{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,24]],"date-time":"2025-10-24T20:51:28Z","timestamp":1761339088463},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: There are many important proteins which bind single-stranded nucleic acids, such as the nucleocapsid protein in HIV and the RecA DNA repair protein in bacteria. The presence of such proteins can strongly alter the secondary structure of the nucleic acid molecules. Therefore, accurate modeling of the interaction between single-stranded nucleic acids and such proteins is essential to fully understand many biological processes.<\/jats:p>\n               <jats:p>Results: We develop a model for predicting nucleic acid secondary structure in the presence of single-stranded binding proteins, and implement it as an extension of the Vienna RNA Package. All parameters needed to model nucleic acid secondary structures in the absence of proteins have been previously determined. This leaves the footprint and sequence-dependent binding affinity of the protein as adjustable parameters of our model. Using this model we are able to predict the probability of the protein binding at any position in the nucleic acid sequence, the impact of the protein on nucleic acid base pairing, the end-to-end distance distribution for the nucleic acid and FRET distributions for fluorophores attached to the nucleic acid.<\/jats:p>\n               <jats:p>Availability: Source code for our modified version of the Vienna RNA package is freely available at http:\/\/bioserv.mps.ohio-state.edu\/Vienna+P, implemented in C and running on Linux.<\/jats:p>\n               <jats:p>Contact: \u00a0bundschuh@mps.ohio-state.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp627","type":"journal-article","created":{"date-parts":[[2009,11,5]],"date-time":"2009-11-05T02:18:51Z","timestamp":1257387531000},"page":"61-67","source":"Crossref","is-referenced-by-count":21,"title":["Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure"],"prefix":"10.1093","volume":"26","author":[{"given":"Robert A.","family":"Forties","sequence":"first","affiliation":[{"name":"1 Department of Physics, 2 Center for RNA Biology and 3 Department of Biochemistry, The Ohio State University, Columbus, OH, USA"}]},{"given":"Ralf","family":"Bundschuh","sequence":"additional","affiliation":[{"name":"1 Department of Physics, 2 Center for RNA Biology and 3 Department of Biochemistry, The Ohio State University, Columbus, OH, USA"},{"name":"1 Department of Physics, 2 Center for RNA Biology and 3 Department of Biochemistry, The Ohio State University, Columbus, OH, USA"},{"name":"1 Department of Physics, 2 Center for RNA Biology and 3 Department of Biochemistry, The Ohio State University, Columbus, OH, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,11,4]]},"reference":[{"key":"2023012507524049900_B1","doi-asserted-by":"crossref","DOI":"10.1201\/9780203833445","volume-title":"Molecular Biology of the Cell","author":"Alberts","year":"2007","edition":"5th"},{"key":"2023012507524049900_B2","doi-asserted-by":"crossref","first-page":"2759","DOI":"10.1529\/biophysj.104.043083","article-title":"Secondary structure and secondary structure dynamics of DNA hairpins complexed with HIV-1 NC protein","volume":"87","author":"Cosa","year":"2004","journal-title":"Biophys. J."},{"key":"2023012507524049900_B3","doi-asserted-by":"crossref","first-page":"2296","DOI":"10.1126\/science.298.5602.2296","article-title":"Breakthrough of the year: small RNAs make big splash","volume":"298","author":"Couzin","year":"2002","journal-title":"Science"},{"key":"2023012507524049900_B4","volume-title":"GNU Scientific Library Reference Manual.","author":"Galassi","year":"2009","edition":"3rd"},{"key":"2023012507524049900_B5","doi-asserted-by":"crossref","first-page":"1324","DOI":"10.1016\/S0006-3495(01)75789-X","article-title":"Force-induced denaturation of RNA","volume":"85","author":"Gerland","year":"2001","journal-title":"Biophys. J."},{"key":"2023012507524049900_B6","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1126\/science.279.5349.384","article-title":"Structure of the HIV-1 nucleocapsid protein bound to the SL3-RNA recognition element","volume":"279","author":"Guzman","year":"1998","journal-title":"Science"},{"key":"2023012507524049900_B7","doi-asserted-by":"crossref","first-page":"6264","DOI":"10.1073\/pnas.93.13.6264","article-title":"Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor","volume":"93","author":"Ha","year":"1996","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012507524049900_B8","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1038\/nature01083","article-title":"Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase","volume":"419","author":"Ha","year":"2002","journal-title":"Nature"},{"key":"2023012507524049900_B9","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1007\/BF00818163","article-title":"Fast folding and comparison of RNA secondary structures","volume":"125","author":"Hofacker","year":"1994","journal-title":"Monatsh. Chem."},{"key":"2023012507524049900_B10","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1002\/recl.19490681203","article-title":"R\u00f6ntgenuntersuchung gel\u00f6ster Fadenmolek\u00fcle","volume":"68","author":"Kratky","year":"1949","journal-title":"Racl. Trav. Chim."},{"key":"2023012507524049900_B11","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1006\/jmbi.1999.2700","article-title":"Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure","volume":"288","author":"Mathews","year":"1999","journal-title":"J. Mol. Biol."},{"key":"2023012507524049900_B12","doi-asserted-by":"crossref","first-page":"7287","DOI":"10.1073\/pnas.0401799101","article-title":"Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure","volume":"101","author":"Mathews","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012507524049900_B13","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1002\/bip.360290621","article-title":"The equilibrium partition-function and base pair binding probabilities for RNA secondary structure","volume":"29","author":"McCaskill","year":"1990","journal-title":"Biopolymers"},{"key":"2023012507524049900_B14","doi-asserted-by":"crossref","first-page":"2530","DOI":"10.1016\/S0006-3495(04)74308-8","article-title":"Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy","volume":"86","author":"Murphy","year":"2004","journal-title":"Biophys. J."},{"key":"2023012507524049900_B15","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1021\/ma60045a006","article-title":"Configurational statistics of polynucleotide chains - single virtual bond treatment","volume":"8","author":"Olson","year":"1975","journal-title":"Macromolecules"},{"key":"2023012507524049900_B16","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4612-5190-3","volume-title":"Principles of Nucleic Acid Structure","author":"Saenger","year":"1984"},{"key":"2023012507524049900_B17","volume-title":"An Introduction to Thermal Physics.","author":"Schroeder","year":"2000"},{"key":"2023012507524049900_B18","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1038\/355318a0","article-title":"The structure of the E. coli recA protein monomer and polymer","volume":"355","author":"Story","year":"1992","journal-title":"Nature"},{"key":"2023012507524049900_B19","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/j.bbrc.2008.05.191","article-title":"Dynamics of an anti-VEGF DNA aptamer: a single-molecule study","volume":"373","author":"Taylor","year":"2008","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"2023012507524049900_B20","article-title":"Statistical mechanics of semiflexible chains","volume-title":"Theoretical and Mathematical Models in Polymer Research.","author":"Thirumalai","year":"1998"},{"key":"2023012507524049900_B21","doi-asserted-by":"crossref","first-page":"14719","DOI":"10.1021\/bi9809425","article-title":"Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs","volume":"37","author":"Xia","year":"1998","journal-title":"Biochemistry"},{"key":"2023012507524049900_B22","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1093\/nar\/9.1.133","article-title":"Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information","volume":"9","author":"Zuker","year":"1981","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/1\/61\/48851040\/bioinformatics_26_1_61.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/1\/61\/48851040\/bioinformatics_26_1_61.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:52:57Z","timestamp":1674633177000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/1\/61\/183122"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,11,4]]},"references-count":22,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp627","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,1,1]]},"published":{"date-parts":[[2009,11,4]]}}}