uni-leipzig-open-access/json/2023.04.07.536000

{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2023,4,12]],"date-time":"2023-04-12T04:02:23Z","timestamp":1681272143444},"posted":{"date-parts":[[2023,4,8]]},"group-title":"Bioinformatics","reference-count":32,"publisher":"Cold Spring Harbor Laboratory","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,4,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>RNA features a highly negatively charged phosphate backbone that attracts a of cloud counter-ions that reduce the electrostatic repulsion in a concentration dependent manner. Ion concentrations thus have a large influence on folding and stability of RNA structures. Despite their well-documented effects, salt effects are not handled by currently available secondary stucture prediction algorithms. Combining Debye-H\u00fcckel potentials for line charges and Manning\u2019s counter-ion condensation theory, Einert<jats:italic>et al<\/jats:italic>. [<jats:italic>Biophys. J<\/jats:italic>.<jats:bold>100<\/jats:bold>: 2745-2753 (2011)] modeled the energetic effects contributions monovalent cations on loops and helices.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The model of Einert<jats:italic>et al<\/jats:italic>. is adapted to match the structure of the dynamic programming recursion of RNA secondary structure prediction algorithms. An empirical term describing the dependence salt dependence of the duplex initiation energy is added to improve co-folding predictions for two or more RNA strands. The slightly modified model is implemented in the<jats:monospace>ViennaRNA<\/jats:monospace>package in such way that only the energy parameters but not the algorithmic structure is affected. A comparison with data from the literature show that predicted free energies and melting temperatures are in reasonable agreement with experiments.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The new feature in the<jats:monospace>ViennaRNA<\/jats:monospace>package makes it possible to study effects of salt concentrations on RNA folding in a systematic manner. Strictly speaking, the model pertains only to mono-valent cations, and thus covers the most important parameter, i.e., the NaCl concentration. It remains a question for future research to what extent unspecific effects of bi- and tri-valent cations can be approximated in a similar manner.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability<\/jats:title><jats:p>Corrections for the concentration of monovalent cations are available in the<jats:monospace>ViennaRNA<\/jats:monospace>package starting from version 2.6.0.<\/jats:p><\/jats:sec>","DOI":"10.1101\/2023.04.07.536000","type":"posted-content","created":{"date-parts":[[2023,4,9]],"date-time":"2023-04-09T04:45:12Z","timestamp":1681015512000},"source":"Crossref","is-referenced-by-count":0,"title":["Salt corrections for RNA secondary structures in the ViennaRNA package"],"prefix":"10.1101","author":[{"ORCID":"http:\/\/orcid.org\/0000-0002-1720-5737","authenticated-orcid":false,"given":"Hua-Ting","family":"Yao","sequence":"first","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-2144-698X","authenticated-orcid":false,"given":"Ronny","family":"Lorenz","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0001-7132-0800","authenticated-orcid":false,"given":"Ivo L.","family":"Hofacker","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-5016-5191","authenticated-orcid":false,"given":"Peter F.","family":"Stadler","sequence":"additional","affiliation":[]}],"member":"246","reference":[{"key":"2023041115500417000_2023.04.07.536000v1.1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-biochem-060409-092720"},{"key":"2023041115500417000_2023.04.07.536000v1.2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.biophys.26.1.113"},{"key":"2023041115500417000_2023.04.07.536000v1.3","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkp892"},{"key":"2023041115500417000_2023.04.07.536000v1.4","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl472"},{"key":"2023041115500417000_2023.04.07.536000v1.5","doi-asserted-by":"publisher","DOI":"10.1261\/rna.5205404"},{"key":"2023041115500417000_2023