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. 2012 Apr 24;51(16):3508-22.
doi: 10.1021/bi3002709. Epub 2012 Apr 10.

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

Jonathan L Chen  1 , Abigael L Dishler, Scott D Kennedy, Ilyas Yildirim, Biao Liu, Douglas H Turner, Martin J Serra
Affiliations
Free PMC article

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

Jonathan L Chen et al. Biochemistry. .
Free PMC article

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 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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Figures

Figure 1
Figure 1
1D 1H imino spectra of r(CCGAAUUUGG)2 from 0 to 45 °C.
Figure 2
Figure 2
1D imino NMR spectra for some RNA duplexes with GU pairs. Spectra were acquired at 0 °C for r(AGGCUU)2 and r(AUGCGU)2; 1 °C for r(AGUCGAUU)2; 5 °C for others.
See this image and copyright information in PMC

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