{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T16:00:05Z","timestamp":1776700805847,"version":"3.51.2"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1010501","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,10,31]],"date-time":"2022-10-31T00:00:00Z","timestamp":1667174400000}}],"reference-count":103,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2022,10,19]],"date-time":"2022-10-19T00:00:00Z","timestamp":1666137600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["11971367"],"award-info":[{"award-number":["11971367"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["11605125"],"award-info":[{"award-number":["11605125"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>The three-dimensional (3D) structure and stability of DNA are essential to understand\/control their biological functions and aid the development of novel materials. In this work, we present a coarse-grained (CG) model for DNA based on the RNA CG model proposed by us, to predict 3D structures and stability for both dsDNA and ssDNA from the sequence. Combined with a Monte Carlo simulated annealing algorithm and CG force fields involving the sequence-dependent base-pairing\/stacking interactions and an implicit electrostatic potential, the present model successfully folds 20 dsDNAs (\u226452nt) and 20 ssDNAs (\u226474nt) into the corresponding native-like structures just from their sequences, with an overall mean RMSD of 3.4\u00c5 from the experimental structures. For DNAs with various lengths and sequences, the present model can make reliable predictions on stability, e.g., for 27 dsDNAs with\/without bulge\/internal loops and 24 ssDNAs including pseudoknot, the mean deviation of predicted melting temperatures from the corresponding experimental data is only ~2.0\u00b0C. Furthermore, the model also quantificationally predicts the effects of monovalent or divalent ions on the structure stability of ssDNAs\/dsDNAs.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1010501","type":"journal-article","created":{"date-parts":[[2022,10,19]],"date-time":"2022-10-19T13:41:46Z","timestamp":1666186906000},"page":"e1010501","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":14,"title":["Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions"],"prefix":"10.1371","volume":"18","author":[{"given":"Zi-Chun","family":"Mu","sequence":"first","affiliation":[]},{"given":"Ya-Lan","family":"Tan","sequence":"additional","affiliation":[]},{"given":"Ben-Gong","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Jie","family":"Liu","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2579-3134","authenticated-orcid":true,"given":"Ya-Zhou","family":"Shi","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,10,19]]},"reference":[{"key":"pcbi.1010501.ref001","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1093\/nar\/gkaa1269","article-title":"Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome","volume":"49","author":"WM Guiblet","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010501.ref002","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1038\/d41586-019-02554-z","article-title":"The structure of DNA","volume":"575","author":"G. Ferry","year":"2019","journal-title":"Nature"},{"key":"pcbi.1010501.ref003","doi-asserted-by":"crossref","first-page":"8419","DOI":"10.1093\/nar\/gkab609","article-title":"DNA G-quadruplex structures: more than simple roadblocks to transcription?","volume":"49","author":"J Robinson","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010501.ref004","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1038\/s41580-020-0236-x","article-title":"The regulation and functions of DNA and RNA G-quadruplexes","volume":"21","author":"D Varshney","year":"2020","journal-title":"Nat Rev Mol Cell Biol"},{"key":"pcbi.1010501.ref005","doi-asserted-by":"crossref","first-page":"17068","DOI":"10.1038\/natrevmats.2017.68","article-title":"DNA nanotechnology","volume":"3","author":"N Seeman","year":"2018","journal-title":"Nat Rev