.04.07.536000v1.6","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.108.131813"},{"key":"2023041115500417000_2023.04.07.536000v1.7","doi-asserted-by":"publisher","DOI":"10.1021\/bi4008275"},{"key":"2023041115500417000_2023.04.07.536000v1.8","doi-asserted-by":"publisher","DOI":"10.1038\/14940"},{"key":"2023041115500417000_2023.04.07.536000v1.9","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1999.3334"},{"key":"2023041115500417000_2023.04.07.536000v1.10","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2002.5422"},{"key":"2023041115500417000_2023.04.07.536000v1.11","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/9.1.133"},{"key":"2023041115500417000_2023.04.07.536000v1.12","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2011.04.038"},{"key":"2023041115500417000_2023.04.07.536000v1.13","first-page":"185","article-title":"Peter und H\u00fcckel: Zur Theorie der Elektrolyte","volume":"24","year":"1923","journal-title":"Physik. Z"},{"key":"2023041115500417000_2023.04.07.536000v1.14","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevE.53.6297"},{"key":"2023041115500417000_2023.04.07.536000v1.15","doi-asserted-by":"publisher","DOI":"10.1063\/1.1672157"},{"key":"2023041115500417000_2023.04.07.536000v1.16","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevE.66.011918"},{"key":"2023041115500417000_2023.04.07.536000v1.17","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0606409103"},{"key":"2023041115500417000_2023.04.07.536000v1.18","doi-asserted-by":"publisher","DOI":"10.1186\/1748-7188-6-26"},{"key":"2023041115500417000_2023.04.07.536000v1.19","doi-asserted-by":"publisher","DOI":"10.1063\/1.1747547"},{"key":"2023041115500417000_2023.04.07.536000v1.20","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx512"},{"key":"2023041115500417000_2023.04.07.536000v1.21","doi-asserted-by":"publisher","DOI":"10.1186\/s13660-017-1317-z"},{"key":"2023041115500417000_2023.04.07.536000v1.22","unstructured":"Moshier, S.L. : Methods and Programs for Mathematical Functions. Prentice-Hall, Hoboken, NJ (1989)"},{"key":"2023041115500417000_2023.04.07.536000v1.23","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1016\/S0009-2614(02)01735-9","article-title":"Temperature dependence of the permittivity of water","volume":"367","year":"2003","journal-title":"Chem Phys Letters"},{"key":"2023041115500417000_2023.04.07.536000v1.24","doi-asserted-by":"publisher","DOI":"10.1016\/j.chemphys.2019.01.016"},{"key":"2023041115500417000_2023.04.07.536000v1.25","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl1073"},{"key":"2023041115500417000_2023.04.07.536000v1.26","doi-asserted-by":"publisher","DOI":"10.1021\/bi961654g"},{"key":"2023041115500417000_2023.04.07.536000v1.27","doi-asserted-by":"publisher","DOI":"10.1021\/bi9809425"},{"key":"2023041115500417000_2023.04.07.536000v1.28","doi-asserted-by":"publisher","DOI":"10.1186\/1748-7188-1-3"},{"key":"2023041115500417000_2023.04.07.536000v1.29","unstructured":"Lorenz, R. , Flamm, C. , Hofacker, I.L. , Stadler, P.F. : Efficient algorithms for co-folding of multiple RNAs. In: Ye, X. , Soares, F. , De Maria, E. , G\u00f3mez Vilda, P. , Cabitza, F. , Fred, A. , Gamboa, H. (eds.) Biomedical Engineering Systems and Technologies. BIOSTEC 2020. Comm. Comp. Inf. Sci., vol. 1400, pp. 10\u20131007978303072379810. Springer, Cham"},{"key":"2023041115500417000_2023.04.07.536000v1.30","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1911632116"},{"key":"2023041115500417000_2023.04.07.536000v1.31","doi-asserted-by":"publisher","DOI":"10.3389\/fchem.2016.00038"},{"key":"2023041115500417000_2023.04.07.536000v1.32","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2013.7"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2023.04.07.536000","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,11]],"date-time":"2023-04-11T22:50:16Z","timestamp":1681253416000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2023.04.07.536000"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,4,8]]},"references-count":32,"URL":"http:\/\/dx.doi.org\/10.1101\/2023.04.07.536000","relation":{},"published":{"date-parts":[[2023,4,8]]},"subtype":"preprint"}}