Walter A E, Turner D H, Kim J, Lyttle M H, Müller P, Mathews D H, Zuker M
Department of Chemistry, University of Rochester, NY 14627-0216.
Proc Natl Acad Sci U S A. 1994 Sep 27;91(20):9218-22. doi: 10.1073/pnas.91.20.9218.
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 [formula: see text] additional free energy change, delta delta G 37 degrees, for binding is roughly the nearest-neighbor delta G 37 degrees for propagation of an uninterrupted helix of equivalent sequence, CGGC. When X and Z are omitted, the delta delta 37 degrees is even more favorable by approximately 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.
一个由与发夹茎5'端4个核苷酸突出端结合的寡聚物组成的RNA模型系统，提供了螺旋 - 螺旋界面的热力学参数。寡聚物以序列依赖的方式，在37℃下与发夹茎相邻结合时的紧密程度比预测与游离四聚体结合的紧密程度高1000倍。对于[公式：见正文]中的界面（/），结合的额外自由能变化，即ΔΔG 37℃，大致相当于等序列CGGC的不间断螺旋延伸的最近邻ΔG 37℃。当省略X和Z时，ΔΔ37℃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贡献，11个RNA二级结构预测的准确率从67%提高到了74%。
