Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters

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• 作者：Jonathan L. Chen ; Abigael L. Dishler ; Scott D. Kennedy ; Ilyas Yildirim ; Biao Liu ; Douglas H. Turner ; Martin J. Serra
• 刊名：Biochemistry
• 出版年：2012
• 出版时间：April 24, 2012
• 年：2012
• 卷：51
• 期：16
• 页码：3508-3522
• 全文大小：509K
• 年卷期：v.51,no.16(April 24, 2012)
• ISSN：1520-4995

文摘

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鈥睪G/3鈥睻U motif were added to the single representation in the previous database. This revises the 螖G掳₃₇ for the 5鈥睪G/3鈥睻U motif from an unfavorable 0.5 kcal/mol to a favorable 鈭?.2 kcal/mol. Similarly, the 螖G掳₃₇ for the 5鈥睻G/3鈥睪U motif changes from 0.3 to 鈭?.6 kcal/mol. The correlation coefficients between predicted and experimental 螖G掳₃₇, 螖H掳, and 螖S掳 for the expanded database are 0.95, 0.89, and 0.87, respectively. The results should improve predictions of RNA secondary structure.