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For: Sengar A, Ouldridge TE, Henrich O, Rovigatti L, Šulc P. A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results. Front Mol Biosci 2021;8:693710. [PMID: 34235181 PMCID: PMC8256390 DOI: 10.3389/fmolb.2021.693710] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Svenšek D, Sočan J, Praprotnik M. Density-Nematic Coupling in Isotropic Solution of DNA: Multiscale Model. Macromol Rapid Commun 2024;45:e2400382. [PMID: 39122482 DOI: 10.1002/marc.202400382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/26/2024] [Indexed: 08/12/2024]
2
Chandrasekhar S, Swope TP, Fadaei F, Hollis DR, Bricker R, Houser D, Portman JJ, Schmidt TL. Bending DNA increases its helical repeat. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.579968. [PMID: 38405957 PMCID: PMC10888926 DOI: 10.1101/2024.02.14.579968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
3
Zhou L, Xiong Y, Dwivedy A, Zheng M, Cooper L, Shepherd S, Song T, Hong W, Le LTP, Chen X, Umrao S, Rong L, Wang T, Cunningham BT, Wang X. Bioinspired designer DNA NanoGripper for virus sensing and potential inhibition. Sci Robot 2024;9:eadi2084. [PMID: 39602515 DOI: 10.1126/scirobotics.adi2084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/25/2024] [Indexed: 11/29/2024]
4
Liu J, Zhou Z, Bo Y, Yan Q, Su X. Harnessing CRISPR/Cas12a Activity and DNA-Based Ultrabright FluoroCube for In Situ Imaging of Metabolically Labeled Cell Membrane Glycoproteins. NANO LETTERS 2024;24:14236-14243. [PMID: 39470128 DOI: 10.1021/acs.nanolett.4c03605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/30/2024]
5
Sample M, Liu H, Diep T, Matthies M, Šulc P. Hairygami: Analysis of DNA Nanostructures' Conformational Change Driven by Functionalizable Overhangs. ACS NANO 2024;18:30004-30016. [PMID: 39421963 DOI: 10.1021/acsnano.4c10796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
6
Walker-Gibbons R, Zhu X, Behjatian A, Bennett TJD, Krishnan M. Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations. Sci Rep 2024;14:20582. [PMID: 39232063 PMCID: PMC11375218 DOI: 10.1038/s41598-024-70641-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 08/20/2024] [Indexed: 09/06/2024]  Open
7
Ji W, Xiong X, Cao M, Zhu Y, Li L, Wang F, Fan C, Pei H. Encoding signal propagation on topology-programmed DNA origami. Nat Chem 2024;16:1408-1417. [PMID: 38886615 DOI: 10.1038/s41557-024-01565-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 05/24/2024] [Indexed: 06/20/2024]
8
Sethi S, Xu T, Sarkar A, Drees C, Jacob C, Walther A. Nuclease-Resistant L-DNA Tension Probes Enable Long-Term Force Mapping of Single Cells and Cell Consortia. Angew Chem Int Ed Engl 2024:e202413983. [PMID: 39212256 DOI: 10.1002/anie.202413983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/26/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
9
Cristofaro S, Querciagrossa L, Soprani L, Fraccia TP, Bellini T, Berardi R, Arcioni A, Zannoni C, Muccioli L, Orlandi S. Simulating the Lyotropic Phase Behavior of a Partially Self-Complementary DNA Tetramer. Biomacromolecules 2024;25:3920-3929. [PMID: 38826125 DOI: 10.1021/acs.biomac.3c01435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
10
Tosti Guerra F, Poppleton E, Šulc P, Rovigatti L. ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems. J Chem Phys 2024;160:205102. [PMID: 38814009 DOI: 10.1063/5.0202829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/04/2024] [Indexed: 05/31/2024]  Open
11
Laeremans W, Segers M, Voorspoels A, Carlon E, Hooyberghs J. Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs cgDNA. J Chem Phys 2024;160:144105. [PMID: 38591677 DOI: 10.1063/5.0197053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/19/2024] [Indexed: 04/10/2024]  Open
12
DeLuca M, Sensale S, Lin PA, Arya G. Prediction and Control in DNA Nanotechnology. ACS APPLIED BIO MATERIALS 2024;7:626-645. [PMID: 36880799 DOI: 10.1021/acsabm.2c01045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
13
Yu S, Chu R, Wu G, Meng X. A Novel Fractional Brownian Dynamics Method for Simulating the Dynamics of Confined Bottle-Brush Polymers in Viscoelastic Solution. Polymers (Basel) 2024;16:524. [PMID: 38399901 PMCID: PMC10891538 DOI: 10.3390/polym16040524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024]  Open
14
Qiao YP, Ren CL. Correlated Hybrid DNA Structures Explored by the oxDNA Model. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024;40:109-117. [PMID: 38154122 DOI: 10.1021/acs.langmuir.3c02231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
15
