Kim J, Walter A E, Turner D H
Department of Chemistry, University of Rochester, New York 14627-0216, USA.
Biochemistry. 1996 Oct 29;35(43):13753-61. doi: 10.1021/bi960913z.
The thermodynamics of RNA helix-helix interfaces with intervening single- and tandem-GA or single-CC mismatches were studied by UV melting experiments. The model system consists of a hairpin with a four- or five-nucleotide 5' overhang which is bound by a short oligomer, creating the helical interface. Single GA interfaces are found to have favorable free energy increments of about 2 kcal/mol. This is similar to those reported for coaxially stacked flush interfaces of AU base pairs [Walter A. E., & Turner, D. H. (1994) Biochemistry 33, 12715-12719]. The free energy increment of the GA mismatches depends little on the sequence of the closing base pairs of the helixes, whether the break in the phosphate backbone is 5' or 3' with respect to the mismatch or whether the chains are extended beyond the helix-helix interface. Surprisingly, interfaces with single-CC mismatches have favorable free energy increments similar to those of GA interfaces, even though CC mismatches in coaxial stacks occur much less frequently in known RNA secondary structures. The results provide experimental support for the assumption that a bonus free energy is required for coaxially stacked helixes with intervening GA mismatches when free energy minimization is used to predict RNA secondary structures.
通过紫外熔解实验研究了具有中间单GA或串联GA错配以及单CC错配的RNA螺旋-螺旋界面的热力学。模型系统由一个带有四或五个核苷酸5'突出端的发夹组成，该发夹由一个短寡聚物结合，形成螺旋界面。发现单GA界面具有约2千卡/摩尔的有利自由能增量。这与报道的AU碱基对同轴堆积平齐界面的自由能增量相似[Walter A. E., & Turner, D. H. (1994) Biochemistry 33, 12715 - 12719]。GA错配的自由能增量几乎不依赖于螺旋封闭碱基对的序列、磷酸主链相对于错配是5'还是3'断裂，也不依赖于链是否延伸到螺旋-螺旋界面之外。令人惊讶的是，具有单CC错配的界面具有与GA界面相似的有利自由能增量，尽管在已知RNA二级结构中同轴堆积中的CC错配出现频率要低得多。这些结果为以下假设提供了实验支持：当使用自由能最小化来预测RNA二级结构时，具有中间GA错配的同轴堆积螺旋需要额外的自由能。
