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Testing the nearest neighbor model for canonical RNA base pairs: revision of GU parameters.

ABSTRACT: 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 ?G°(37) for the 5'GG/3'UU motif from an unfavorable 0.5 kcal/mol to a favorable -0.2 kcal/mol. Similarly, the ?G°(37) for the 5'UG/3'GU motif changes from 0.3 to -0.6 kcal/mol. The correlation coefficients between predicted and experimental ?G°(37), ?H°, and ?S° for the expanded database are 0.95, 0.89, and 0.87, respectively. The results should improve predictions of RNA secondary structure.

SUBMITTER: Chen JL

PROVIDER: S-EPMC3335265 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature

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Testing the nearest neighbor model for canonical RNA base pairs: revision of GU parameters.

Chen Jonathan L JL Dishler Abigael L AL Kennedy Scott D SD Yildirim Ilyas I Liu Biao B Turner Douglas H DH Serra Martin J MJ

Biochemistry 20120410 16

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 databas ...[more]

PMID: 22490167

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