Shimizu M, Hanvey J C, Wells R D
Department of Biochemistry, School of Medicine, University of Alabama, Birmingham 35294.
Biochemistry. 1990 May 15;29(19):4704-13. doi: 10.1021/bi00471a027.
A polypurine.polypyrimidine (Pur.Pyr) sequence with a central interruption in a plasmid can adopt multiple non-B-DNA conformations depending on the conditions as revealed by specific chemical probes (OsO4, diethyl pyrocarbonate, and dimethyl sulfate) and two-dimensional electrophoresis. The relatively long mirror repeat Pur.Pyr sequences (GAA)9TTC(GAA)8 and (GGA)9TCC(GGA)8 form single canonical intramolecular triplexes at pH 7.0-6.0 in negatively supercoiled plasmids as isolated from Escherichia coli. With a lowering of the pH and/or an increase in the degree of negative supercoiling, these sequences undergo a novel conformational change as revealed by diethyl pyrocarbonate hypermodification of adenines in the middle of the polypurine strand and OsO4 reaction with thymines in the center and the quarter points of the polypyrimidine strand. To evaluate this structure, a family of related Pur.Pyr sequences were cloned and studied. The non mirror repeat sequence (GGA)9TCC(GAA)8 forms a non-B conformation only under acidic pH conditions, but the structural properties are different from those of the mirror repeat sequences. Furthermore, when the central interruptions of a mirror repeat sequence were increased from 3 to 9 bp, two canonical triplexes formed independently at pH 5.0 [at the (GAA)9 and (GAA)8 regions in the sequence (GAA)9TTAATTCGC(GAA)8]. Thus, if an interruption is sufficiently long, the two halves of the Pur.Pyr sequence do not interact with each other. Novel types of folded DNA geometries which explain these results are described.
质粒中具有中央间断的聚嘌呤-聚嘧啶（Pur.Pyr）序列，根据特定化学探针（四氧化锇、焦碳酸二乙酯和硫酸二甲酯）及二维电泳所揭示的条件，可呈现多种非B-DNA构象。相对较长的镜像重复Pur.Pyr序列（GAA）9TTC（GAA）8和（GGA）9TCC（GGA）8，在从大肠杆菌分离得到的负超螺旋质粒中，于pH 7.0 - 6.0时形成单一标准的分子内三链体。随着pH值降低和/或负超螺旋程度增加，这些序列会发生一种新的构象变化，这可通过聚嘌呤链中部腺嘌呤的焦碳酸二乙酯超修饰以及聚嘧啶链中心和四分之一点处胸腺嘧啶与四氧化锇的反应揭示出来。为评估这种结构，克隆并研究了一系列相关的Pur.Pyr序列。非镜像重复序列（GGA）9TCC（GAA）8仅在酸性pH条件下形成非B构象，但其结构特性与镜像重复序列不同。此外，当镜像重复序列的中央间断从3 bp增加到9 bp时，在pH 5.0时会独立形成两个标准三链体[在序列（GAA）9TTAATTCGC（GAA）8的（GAA）9和（GAA）⑧区域]。因此，如果间断足够长，Pur.Pyr序列的两半不会相互作用。文中描述了解释这些结果的新型折叠DNA几何结构。