Mater"},{"key":"pcbi.1010501.ref006","doi-asserted-by":"crossref","first-page":"6459","DOI":"10.1021\/acs.chemrev.7b00663","article-title":"DNA nanotechnology-enabled drug delivery dystems","volume":"119","author":"Q Hu","year":"2019","journal-title":"Chem Rev"},{"key":"pcbi.1010501.ref007","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/s43586-020-00009-8","article-title":"DNA origami","volume":"1","author":"S Dey","year":"2021","journal-title":"Nat Rev Methods Primers"},{"key":"pcbi.1010501.ref008","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1038\/s41392-021-00727-9","article-title":"The biological applications of DNA nanomaterials: current challenges and future directions","volume":"6","author":"W Ma","year":"2021","journal-title":"Signal Transduct Target Ther"},{"key":"pcbi.1010501.ref009","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1146\/annurev.biophys.32.110601.141800","article-title":"The thermodynamics of DNA structural motifs","volume":"33","author":"J SantaLucia","year":"2004","journal-title":"Annu Rev Biophys Biomol Struct"},{"key":"pcbi.1010501.ref010","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1016\/j.sbi.2012.04.007","article-title":"Recent developments in single-molecule DNA mechanics","volume":"22","author":"Z Bryant","year":"2012","journal-title":"Curr Opin Struct Biol"},{"key":"pcbi.1010501.ref011","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.jsb.2016.06.022","article-title":"Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers","volume":"197","author":"F Kriegel","year":"2017","journal-title":"J Struct Biol"},{"key":"pcbi.1010501.ref012","doi-asserted-by":"crossref","first-page":"5726","DOI":"10.1093\/nar\/gkac445","article-title":"Twisting DNA by salt","volume":"50","author":"S Cruz-Leon","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010501.ref013","doi-asserted-by":"crossref","first-page":"058101","DOI":"10.1103\/PhysRevLett.124.058101","article-title":"Opposite effects of high-valent cations on the elasticities of DNA and RNA duplexes revealed by magnetic tweezers","volume":"124","author":"H Fu","year":"2020","journal-title":"Phys Rev Lett"},{"key":"pcbi.1010501.ref014","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1016\/S0006-3495(01)75770-0","article-title":"Stretching single-stranded DNA: interplay of electrostatic, base-pairing, and base-pair stacking interactions","volume":"81","author":"Y Zhang","year":"2001","journal-title":"Biophys J"},{"key":"pcbi.1010501.ref015","doi-asserted-by":"crossref","first-page":"047801","DOI":"10.1103\/PhysRevLett.122.047801","article-title":"Direct measurement of length scale dependence of the hydrophobic free energy of a single collapsed polymer nanosphere","volume":"122","author":"W Di","year":"2019","journal-title":"Phys Rev Lett"},{"key":"pcbi.1010501.ref016","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1021\/acs.jpcb.9b09106","article-title":"Modeling DNA flexibility: comparison of force fields from atomistic to multiscale levels","volume":"124","author":"V Minhas","year":"2020","journal-title":"J Phys Chem B"},{"key":"pcbi.1010501.ref017","doi-asserted-by":"crossref","first-page":"e2021263118","DOI":"10.1073\/pnas.2021263118","article-title":"Accurate modeling of DNA conformational flexibility by a multivariate Ising model","volume":"118","author":"K Liebl","year":"2021","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1010501.ref018","doi-asserted-by":"crossref","first-page":"17395","DOI":"10.1021\/jacs.1c05219","article-title":"Determining sequence-dependent DNA oligonucleotide hybridization and dehybridization mechanisms using coarse-grained molecular simulation, markov state models, and infrared spectroscopy","volume":"143","author":"MS Jones","year":"2021","journal-title":"J Am Chem Soc"},{"key":"pcbi.1010501.ref019","doi-asserted-by":"crossref","first-page":"W35","DOI":"10.1093\/nar\/gkz412","article-title":"HNADOCK: a nucleic acid docking server for modeling RNA\/DNA-RNA\/DNA 3D complex structures","volume":"47","author":"J