Thermodynamic Characterization of RNA Duplexes Containing Naturally Occurring 1 × 2 Nucleotide Internal Loops

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• 作者：Jaya Badhwar ; Saradasri Karri ; Cody K. Cass ; Erica L. Wunderlich ; Brent M. Znosko
• 刊名：Biochemistry
• 出版年：2007
• 出版时间：December 18, 2007
• 年：2007
• 卷：46
• 期：50
• 页码：14715 - 14724
• 全文大小：67K
• 年卷期：v.46,no.50(December 18, 2007)
• ISSN：1520-4995

文摘

Thermodynamic data for RNA 1 × 2 nucleotide internal loops are lacking. Thermodynamicdata that are available for 1 × 2 loops, however, are for loops that rarely occur in nature. In order toidentify the most frequently occurring 1 × 2 nucleotide internal loops, a database of 955 RNA secondarystructures was compiled and searched. Twenty-four RNA duplexes containing the most common 1 × 2nucleotide loops were optically melted, and the thermodynamic parameters H, S, G₃₇, and T_M foreach duplex were determined. This data set more than doubles the number of 1 × 2 nucleotide loopspreviously studied. A table of experimental free energy contributions for frequently occurring 1 × 2nucleotide loops (as opposed to a predictive model) is likely to result in better prediction of RNA secondarystructure from sequence. In order to improve free energy calculations for duplexes containing 1 × 2nucleotide loops that do not have experimental free energy contributions, the data collected here werecombined with data from 21 previously studied 1 × 2 loops. Using linear regression, the entire datasetwas used to derive nearest neighbor parameters that can be used to predict the thermodynamics of previouslyunmeasured 1 × 2 nucleotide loops. The G_37,loop and H_loop nearest neighbor parameters derived herewere compared to values that were published previously for 1 × 2 nucleotide loops but were derivedfrom either a significantly smaller dataset of 1 × 2 nucleotide loops or from internal loops of varioussizes [Lu, Z. J., Turner, D. H., and Mathews, D. H. (2006) Nucleic Acids Res. 34, 4912-4924]. Most ofthese values were found to be within experimental error, suggesting that previous approximations andassumptions associated with the derivation of those nearest neighbor parameters were valid. S_loop nearestneighbor parameters are also reported for 1 × 2 nucleotide loops. Both the experimental thermodynamicsand the nearest neighbor parameters reported here can be used to improve secondary structure predictionfrom sequence.