Sharma G, Seth A, Giri RP, Hayen N, Murphy BM, Ghosh SK. Ionic Liquid-Induced Assembly of DNA at Air-Water Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023;39:16079-16089. [PMID: 37922422 DOI: 10.1021/acs.langmuir.3c02212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
16
Karna D, Mano E, Ji J, Kawamata I, Suzuki Y, Mao H. Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies. Nat Commun 2023;14:6459. [PMID: 37833326 PMCID: PMC10575982 DOI: 10.1038/s41467-023-41604-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 09/06/2023] [Indexed: 10/15/2023]  Open
17
Erban R, Togashi Y. Asymmetric Periodic Boundary Conditions for All-Atom Molecular Dynamics and Coarse-Grained Simulations of Nucleic Acids. J Phys Chem B 2023;127:8257-8267. [PMID: 37713594 PMCID: PMC10544013 DOI: 10.1021/acs.jpcb.3c03887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/31/2023] [Indexed: 09/17/2023]
18
Micheloni M, Petrolli L, Lattanzi G, Potestio R. Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations. Biophys J 2023;122:3314-3322. [PMID: 37455429 PMCID: PMC10465705 DOI: 10.1016/j.bpj.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 01/16/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]  Open
19
Gilbert BR, Thornburg ZR, Brier TA, Stevens JA, Grünewald F, Stone JE, Marrink SJ, Luthey-Schulten Z. Dynamics of chromosome organization in a minimal bacterial cell. Front Cell Dev Biol 2023;11:1214962. [PMID: 37621774 PMCID: PMC10445541 DOI: 10.3389/fcell.2023.1214962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/10/2023] [Indexed: 08/26/2023]  Open
20
Shirt-Ediss B, Connolly J, Elezgaray J, Torelli E, Navarro SA, Bacardit J, Krasnogor N. Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists. Comput Struct Biotechnol J 2023;21:3615-3626. [PMID: 37520280 PMCID: PMC10371787 DOI: 10.1016/j.csbj.2023.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023]  Open
21
Yu S, Zhao J, Chu R, Li X, Wu G, Meng X. Anomalous Diffusion of Polyelectrolyte Segments on Supported Charged Lipid Bilayers. ENTROPY (BASEL, SWITZERLAND) 2023;25:e25050796. [PMID: 37238551 DOI: 10.3390/e25050796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/04/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023]
22
Qiao YP, Ren CL, Ma YQ. Two Different Ways of Stress Release in Supercoiled DNA Minicircles under DNA Nick. J Phys Chem B 2023;127:4015-4021. [PMID: 37126597 DOI: 10.1021/acs.jpcb.2c08618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
23
Cervantes-Salguero K, Gutiérrez Fosado YA, Megone W, Gautrot JE, Palma M. Programmed Self-Assembly of DNA Nanosheets with Discrete Single-Molecule Thickness and Interfacial Mechanics: Design, Simulation, and Characterization. Molecules 2023;28:3686. [PMID: 37175096 PMCID: PMC10180480 DOI: 10.3390/molecules28093686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/05/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023]  Open
24
Huang J, Gambietz S, Saccà B. Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023;19:e2202253. [PMID: 35775957 DOI: 10.1002/smll.202202253] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/02/2022] [Indexed: 06/15/2023]
25
Udono H, Gong J, Sato Y, Takinoue M. DNA Droplets: Intelligent, Dynamic Fluid. Adv Biol (Weinh) 2023;7:e2200180. [PMID: 36470673 DOI: 10.1002/adbi.202200180] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/14/2022] [Indexed: 12/12/2022]
26
Zhou C, Yang D, Sensale S, Sharma P, Wang D, Yu L, Arya G, Ke Y, Wang P. A bistable and reconfigurable molecular system with encodable bonds. SCIENCE ADVANCES 2022;8:eade3003. [PMID: 36399380 PMCID: PMC9674029 DOI: 10.1126/sciadv.ade3003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
27
Fontana F, Bellini T, Todisco M. Liquid Crystal Ordering in DNA Double Helices with Backbone Discontinuities. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
28
Marrink SJ, Monticelli L, Melo MN, Alessandri R, Tieleman DP, Souza PCT. Two decades of Martini: Better beads, broader scope. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
29
Design and simulation of DNA, RNA and hybrid protein-nucleic acid nanostructures with oxView. Nat Protoc 2022;17:1762-1788. [PMID: 35668321 DOI: 10.1038/s41596-022-00688-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/18/2022] [Indexed: 11/08/2022]
30
Piskunen P, Latham R, West CE, Castronovo M, Linko V. Integrating CRISPR/Cas systems with programmable DNA nanostructures for delivery and beyond. iScience 2022;25:104389. [PMID: 35633938 PMCID: PMC9130510 DOI: 10.1016/j.isci.2022.104389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
31
OxDNA to Study Species Interactions. ENTROPY 2022;24:e24040458. [PMID: 35455121 PMCID: PMC9029285 DOI: 10.3390/e24040458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 02/01/2023]
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