He","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010501.ref020","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1016\/j.bpj.2017.02.022","article-title":"Understanding the relative flexibility of RNA and DNA duplexes: stretching and twist-stretch coupling","volume":"112","author":"L Bao","year":"2017","journal-title":"Biophys J"},{"key":"pcbi.1010501.ref021","doi-asserted-by":"crossref","first-page":"125103","DOI":"10.1063\/1.4915539","article-title":"Flexibility of short DNA helices with finite-length effect: From base pairs to tens of base pairs","volume":"142","author":"YY Wu","year":"2015","journal-title":"J Chem Phys"},{"key":"pcbi.1010501.ref022","doi-asserted-by":"crossref","first-page":"115101","DOI":"10.1063\/1.4944067","article-title":"The thermodynamics and kinetics of a nucleotide base pair","volume":"144","author":"Y Wang","year":"2016","journal-title":"J Chem Phys"},{"key":"pcbi.1010501.ref023","doi-asserted-by":"crossref","first-page":"042409","DOI":"10.1103\/PhysRevE.103.042409","article-title":"Thermodynamic and kinetic properties of a single base pair in A-DNA and B-DNA","volume":"103","author":"T Liu","year":"2021","journal-title":"Phys Rev E"},{"key":"pcbi.1010501.ref024","doi-asserted-by":"crossref","first-page":"7998","DOI":"10.1093\/nar\/gky599","article-title":"The temperature dependence of the helical twist of DNA","volume":"46","author":"F Kriegel","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010501.ref025","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1021\/acs.jpcb.0c09237","article-title":"Thermodynamics of DNA hybridization from atomistic simulations","volume":"125","author":"GH Zerze","year":"2021","journal-title":"J Phys Chem B"},{"key":"pcbi.1010501.ref026","doi-asserted-by":"crossref","first-page":"062411","DOI":"10.1103\/PhysRevE.103.062411","article-title":"Effect of loop sequence on unzipping of short DNA hairpins","volume":"103","author":"A Upadhyaya","year":"2021","journal-title":"Phys Rev E"},{"key":"pcbi.1010501.ref027","doi-asserted-by":"crossref","first-page":"217801","DOI":"10.1103\/PhysRevLett.118.217801","article-title":"Twist-bend coupling and the torsional response of double-stranded DNA","volume":"118","author":"SK Nomidis","year":"2017","journal-title":"Phys Rev Lett"},{"key":"pcbi.1010501.ref028","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1126\/science.8036491","article-title":"Fluctuations and supercoiling of DNA","volume":"265","author":"JF Marko","year":"1994","journal-title":"Science"},{"key":"pcbi.1010501.ref029","doi-asserted-by":"crossref","first-page":"032414","DOI":"10.1103\/PhysRevE.99.032414","article-title":"Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond","volume":"99","author":"SK Nomidis","year":"2019","journal-title":"Phys Rev E"},{"key":"pcbi.1010501.ref030","doi-asserted-by":"crossref","first-page":"235103","DOI":"10.1063\/1.4729371","article-title":"On the origin of the unusual behavior in the stretching of single-stranded DNA","volume":"136","author":"NM Toan","year":"2012","journal-title":"J Chem Phys"},{"key":"pcbi.1010501.ref031","doi-asserted-by":"crossref","first-page":"3406","DOI":"10.1093\/nar\/gkg595","article-title":"Mfold web server for nucleic acid folding and hybridization prediction","volume":"31","author":"M. Zuker","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010501.ref032","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1002\/wcms.1169","article-title":"The power of coarse graining in biomolecular simulations","volume":"4","author":"HI Ingolfsson","year":"2014","journal-title":"Wiley Interdiscip Rev Comput Mol Sci"},{"key":"pcbi.1010501.ref033","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.sbi.2015.11.011","article-title":"Multiscale simulation of DNA","volume":"37","author":"PD Dans","year":"2016","journal-title":"Curr Opin Struct Biol"},{"key":"pcbi.1010501.ref034","doi-asserted-by":"crossref","first-page":"645527","DOI":"10.3389\/fmolb.2021.645527","article-title":"Bottom-up coarse-grained