Document Detail


Testing the nearest neighbor model for canonical RNA base pairs: revision of GU parameters.
MedLine Citation:
PMID:  22490167     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
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:
Type:  Journal Article; Research Support, N.I.H., Extramural     Date:  2012-04-10
Journal Detail:
Title:  Biochemistry     Volume:  51     ISSN:  1520-4995     ISO Abbreviation:  Biochemistry     Publication Date:  2012 Apr 
Date Detail:
Created Date:  2013-02-07     Completed Date:  2013-04-03     Revised Date:  2013-07-18    
Medline Journal Info:
Nlm Unique ID:  0370623     Medline TA:  Biochemistry     Country:  United States    
Other Details:
Languages:  eng     Pagination:  3508-22     Citation Subset:  IM    
Affiliation:
Department of Chemistry, University of Rochester, Rochester, NY 14627, USA.
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MeSH Terms
Descriptor/Qualifier:
Base Pairing*
Base Sequence
Molecular Sequence Data
Nucleic Acid Conformation
RNA / chemistry*
Thermodynamics
Grant Support
ID/Acronym/Agency:
GM22939/GM/NIGMS NIH HHS; R01 GM022939/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
63231-63-0/RNA
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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