COAXIAL STACKING OF HELIXES ENHANCES BINDING OF OLIGORIBONUCLEOTIDES AND IMPROVES PREDICTIONS OF RNA FOLDING
COAXIAL STACKING OF HELIXES ENHANCES BINDING OF OLIGORIBONUCLEOTIDES AND IMPROVES PREDICTIONS OF RNA FOLDING
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DOI：
10.1073/pnas.91.20.9218
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发表时间：
1994-09-27
影响因子：
11.1
通讯作者：
ZUKER, M
中科院分区：
文献类型：
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作者：
WALTER, AE;TURNER, DH;ZUKER, M
一个由与发夹茎5'端的4个核苷酸突出端结合的寡聚体组成的RNA模型系统，为螺旋 - 螺旋界面提供了热力学参数。以序列依赖的方式，在37℃时，寡聚体在发夹茎附近的结合比预测的与游离四聚体的结合紧密多达1000倍。对于[图形]中的界面（/），其中X和Z是未配对的核苷酸，结合的额外自由能变化ΔΔG°(37)大致是等效序列不间断螺旋延伸的最近邻ΔG°(37)，[图形]当X和Z缺失时，ΔΔG°(37)甚至更有利，约为1千卡/摩尔（1卡 = 4.184焦耳）。平均而言，通过纳入类似的堆积作用，11个RNA二级结构的预测准确率从67%提高到74%。
An RNA model system consisting of an oligomer binding to a 4-nt overhang at the 5' end of a hairpin stem provides thermodynamic parameters for helix-helix interfaces. In a sequence-dependent manner, oligomers bind up to 1000-fold more tightly adjacent to the hairpin stem than predicted for binding to a free tetramer at 37 degrees C. For the interface (/) in[GRAPHICS]where X and Z are unpaired nucleotides, the additional free energy change, Delta Delta G degrees(37), for binding is roughly the nearest-neighbor Delta G degrees(37), for propagation of an uninterrupted helix of equivalent sequence,[GRAPHICS]When X and Z are omitted, the Delta Delta G degrees(37), is even more favorable by approximate to 1 kcal/mol (1 cal = 4.184j). On average, predictions of 11 RNA secondary structures improve from 67 to 74% accuracy by inclusion of similar stacking contributions.