modeling of DNA","volume":"8","author":"T Sun","year":"2021","journal-title":"Front Mol Biosci"},{"key":"pcbi.1010501.ref035","doi-asserted-by":"crossref","first-page":"1102","DOI":"10.1093\/nar\/gkx1262","article-title":"A coarse-grained model for DNA origami","volume":"46","author":"RV Reshetnikov","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010501.ref036","doi-asserted-by":"crossref","first-page":"125101","DOI":"10.1063\/1.3480685","article-title":"Analysis of a DNA simulation model through hairpin melting experiments","volume":"133","author":"MC Linak","year":"2010","journal-title":"J Chem Phys"},{"key":"pcbi.1010501.ref037","doi-asserted-by":"crossref","first-page":"e29","DOI":"10.1093\/nar\/gkaa015","article-title":"A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level","volume":"48","author":"J Walther","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010501.ref038","doi-asserted-by":"crossref","first-page":"2891","DOI":"10.1021\/ct500193u","article-title":"A coarse-grained model of unstructured single-stranded DNA derived from atomistic simulation and single-molecule experiment","volume":"10","author":"C Maffeo","year":"2014","journal-title":"J Chem Theory Comput"},{"key":"pcbi.1010501.ref039","doi-asserted-by":"crossref","first-page":"1711","DOI":"10.1021\/ct900653p","article-title":"A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics","volume":"6","author":"PD Dans","year":"2010","journal-title":"J Chem Theory Comput"},{"key":"pcbi.1010501.ref040","doi-asserted-by":"crossref","first-page":"3932","DOI":"10.1021\/acs.jctc.5b00286","article-title":"Martini coarse-grained force field: Extension to DNA","volume":"11","author":"JJ Uusitalo","year":"2015","journal-title":"J Chem Theory Comput"},{"key":"pcbi.1010501.ref041","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1038\/s41592-021-01098-3","article-title":"Martini 3: a general purpose force field for coarse-grained molecular dynamics","volume":"18","author":"PCT Souza","year":"2021","journal-title":"Nat Methods"},{"key":"pcbi.1010501.ref042","doi-asserted-by":"crossref","first-page":"3239","DOI":"10.1021\/acs.jctc.2c00138","article-title":"Accurate sequence-dependent coarse-grained model for conformational and elastic properties of double-stranded DNA","volume":"18","author":"S Assenza","year":"2022","journal-title":"J Chem Theory Comput"},{"key":"pcbi.1010501.ref043","doi-asserted-by":"crossref","first-page":"144903","DOI":"10.1063\/1.4822042","article-title":"An experimentally-informed coarse-grained 3-Site-Per-Nucleotide model of DNA: structure, thermodynamics, and dynamics of hybridization","volume":"139","author":"DM Hinckley","year":"2013","journal-title":"J Chem Phys"},{"key":"pcbi.1010501.ref044","doi-asserted-by":"crossref","first-page":"084901","DOI":"10.1063\/1.2431804","article-title":"A coarse grain model for DNA","volume":"126","author":"TAt Knotts","year":"2007","journal-title":"J Chem Phys"},{"key":"pcbi.1010501.ref045","doi-asserted-by":"crossref","first-page":"165103","DOI":"10.1063\/1.4897649","article-title":"Coarse-grained modeling of DNA curvature","volume":"141","author":"GS Freeman","year":"2014","journal-title":"J Chem Phys"},{"key":"pcbi.1010501.ref046","doi-asserted-by":"crossref","first-page":"085101","DOI":"10.1063\/1.3552946","article-title":"Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model","volume":"134","author":"TE Ouldridge","year":"2011","journal-title":"J Chem Phys"},{"key":"pcbi.1010501.ref047","doi-asserted-by":"crossref","first-page":"10726","DOI":"10.1093\/nar\/gkaa854","article-title":"Understanding DNA interactions in crowded environments with a coarse-grained model","volume":"48","author":"F Hong","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010501.ref048","doi-asserted-by":"crossref","first-page":"W491","DOI":"10.1093\/nar\/gkab324","article-title":"OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures","volume":"49","author":"E