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NMR Structure of an 8x8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to 3D Predictions

机译:核磁共振结构的两侧各有三个沃森-克里克对的8x8核苷酸RNA内部环和与3D预测的比较

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摘要

The prediction of RNA 3D structure from sequence alone is a long-standing goal. High resolution, experimentally determined structures of simple noncanonical pairings and motifs are critical to the development of prediction programs. Here, we present the NMR structure of the duplex, (5′CCAGAAACGGAUGGA)2, which contains an 8x8 nucleotide internal loop flanked by three Watson-Crick pairs on each side. The loop is comprised of a central 5′AC/3′CA nearest neighbor flanked by two 3RRs motifs, a known stable motif consisting of three consecutive sheared GA pairs. Hydrogen bonding patterns between base pairs in the loop, all-atom RMSD for the loop, and deformation index were used to compare the structure to automated predictions by MC-sym, RNA FARFAR, and RNAComposer.
机译:长期仅靠序列预测RNA 3D结构是一个长期的目标。高分辨率,实验确定的简单非典型配对和图案的结构对于预测程序的开发至关重要。在这里,我们介绍了双链体(5'CCAGAAACGGAUGGA)2的NMR结构,该结构包含一个8x8核苷酸的内部环,两侧各有3个Watson-Crick对。该环由中央的5'AC / 3'CA最近邻组成,两侧有两个3RRs基序,这是一个已知的稳定基序,由三个连续的剪切GA对组成。环中碱基对之间的氢键模式,环中的全原子RMSD和变形指数用于比较结构与MC-sym,RNA FARFAR和RNAComposer的自动预测。

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