| Testing the nearest neighbor model for canonical RNA base pairs: revision of GU parameters. | |
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MedLine Citation:
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PMID: 22490167 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Thermodynamic parameters for GU pairs are important for predicting the secondary structures of RNA and for finding genomic sequences that code for structured RNA. Optical melting curves were measured for 29 RNA duplexes with GU pairs to improve nearest neighbor parameters for predicting stabilities of helixes. The updated model eliminates a prior penalty assumed for terminal GU pairs. Six additional duplexes with the 5'GG/3'UU motif were added to the single representation in the previous database. This revises the ΔG°(37) for the 5'GG/3'UU motif from an unfavorable 0.5 kcal/mol to a favorable -0.2 kcal/mol. Similarly, the ΔG°(37) for the 5'UG/3'GU motif changes from 0.3 to -0.6 kcal/mol. The correlation coefficients between predicted and experimental ΔG°(37), ΔH°, and ΔS° for the expanded database are 0.95, 0.89, and 0.87, respectively. The results should improve predictions of RNA secondary structure. |
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Authors:
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Jonathan L Chen; Abigael L Dishler; Scott D Kennedy; Ilyas Yildirim; Biao Liu; Douglas H Turner; Martin J Serra |
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Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Extramural Date: 2012-04-10 |
Journal Detail:
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Title: Biochemistry Volume: 51 ISSN: 1520-4995 ISO Abbreviation: Biochemistry Publication Date: 2012 Apr |
Date Detail:
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Created Date: 2013-02-07 Completed Date: 2013-04-03 Revised Date: 2013-05-20 |
Medline Journal Info:
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Nlm Unique ID: 0370623 Medline TA: Biochemistry Country: United States |
Other Details:
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Languages: eng Pagination: 3508-22 Citation Subset: IM |
Affiliation:
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Department of Chemistry, University of Rochester, Rochester, NY 14627, USA. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Base Pairing* Base Sequence Molecular Sequence Data Nucleic Acid Conformation RNA / chemistry* Thermodynamics |
| Grant Support | |
ID/Acronym/Agency:
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GM22939/GM/NIGMS NIH HHS |
| Chemical | |
Reg. No./Substance:
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63231-63-0/RNA |
| Comments/Corrections | |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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