Poppleton","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010501.ref049","doi-asserted-by":"crossref","first-page":"178101","DOI":"10.1103\/PhysRevLett.104.178101","article-title":"DNA nanotweezers studied with a coarse-grained model of DNA","volume":"104","author":"TE Ouldridge","year":"2010","journal-title":"Phys Rev Lett"},{"key":"pcbi.1010501.ref050","doi-asserted-by":"crossref","first-page":"3763","DOI":"10.1021\/acs.jctc.8b00091","article-title":"Sequence-dependent three interaction site model for single- and double-stranded DNA","volume":"14","author":"D Chakraborty","year":"2018","journal-title":"J Chem Theory Comput"},{"key":"pcbi.1010501.ref051","doi-asserted-by":"crossref","first-page":"4901","DOI":"10.1021\/jp401087x","article-title":"Coarse-grained model for predicting RNA folding thermodynamics","volume":"117","author":"NA Denesyuk","year":"2013","journal-title":"J Phys Chem B"},{"key":"pcbi.1010501.ref052","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1038\/ncomms1481","article-title":"Capturing the essence of folding and functions of biomolecules using coarse-grained models","volume":"2","author":"C Hyeon","year":"2011","journal-title":"Nat Commun"},{"key":"pcbi.1010501.ref053","doi-asserted-by":"crossref","first-page":"5936","DOI":"10.3390\/molecules27185936","article-title":"3dDNA: A computational method of building DNA 3D structures","volume":"27","author":"Y Zhang","year":"2022","journal-title":"Molecules"},{"key":"pcbi.1010501.ref054","doi-asserted-by":"crossref","first-page":"167452","DOI":"10.1016\/j.jmb.2022.167452","article-title":"3dRNA: 3D structure prediction from linear to circular RNAs","volume":"434","author":"Y Zhang","year":"2022","journal-title":"J Mol Biol"},{"key":"pcbi.1010501.ref055","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1038\/srep00734","article-title":"Automated and fast building of three-dimensional RNA structures","volume":"2","author":"Y Zhao","year":"2012","journal-title":"Sci Rep"},{"key":"pcbi.1010501.ref056","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.1038\/s41598-017-01348-5","article-title":"Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors","volume":"7","author":"I Jeddi","year":"2017","journal-title":"Sci Rep"},{"key":"pcbi.1010501.ref057","doi-asserted-by":"crossref","first-page":"098101","DOI":"10.1103\/PhysRevLett.110.098101","article-title":"Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix","volume":"110","author":"Y He","year":"2013","journal-title":"Phys Rev Lett"},{"key":"pcbi.1010501.ref058","doi-asserted-by":"crossref","first-page":"243111","DOI":"10.1063\/1.4932082","article-title":"Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach","volume":"143","author":"Y He","year":"2015","journal-title":"J Chem Phys"},{"key":"pcbi.1010501.ref059","doi-asserted-by":"crossref","first-page":"5020","DOI":"10.1021\/ct4006689","article-title":"DNA duplex formation with a coarse-grained model","volume":"10","author":"M Maciejczyk","year":"2014","journal-title":"J Chem Theory Comput"},{"key":"pcbi.1010501.ref060","doi-asserted-by":"crossref","first-page":"8047","DOI":"10.1021\/jp400786b","article-title":"Coarse-grained simulations of RNA and DNA duplexes","volume":"117","author":"T Cragnolini","year":"2013","journal-title":"J Phys Chem B"},{"key":"pcbi.1010501.ref061","doi-asserted-by":"crossref","first-page":"11957","DOI":"10.1021\/jp102497y","article-title":"HiRE-RNA: a high resolution coarse-grained energy model for RNA","volume":"114","author":"S Pasquali","year":"2010","journal-title":"J Phys Chem B"},{"key":"pcbi.1010501.ref062","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1146\/annurev-biochem-060409-092720","article-title":"Understanding nucleic acid-ion interactions","volume":"83","author":"J Lipfert","year":"2014","journal-title":"Annu Rev Biochem"},{"key":"pcbi.1010501.ref063","doi-asserted-by":"crossref","first-page":"6629","DOI":"10.1093\/nar\/gkl810","article-title":"Electrostatic free energy landscapes for nucleic acid helix assembly","volume":"34","author":"ZJ Tan","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010501.ref064","doi-asserted-by":"crossref","first-page":"6156","DOI":"10.1093\/nar\/gkv570","article-title":"Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA","volume":"43","author":"YY Wu","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010501.ref065","doi-asserted-by":"crossref","first-page":"eabn1384","DOI":"10.1126\/sciadv.abn1384","article-title":"Twist-diameter coupling drives DNA twist changes with salt and temperature","volume":"8","author":"C Zhang","year":"2022","journal-title":"Sci Adv"},{"key":"pcbi.1010501.ref066","doi-asserted-by":"crossref","first-page":"105102","DOI":"10.1063\/1.4894752","article-title":"A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect","volume":"141","author":"YZ Shi","year":"2014","journal-title":"J Chem Phys"},{"key":"pcbi.1010501.ref067","doi-asserted-by":"crossref","first-page":"2654","DOI":"10.1016\/j.bpj.2015.11.006","article-title":"Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions","volume":"109","author":"YZ Shi","year":"2015","journal-title":"Biophys J"},{"key":"pcbi.1010501.ref068","doi-asserted-by":"crossref","first-page":"1532","DOI":"10.1261\/rna.071662.119","article-title":"Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway","volume":"25","author":"L Jin","year":"2019","journal-title":"RNA"},{"key":"pcbi.1010501.ref069","doi-asserted-by":"crossref","first-page":"e1006222","DOI":"10.1371\/journal.pcbi.1006222","article-title":"Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions","volume":"14","author":"YZ Shi","year":"2018","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1010501.ref070","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1016\/j.bpj.2018.08.030","article-title":"Modeling structure, stability, and flexibility of double-stranded RNAs in salt solutions","volume":"115","author":"L Jin","year":"2018","journal-title":"Biophys J"},{"key":"pcbi.1010501.ref071","doi-asserted-by":"crossref","first-page":"3555","DOI":"10.1021\/bi951907q","article-title":"Improved nearest-neighbor parameters for predicting DNA duplex stability","volume":"35","author":"J SantaLucia","year":"1996","journal-title":"Biochemistry"},{"key":"pcbi.1010501.ref072","doi-asserted-by":"crossref","first-page":"125107","DOI":"10.1063\/1.2895050","article-title":"Discrete state model and accurate estimation of loop entropy of RNA secondary structures","volume":"128","author":"J Zhang","year":"2008","journal-title":"J Chem Phys"},{"key":"pcbi.1010501.ref073","doi-asserted-by":"crossref","first-page":"118702","DOI":"10.1088\/0256-307X\/27\/11\/118702","article-title":"An RNA base discrete state model toward tertiary structure prediction","volume":"27","author":"J Zhang","year":"2010","journal-title":"Chin Phys Lett"},{"key":"pcbi.1010501.ref074","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1017\/S0033583500002031","article-title":"The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides","volume":"11","author":"GS Manning","year":"1978","journal-title":"Q Rev Biophys"},{"key":"pcbi.1010501.ref075","doi-asserted-by":"crossref","first-page":"44903","DOI":"10.1063\/1.1842059","article-title":"Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte","volume":"122","author":"ZJ Tan","year":"2005","journal-title":"J Chem Phys"},{"key":"pcbi.1010501.ref076","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1007\/978-94-017-9245-5_11","article-title":"RNA folding: structure prediction, folding kinetics and ion electrostatics","volume":"827","author":"Z Tan","year":"2015","journal-title":"Adv Exp Med Biol"},{"key":"pcbi.1010501.ref077","doi-asserted-by":"crossref","first-page":"4874","DOI":"10.1021\/ct4005036","article-title":"Evolutionary algorithm in the optimization of a coarse-grained force field","volume":"9","author":"F Leonarski","year":"2013","journal-title":"J Chem Theory Comput"},{"key":"pcbi.1010501.ref078","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1126\/science.220.4598.671","article-title":"Optimization by simulated annealing","volume":"220","author":"S