{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T09:22:50Z","timestamp":1775121770842,"version":"3.50.1"},"reference-count":28,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2009,3,13]],"date-time":"2009-03-13T00:00:00Z","timestamp":1236902400000},"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.1000313","type":"journal-article","created":{"date-parts":[[2009,3,12]],"date-time":"2009-03-12T21:30:23Z","timestamp":1236893423000},"page":"e1000313","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":40,"title":["Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter"],"prefix":"10.1371","volume":"5","author":[{"given":"Boian S.","family":"Alexandrov","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vladimir","family":"Gelev","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sang Wook","family":"Yoo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alan R.","family":"Bishop","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kim \u00d8.","family":"Rasmussen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anny","family":"Usheva","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2009,3,13]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1038\/19999","article-title":"Structural basis for initiation of transcription from an RNA polymerase-promoter complex.","volume":"399","author":"GM Cheetham","year":"1999","journal-title":"Nature"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1002\/(SICI)1521-1878(200004)22:4<316::AID-BIES2>3.0.CO;2-B","article-title":"Peeling by binding or twisting by cranking: models for promoter opening and transcription initiation by RNA polymerase II.","volume":"22","author":"U Fiedler","year":"2000","journal-title":"Bioessays"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1002\/j.1460-2075.1994.tb06273.x","article-title":"Transcription initiation by RNA polymerase II does not require hydrolysis of the beta-gamma phosphoanhydride bond of ATP.","volume":"13","author":"HT Timmers","year":"1994","journal-title":"EMBO J"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1016\/0092-8674(93)90140-L","article-title":"DNA topology and a minimal set of basal factors for transcription by RNA polymerase II.","volume":"73","author":"JD Parvin","year":"1993","journal-title":"Cell"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"10745","DOI":"10.1073\/pnas.200365097","article-title":"An initiation element in the yeast CUP1 promoter is recognized by RNA polymerase II in the absence of TATA box-binding protein if the DNA is negatively supercoiled.","volume":"97","author":"CJ Leblanc Bp Fau - Benham","year":"2000","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"13571","DOI":"10.1073\/pnas.93.24.13571","article-title":"YY1 transcriptional initiator: protein interactions and association with a DNA site containing unpaired strands.","volume":"93","author":"A Usheva","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"30101","DOI":"10.1016\/S0021-9258(18)43780-5","article-title":"Initiation of transcription by RNA polymerase II is limited by melting of the promoter DNA in the region immediately upstream of the initiation site.","volume":"269","author":"G Pan","year":"1994","journal-title":"J Biol Chem"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1584","DOI":"10.1093\/nar\/gkh335","article-title":"DNA dynamically directs its own transcription initiation.","volume":"32","author":"CH Choi","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"2755","DOI":"10.1103\/PhysRevLett.62.2755","article-title":"Statistical mechanics of a nonlinear model for DNA denaturation.","volume":"62","author":"M Peyrard","year":"1989","journal-title":"Phys Rev Lett"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"3585","DOI":"10.1103\/PhysRevE.58.3585","article-title":"Experimental tests of the Peyrard-Bishop model applied to the melting of very short DNA chains.","volume":"58","author":"A Campa","year":"1998","journal-title":"Phys Rev E"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"153901","DOI":"10.1063\/1.2358846","article-title":"Helicase mediated active DNA unwinding in a stochastic field.","volume":"89","author":"T Das","year":"2006","journal-title":"Appl Phys Lett"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"248101","DOI":"10.1103\/PhysRevLett.96.248101","article-title":"Probing the mechanical unzipping of DNA.","volume":"96","author":"NK Voulgarakis","year":"2006","journal-title":"Phys Rev Lett"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"035504","DOI":"10.1103\/PhysRevLett.94.035504","article-title":"Bubble nucleation and cooperativity in DNA melting.","volume":"94","author":"S Ares","year":"2005","journal-title":"Phys Rev Lett"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1529\/biophysj.107.123471","article-title":"Profiling the thermodynamic softness of adenoviral promoters.","volume":"95","author":"CH Choi","year":"2008","journal-title":"Biophys J"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"050901","DOI":"10.1103\/PhysRevE.74.050901","article-title":"Bubble statistics and dynamics in double-stranded DNA.","volume":"74","author":"BS Alexandrov","year":"2006","journal-title":"Phys Rev E"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"R44","DOI":"10.1103\/PhysRevE.47.R44","article-title":"Entropy-driven DNA denaturation.","volume":"47","author":"T Dauxois","year":"1993","journal-title":"Phys Rev E"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1016\/j.ceb.2008.03.003","article-title":"The RNA polymerase II core promoter\u2014the gateway to transcription.","volume":"20","author":"T Juven-Gershon","year":"2008","journal-title":"Curr Opin Cell Biol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1038\/nrg2026","article-title":"Mammalian RNA polymerase II core promoters: insights from genome-wide studies.","volume":"8","author":"A Sandelin","year":"2007","journal-title":"Nat Rev Genet"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1038\/328089a0","article-title":"A single mode of DNA base-pair opening drives imino proton exchange.","volume":"328","author":"M Gueron","year":"1987","journal-title":"Nature"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"218104","DOI":"10.1103\/PhysRevLett.95.218104","article-title":"Can one predict DNA transcription start sites by studying bubbles?","volume":"95","author":"TS van Erp","year":"2005","journal-title":"Phys Rev Lett"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"239801","DOI":"10.1103\/PhysRevLett.96.239801","article-title":"Comment on \u201cCan one predict DNA transcription start sites by studying bubbles?\u201d","volume":"96","author":"CH Choi","year":"2006","journal-title":"Phys Rev Lett"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1023\/A:1011250219293","article-title":"H\u00b7\u00b7\u00b7N hydrogen bond lengths in double stranded DNA from internucleotide dipolar couplings.","volume":"19","author":"Z Wu","year":"2001","journal-title":"J Biomol NMR"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1016\/S0167-4781(00)00109-3","article-title":"The genomic structure and promoter analysis of the human ABF-1 gene.","volume":"1492","author":"B Mitchell","year":"2000","journal-title":"Biochim Biophys Acta"},{"key":"ref24","first-page":"1549","article-title":"PU.1 (Spi-1) autoregulates its expression in myeloid cells.","volume":"11","author":"H Chen","year":"1995","journal-title":"Oncogene"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"2085","DOI":"10.1101\/gad.1654808","article-title":"PU.1 expression is modulated by the balance of functional sense and antisense RNAs regulated by a shared cis-regulatory element.","volume":"22","author":"AK Ebralidze","year":"2008","journal-title":"Genes Dev"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"6957","DOI":"10.1074\/jbc.274.11.6957","article-title":"High base pair opening rates in tracts of GC base pairs.","volume":"274","author":"U Dornberger","year":"1999","journal-title":"J Biol Chem"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1016\/0022-2836(70)90121-X","article-title":"Physicochemical studies on polydeoxyribonucleotides containing defined repeating nucleotide sequences.","volume":"54","author":"RD Wells","year":"1970","journal-title":"J Mol Biol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"2595","DOI":"10.1039\/b719370j","article-title":"Nature and magnitude of aromatic stacking of nucleic acid bases.","volume":"10","author":"J Sponer","year":"2008","journal-title":"Phys Chem Chem Phys"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000313","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,10,3]],"date-time":"2021-10-03T05:02:49Z","timestamp":1633237369000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000313"}},"subtitle":[],"editor":[{"given":"James M.","family":"Briggs","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2009,3,13]]},"references-count":28,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2009,3,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000313","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,3,13]]}}}