)
- A Differentiable Model of Nucleic Acid Dynamics (arXiv)
- Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted
- Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells (ResearchSquare)
- K. Zhou, M. Chung, J. Cheng, J.T. Powell, J. Liu, Y. Xiong, M.A. Schwartz and C. Lin, submitted.
- DNA nanodevice for analysis of force-activated protein extension and interactions (bioRxiv)
- W.-S. Wei, T.E. Videbæk, D. Hayakawa, R. Saha, W.B. Rogers, S. Fraden, submitted
- Economical and versatile subunit design principles for self-assembled DNA origami structures (arXiv)
We are also maintaining a list of all published papers using oxDNA at publons.