未配对碱基对三臂DNA接头构象和稳定性的影响。

Effects of unpaired bases on the conformation and stability of three-arm DNA junctions.

作者信息

Zhong M, Rashes M S, Leontis N B, Kallenbach N R

机构信息

Department of Chemistry, New York University, New York 10003.

出版信息

Biochemistry. 1994 Mar 29;33(12):3660-7. doi: 10.1021/bi00178a024.

DOI:10.1021/bi00178a024

PMID:8142364

Abstract

Three-arm DNA junctions, in which three double helices intersect at a branch, have unique structure and reactivity of bases at and near the branch. Their solution conformation is asymmetric in the presence of Mg2+, while bases at the branch are sensitive to single-strand-specific agents. Following the surprising report that unpaired bases at the branch stabilize three-arm junctions, we have investigated the geometry and thermodynamics of three-arm junctions containing pendant T and A bases. The results are consistent with additional structure formation in junctions containing up to four pendant bases at the branch: relative to the tight junction, the thermal stability of junctions with two T's or A's at the branch increases; bases near the branch become less reactive to single-strand-reactive probes; and the enthalpy of formation is more negative. The interaction of ethidium observed at the branch in three-arm junctions is enhanced in junctions with unpaired bases at the branch. The geometry of three-arm junctions is perturbed by the presence of pendant bases, as seen by measuring the electrophoretic mobility of junctions to which long duplex arms are appended pairwise.

摘要

三链 DNA 连接体是由三条双螺旋在一个分支点处相交形成的，其在分支点及附近具有独特的碱基结构和反应活性。在镁离子存在的情况下，它们在溶液中的构象是不对称的，而分支点处的碱基对单链特异性试剂敏感。在有关于分支点处未配对碱基可稳定三链连接体的惊人报道之后，我们研究了含有悬垂 T 和 A 碱基的三链连接体的几何结构和热力学性质。结果表明，在分支点处含有多达四个悬垂碱基的连接体中会形成额外的结构：相对于紧密连接体，分支点处有两个 T 或 A 的连接体的热稳定性增加；分支点附近的碱基对单链反应性探针的反应性降低；并且形成焓更负。在三链连接体分支点处观察到的溴化乙锭相互作用在分支点处有未配对碱基的连接体中增强。通过测量两两连接有长双链臂的连接体的电泳迁移率可以看出，悬垂碱基的存在会扰乱三链连接体的几何结构。