Stability of RNA hairpins closed by wobble base pairs
Stability of RNA hairpins closed by wobble base pairs
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DOI：
10.1021/bi972050v
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发表时间：
1998-01-27
期刊：
影响因子：
2.9
通讯作者：
Serra, MJ
中科院分区：
文献类型：
--
作者：
Giese, MR;Betschart, K;Serra, MJ
报道了GGXAN（m）AVCC型RNA序列在1 M NaCl中形成发夹的热力学参数，其中XY是摆动碱基对，GU或UG，下划线的环序列是3 - 8个核苷酸。最近邻分析表明环形成的自由能取决于环的大小和闭合碱基对。由UC碱基对闭合的发夹环平均比由GU碱基对闭合的发夹稳定性低1.3 kcal/mol。由UG闭合的发夹环具有与由Au/UA碱基对闭合的发夹环大致相同的稳定性，而由GU闭合的发夹环比由GC/CG碱基对闭合的发夹环稳定约0.7 kcal/mol。这些结果与先前开发的模型[Serra等人（1997）Biochemistry 36，4844]相结合以预测由Watson-Crick碱基对闭合的发夹环的稳定性，允许以下模型预测发夹环的稳定性：Δ G度（37 L）（n）= Δ G度（37 L）（n）+ Δ G度（37 mm）+0.6（如果由Au、UA或UB关闭）-0.7（如果由GU闭合- 0.7（如果第一失配是GA或UU，除了由GU闭合的环），这里，Δ G度（37 μ L（n））是起始具有CC或GC对的rt核苷酸的环的自由能增量，并且Δ G度（37 μ L）是第一错配与闭合碱基对相互作用的自由能。Δ G度（37 μ L）（n）分别为4.9、5.0、5.0、5.0、4.9和5.5 kcal/mol。对于n = 3的发夹环，Δ G（37 μ L）（0）（3）= +4.8 +0.6（如果被Au：VA或UG封闭）kcal/mol。热力学参数发夹形成在1 M NaCl的13个自然发生的RNA发夹序列关闭摆动碱基对的报告。该模型为研究的大多数发夹结构提供了良好的T-M和Δ G度（37）一致性。热力学值为五个终端错配相邻摆动碱基对也报道。
Thermodynamic parameters are reported for hairpin formation ill 1 M NaCl by RNA sequences of the type GGXAN(m)AVCC, where XY is the wobble base pair, GU or UG, and the underlined loop sequences are three to eight nucleotides, A nearest-neighbor analysis indicates the free energy of loop formation is dependent upon loop size and closing base pair. Hairpin loops closed by UC base pairs are on average 1.3 kcal/mol less stable than hairpins closed by GU base pairs. The hairpin loops closed by UG have approximately the same stability as hairpin loops closed by AU/UA base pairs, while the loops closed by GU are approximately 0.7 kcal/mol more stable than hairpins loops closed by GC/CG base pairs. These results, combined with the model previously developed [Serra et al. (1997) Biochemistry 36, 4844] to predict the stability for hairpin loops closed by Watson-Crick base pairs, allow for the following model to predict the stability of hairpin loops: Delta G degrees(37L)(n) = Delta G degrees(37iL)(n) + Delta G degrees(37mm) + 0.6 (if closed by AU, UA, or UB) -0.7 (if closed by GU - 0.7 (if first mismatch is GA or UU except for loops closed by GU), Here, Delta G degrees 37iL(n) is the free energy increment for initiating a loop of rt nucleotides with a CC or GC pair, and Delta G degrees(37mm) is the free energy for the interaction of the first mismatch with the closing base pair, Fur hairpin]oops of n = 4-9, Delta G degrees(37iL)(n) is 4.9, 5.0, 5.0, 5.0, 4.9, and 5.5 kcal/mol, respectively. For hairpin loops of n = 3, Delta G(37iL)(0)(3) = +4.8 + 0.6 (if closed by AU: VA, or UG) kcal/mol. Thermodynamic parameters for hairpin formation in 1 M NaCl for 13 naturally occurring RNA hairpin sequences closed by wobble base pairs are reported. The model provides good agreement fnr both T-M and Delta G degrees(37) for most hairpins studied. Thermodynamic values for five terminal mismatches adjacent to wobble base pairs are also reported.