{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T12:38:25Z","timestamp":1775911105975,"version":"3.50.1"},"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2014,4,10]],"date-time":"2014-04-10T00:00:00Z","timestamp":1397088000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1003562","type":"journal-article","created":{"date-parts":[[2014,4,10]],"date-time":"2014-04-10T20:52:48Z","timestamp":1397163168000},"page":"e1003562","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":59,"title":["Atomistic Picture for the Folding Pathway of a Hybrid-1 Type Human Telomeric DNA G-quadruplex"],"prefix":"10.1371","volume":"10","author":[{"given":"Yunqiang","family":"Bian","sequence":"first","affiliation":[]},{"given":"Cheng","family":"Tan","sequence":"additional","affiliation":[]},{"given":"Jun","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Yuebiao","family":"Sheng","sequence":"additional","affiliation":[]},{"given":"Jian","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Wei","family":"Wang","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2014,4,10]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1016\/j.tcb.2009.05.002","article-title":"G-quadruplex structures: in vivo evidence and function","volume":"19","author":"HJ Lipps","year":"2009","journal-title":"Trends Cell Biol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1126\/science.1147182","article-title":"Telomeric repeatccontaining RNA and RNA surveillance factors at mammalian chromosome ends","volume":"318","author":"CM Azzalin","year":"2007","journal-title":"Science"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"16072","DOI":"10.1073\/pnas.1006026107","article-title":"G-quadruplex struc- tures in RNA stimulate mitochondrial transcription termination and primer formation","volume":"107","author":"PH Wanrooij","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1002\/anie.200300589","article-title":"G-quartets 40 years later: From 5-gmp to molecular biology and supramolecular chemistry","volume":"43","author":"JT Davis","year":"2004","journal-title":"Angew Chem Int Ed"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1006\/jtbi.1994.1163","article-title":"On the conformational stability of oligonucleotide duplexes and tRNA molecules","volume":"169","author":"P Ponnuswamy","year":"1994","journal-title":"J Theor Biol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"8759","DOI":"10.1021\/jp991614x","article-title":"DNA, RNA, and DNA\/RNA oligomer duplexes: A comparative study of their stability, heat, hydration, and Mg2+ binding properties","volume":"103","author":"BI Kankia","year":"1999","journal-title":"J Phys Chem B"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"6507","DOI":"10.1021\/bi026997v","article-title":"Stability of intramolecular DNA quadruplexes:comparison with DNA duplexes","volume":"42","author":"A Risitano","year":"2003","journal-title":"Biochemistry"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1073\/pnas.0404448102","article-title":"Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution","volume":"102","author":"Y Bai","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1021\/bi061375l","article-title":"Folding cooperativity in RNA and DNA is dependent on position in the helix","volume":"46","author":"NA Siegfried","year":"2007","journal-title":"Biochemistry"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1016\/j.jmb.2009.08.044","article-title":"Metal ion dependence of cooperative collapse transitions in RNA","volume":"393","author":"S Moghaddam","year":"2009","journal-title":"J Mol Biol"},{"key":"ref11","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":"ref12","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":"ref13","doi-asserted-by":"crossref","first-page":"5482","DOI":"10.1093\/nar\/gkn517","article-title":"Stability and kinetics of G-quadruplex structures","volume":"36","author":"AN Lane","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"5402","DOI":"10.1093\/nar\/gkl655","article-title":"Quadruplex DNA: sequence, topology and structure","volume":"34","author":"S Burge","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1016\/j.sbi.2006.05.011","article-title":"DNA architecture: from g to z","volume":"16","author":"AT Phan","year":"2006","journal-title":"Curr Opin Struct Biol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.ymeth.2012.04.005","article-title":"Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures","volume":"57","author":"J \u0160poner","year":"2012","journal-title":"Methods"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1016\/j.sbi.2009.04.001","article-title":"The structures of quadruplex nucleic acids and their drug complexes","volume":"19","author":"S Neidle","year":"2009","journal-title":"Curr Opin Struct Biol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"5293","DOI":"10.1039\/c1cs15117g","article-title":"Methods for investigating G-quadruplex DNA\/ligand interactions","volume":"40","author":"P Murat","year":"2011","journal-title":"Chem Soc Rev"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1038\/nrg3296","article-title":"DNA secondary structures: stability and function of G-quadruplex structures","volume":"13","author":"ML Bochman","year":"2012","journal-title":"Nat Rev Genet"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"9657","DOI":"10.1021\/ja300605n","article-title":"Energetic basis of human telomeric DNA folding into G-Quadruplex structures","volume":"134","author":"M Bon\u010dina","year":"2012","journal-title":"J Am Chem Soc"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1021\/ja2096255","article-title":"Toward a digital gene response: RNA G- Quadruplexes with fewer quartets fold with higher cooperativity","volume":"134","author":"MA Mullen","year":"2012","journal-title":"J Am Chem Soc"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"15324","DOI":"10.1021\/ja303499m","article-title":"Human telomere sequence DNA in water-free and high-viscosity solvents: G-Quadruplex folding governed by kramers rate theory","volume":"134","author":"FM Lannan","year":"2012","journal-title":"J Am Chem Soc"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"16834","DOI":"10.1021\/ja307543z","article-title":"Populated intermediates in the thermal unfolding of the human telomeric quadruplex","volume":"134","author":"RD Gray","year":"2012","journal-title":"J Am Chem Soc"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"2235","DOI":"10.1021\/ja309668t","article-title":"Long-loop G-Quadruplexes are misfolded population minorities with fast transition kinetics in human telomeric