Kirkpatrick","year":"1983","journal-title":"Science"},{"key":"pcbi.1010501.ref079","doi-asserted-by":"crossref","first-page":"e1005032","DOI":"10.1371\/journal.pcbi.1005032","article-title":"Structure prediction of RNA loops with a probabilistic approach","volume":"12","author":"J Li","year":"2016","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1010501.ref080","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1007\/BF01022990","article-title":"The pivot algorithm: A highly efficient Monte Carlo method for the self-avoiding walk","volume":"50","author":"N Madras","year":"1988","journal-title":"J Stat Phys"},{"key":"pcbi.1010501.ref081","doi-asserted-by":"crossref","first-page":"661367","DOI":"10.3389\/fphy.2021.661367","article-title":"Using Monte Carlo to simulate complex polymer systems: recent progress and outlook","volume":"9","author":"VG Mavrantzas","year":"2021","journal-title":"Front Phys"},{"key":"pcbi.1010501.ref082","doi-asserted-by":"crossref","first-page":"104102","DOI":"10.1088\/0953-8984\/22\/10\/104102","article-title":"Extracting bulk properties of self-assembling systems from small simulations","volume":"22","author":"TE Ouldridge","year":"2010","journal-title":"J Phys Condens Matter"},{"key":"pcbi.1010501.ref083","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.bpj.2017.11.003","article-title":"Translational entropy and DNA duplex stability","volume":"114","author":"PL Privalov","year":"2018","journal-title":"Biophys J"},{"key":"pcbi.1010501.ref084","doi-asserted-by":"crossref","first-page":"3446","DOI":"10.1038\/s41467-020-17128-1","article-title":"Structural basis of seamless excision and specific targeting by piggyBac transposase","volume":"11","author":"Q Chen","year":"2020","journal-title":"Nat Commun"},{"key":"pcbi.1010501.ref085","doi-asserted-by":"crossref","first-page":"3228","DOI":"10.1093\/nar\/gkh645","article-title":"Global structure of a DNA three-way junction by solution NMR: towards prediction of 3H fold","volume":"32","author":"B Wu","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010501.ref086","doi-asserted-by":"crossref","first-page":"4042","DOI":"10.1021\/bi00230a031","article-title":"Thermodynamic characterization of deoxyribooligonucleotide duplexes containing bulges","volume":"30","author":"DA LeBlanc","year":"1991","journal-title":"Biochemistry"},{"key":"pcbi.1010501.ref087","doi-asserted-by":"crossref","first-page":"4283","DOI":"10.1021\/bi00436a025","article-title":"Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC","volume":"28","author":"AP Williams","year":"1989","journal-title":"Biochemistry"},{"key":"pcbi.1010501.ref088","doi-asserted-by":"crossref","first-page":"3468","DOI":"10.1021\/bi9825091","article-title":"Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches","volume":"38","author":"N Peyret","year":"1999","journal-title":"Biochemistry"},{"key":"pcbi.1010501.ref089","doi-asserted-by":"crossref","first-page":"6448","DOI":"10.1021\/acs.biochem.7b00930","article-title":"Differential effects of strand asymmetry on the energetics and structural flexibility of DNA internal loops","volume":"56","author":"T Tran","year":"2017","journal-title":"Biochemistry"},{"key":"pcbi.1010501.ref090","doi-asserted-by":"crossref","first-page":"1939","DOI":"10.1021\/jp5116417","article-title":"Loop contributions to the folding thermodynamics of DNA straight hairpin loops and pseudoknots","volume":"119","author":"C Reiling","year":"2015","journal-title":"J Phys Chem B"},{"key":"pcbi.1010501.ref091","doi-asserted-by":"crossref","first-page":"9945","DOI":"10.1021\/jp0260853","article-title":"Folding of intramolecular DNA hairpin loops: enthalpy-entropy compensations and hydration contributions and hydration contributions","volume":"106","author":"D Rentzeperis","year":"2002","journal-title":"J Phys Chem B"},{"key":"pcbi.1010501.ref092","doi-asserted-by":"crossref","first-page":"6276","DOI":"10.1021\/bi00239a028","article-title":"Coupling of sequential transitions in a DNA double hairpin: energetics, ion binding, and hydration","volume":"30","author":"D Rentzeperis","year":"1991","journal-title":"Biochemistry"},{"key":"pcbi.1010501.ref093","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1016\/S0300-9084(85)80156-5","article-title":"Hairpin formation in synthetic oligonucleotides","volume":"67","author":"CW Hilbers","year":"1985","journal-title":"Biochimie"},{"key":"pcbi.1010501.ref094","doi-asserted-by":"crossref","first-page":"1489","DOI":"10.1093\/nar\/18.6.1489","article-title":"Perturbation of DNA hairpins containing the EcoRI recognition site by hairpin loops of varying size and composition: physical (NMR and UV) and enzymatic (EcoRI) studies","volume":"18","author":"MW Germann","year":"1990","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010501.ref095","doi-asserted-by":"crossref","first-page":"2400","DOI":"10.1103\/PhysRevLett.85.2400","article-title":"Sequence dependent rigidity of single stranded DNA","volume":"85","author":"NL Goddard","year":"2000","journal-title":"Phys Rev Lett"},{"key":"pcbi.1010501.ref096","doi-asserted-by":"crossref","first-page":"1098","DOI":"10.1093\/nar\/gkm1083","article-title":"Loop dependence of the stability and dynamics of nucleic acid hairpins","volume":"36","author":"SV Kuznetsov","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010501.ref097","doi-asserted-by":"crossref","first-page":"3537","DOI":"10.1021\/bi034621r","article-title":"Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures","volume":"43","author":"R Owczarzy","year":"2004","journal-title":"Biochemistry"},{"key":"pcbi.1010501.ref098","doi-asserted-by":"crossref","first-page":"e1008309","DOI":"10.1371\/journal.pcbi.1008309","article-title":"AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses","volume":"17","author":"F Stefaniak","year":"2021","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1010501.ref099","doi-asserted-by":"crossref","first-page":"e63","DOI":"10.1093\/nar\/gkv141","article-title":"3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures","volume":"43","author":"J Wang","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010501.ref100","doi-asserted-by":"crossref","first-page":"2777","DOI":"10.1038\/s41467-021-23100-4","article-title":"Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement","volume":"12","author":"P Xiong","year":"2021","journal-title":"Nat Commun"},{"key":"pcbi.1010501.ref101","doi-asserted-by":"crossref","first-page":"1857","DOI":"10.1093\/bioinformatics\/btq295","article-title":"Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function","volume":"26","author":"H Zhao","year":"2010","journal-title":"Bioinformatics"},{"key":"pcbi.1010501.ref102","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/j.bpj.2021.11.016","article-title":"rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation","volume":"121","author":"YL Tan","year":"2022","journal-title":"Biophys J"},{"key":"pcbi.1010501.ref103","doi-asserted-by":"crossref","first-page":"e1006514","DOI":"10.1371\/journal.pcbi.1006514","article-title":"RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks","volume":"14","author":"J Li","year":"2018","journal-title":"PLoS Comput Biol"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1010501","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,10,31]],"date-time":"2022-10-31T00:00:00Z","timestamp":1667174400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010501","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,10,31]],"date-time":"2022-10-31T14:00:51Z","timestamp":1667224851000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010501"}},"subtitle":[],"editor":[{"given":"Alexander","family":"MacKerell","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,10,19]]},"references-count":103,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2022,10,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1010501","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.08.22.504895","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,10,19]]}}}