Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA.
Nucleic Acids Res. 2011 May;39(10):4265-74. doi: 10.1093/nar/gkq1362. Epub 2011 Jan 25.
Heterocyclic diamidines are compounds with antiparasitic properties that target the minor groove of kinetoplast DNA. The mechanism of action of these compounds is unknown, but topological changes to DNA structures are likely to be involved. In this study, we have developed a polyacrylamide gel electrophoresis-based screening method to determine topological effects of heterocyclic diamidines on four minor groove target sequences: AAAAA, TTTAA, AAATT and ATATA. The AAAAA and AAATT sequences have the largest intrinsic bend, whereas the TTTAA and ATATA sequences are relatively straight. The changes caused by binding of the compounds are sequence dependent, but generally the topological effects on AAAAA and AAATT are similar as are the effects on TTTAA and ATATA. A total of 13 compounds with a variety of structural differences were evaluated for topological changes to DNA. All compounds decrease the mobility of the ATATA sequence that is consistent with decreased minor groove width and bending of the relatively straight DNA into the minor groove. Similar, but generally smaller, effects are seen with TTTAA. The intrinsically bent AAAAA and AAATT sequences, which have more narrow minor grooves, have smaller mobility changes on binding that are consistent with increased or decreased bending depending on compound structure.
杂环二脒类化合物具有抗寄生虫特性，靶向动基体 DNA 的小沟。这些化合物的作用机制尚不清楚，但 DNA 结构的拓扑变化可能与之相关。在这项研究中，我们开发了一种基于聚丙烯酰胺凝胶电泳的筛选方法，以确定杂环二脒类化合物对四个小沟靶序列（AAAAA、TTTAA、AAATT 和 ATATA）的拓扑效应。AAAAA 和 AAATT 序列具有最大的固有弯曲度，而 TTTAA 和 ATATA 序列相对较直。结合化合物引起的变化与序列有关，但一般来说，AAAAA 和 AAATT 的拓扑效应相似，TTTAA 和 ATATA 的效应也相似。共评估了 13 种具有多种结构差异的化合物对 DNA 的拓扑变化。所有化合物均降低 ATATA 序列的迁移率，这与较小的小沟宽度一致，并使相对直的 DNA 弯曲进入小沟。TTTAA 也有类似但通常较小的影响。具有更窄小沟的固有弯曲的 AAAAA 和 AAATT 序列在结合时的迁移率变化较小，这与化合物结构有关的弯曲增加或减少一致。