sequences","volume":"135","author":"D Koirala","year":"2013","journal-title":"J Am Chem Soc"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"6423","DOI":"10.1021\/ja4019176","article-title":"Direct measurement of sequential folding pathway and energy landscape of human telomeric G-quadruplex structures","volume":"135","author":"W Li","year":"2013","journal-title":"J Am Chem Soc"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"5157","DOI":"10.1021\/ja210399h","article-title":"Tertiary DNA structure in the single- stranded htert promoter fragment unfolds and refolds by parallel pathways via cooperative or sequential events","volume":"134","author":"Z Yu","year":"2012","journal-title":"J Am Chem Soc"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1787","DOI":"10.1016\/S0006-3495(03)74608-6","article-title":"Formation pathways of a Guanine-Quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates","volume":"85","author":"R \u0160te","year":"2003","journal-title":"Biophys J"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"3003","DOI":"10.1021\/ct100253m","article-title":"Structural dynamics of thrombin-binding DNA aptamer d(<named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"gene\" xlink:type=\"simple\">GGTTGGTGTGGTTGG<\/named-content>) quadruplex DNA studied by largescale explicit solvent simulations","volume":"6","author":"R Reshetnikov","year":"2010","journal-title":"J Chem Theory Comput"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1093\/nass\/nrm120","article-title":"Folding pathways of human telomeric hybrid G-quadruplex structure","volume":"51","author":"T Mashimo","year":"2007","journal-title":"Nucleic Acids Symp Ser (Oxf)"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"14910","DOI":"10.1021\/ja105806u","article-title":"Folding pathways of human telomeric type-1 and type-2 G-Quadruplex structures","volume":"132","author":"T Mashimo","year":"2010","journal-title":"J Am Chem Soc"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/j.bbrc.2008.12.006","article-title":"Force-induced unfolding of human telomeric G-quadruplex: A steered molecular dynamics simulation study","volume":"379","author":"H Li","year":"2009","journal-title":"Biochem Biophys Res Commun"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"2269","DOI":"10.1002\/anie.201206522","article-title":"The G-Triplex DNA","volume":"52","author":"V Limongelli","year":"2013","journal-title":"Angew Chem Int Ed"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"9963","DOI":"10.1021\/ja062791w","article-title":"Structure of the human telomere in K+ solution: An intramolecular (3+1) G-Quadruplex scaffold","volume":"128","author":"KN Luu","year":"2006","journal-title":"J Am Chem Soc"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"4191","DOI":"10.1093\/nar\/gkn379","article-title":"Kinetics and mechanism of K+- and Na+-induced folding of models of human telomeric DNA into G-quadruplex structures","volume":"36","author":"RD Gray","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"126601","DOI":"10.1088\/0034-4885\/71\/12\/126601","article-title":"Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science","volume":"71","author":"A Laio","year":"2008","journal-title":"Rep Prog Phys"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"4553","DOI":"10.1021\/jp067873l","article-title":"A bias-exchange approach to protein folding","volume":"111","author":"S Piana","year":"2007","journal-title":"J Phys Chem B"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"6882","DOI":"10.1021\/ja1109425","article-title":"Atomistic analysis of pseudoknotted RNA unfolding","volume":"133","author":"Y Zhang","year":"2011","journal-title":"J Am Chem Soc"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"1538","DOI":"10.1021\/ja0771641","article-title":"Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins","volume":"130","author":"C Hyeon","year":"2008","journal-title":"J Am Chem Soc"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"20634","DOI":"10.1021\/ja2092823","article-title":"Folding of human telomerase RNA pseudoknot using ionjump and temperature-quench simulations","volume":"133","author":"S Biyun","year":"2011","journal-title":"J Am Chem Soc"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"e1001118","DOI":"10.1371\/journal.pcbi.1001118","article-title":"Multi-scaled explorations of binding- induced folding of intrinsically disordered protein inhibitor ia3 to its target enzyme","volume":"7","author":"J Wang","year":"2011","journal-title":"PLoS Comput Biol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"E2342","DOI":"10.1073\/pnas.1220699110","article-title":"Quantifying the topography of the intrinsic energy landscape of exible biomolecular recognition","volume":"110","author":"X Chu","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"E3743","DOI":"10.1073\/pnas.1308381110","article-title":"Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein","volume":"110","author":"Y Wang","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"7128","DOI":"10.1093\/nar\/gkt412","article-title":"Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations","volume":"41","author":"P Stadlbauer","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"1028","DOI":"10.1016\/j.bpj.2012.08.012","article-title":"Single-stranded DNA within nanopores: Conformational dynamics and implications for sequencing; a molecular dynamics simulation study","volume":"103","author":"AT Guy","year":"2012","journal-title":"Biophys J"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1021\/ct700301q","article-title":"Gromacs 4: Algorithms for highly e_cient, load-balanced, and scalable molecular simulation","volume":"4","author":"B Hess","year":"2008","journal-title":"J Chem Theory Comput"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1961","DOI":"10.1016\/j.cpc.2009.05.011","article-title":"Plumed: A portable plugin for free-energy calculations with molecular dynamics","volume":"180","author":"M Bonomi","year":"2009","journal-title":"Comput Phys Commun"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003562","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T21:04:37Z","timestamp":1540328677000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003562"}},"subtitle":[],"editor":[{"given":"Alexander Donald","family":"MacKerell","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2014,4,10]]},"references-count":46,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2014,4,10]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003562","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,4,10]]}}}