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溶液中DNA发夹的三维结构：对d(CGCGTTTTCGCG)的二维核磁共振研究和距离几何计算

Three-dimensional structure of a DNA hairpin in solution: two-dimensional NMR studies and distance geometry calculations on d(CGCGTTTTCGCG).

作者信息

Hare D R, Reid B R

出版信息

Biochemistry. 1986 Sep 9;25(18):5341-50. doi: 10.1021/bi00366a053.

DOI:10.1021/bi00366a053
PMID:3768352
Abstract

The three-dimensional structure of d(CGCGTTTTCGCG) in solution has been determined from proton NMR data by using distance geometry methods. The rate of dipolar cross-relaxation between protons close together in space is used to calculate distances between proton pairs within 5 A of each other; these distances are used as input to a distance geometry algorithm that embeds this distance matrix in three-dimensional space. The resulting refined structures that best agree with the input distances are all very similar to each other and show that the DNA sequence forms a hairpin in solution; the bases of the loop region are stacked, and the stem region forms a right-handed helix. The advantages and limitations of the technique, as well as the computer requirements of the algorithm, are discussed.

摘要

通过使用距离几何方法，根据质子核磁共振数据确定了溶液中d(CGCGTTTTCGCG)的三维结构。利用空间中彼此靠近的质子之间的偶极交叉弛豫速率来计算相互距离在5埃以内的质子对之间的距离；这些距离被用作距离几何算法的输入，该算法将此距离矩阵嵌入三维空间。与输入距离最相符的最终优化结构彼此非常相似，表明该DNA序列在溶液中形成发夹结构；环区的碱基堆积在一起，茎区形成右手螺旋。文中讨论了该技术的优缺点以及算法对计算机的要求。

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