154D

DNA DISTORTION IN BIS-INTERCALATED COMPLEXES

154D の概要

• エントリーDOI: 10.2210/pdb154d/pdb
• 分子名称: DNA (5'-D(*(CBR)P*GP*CP*G)-3'), BIS-(N-ETHYLPYRIDINIUM-(3-METHOXYCARBAZOLE))HEXANE-1,6-DIAMINE (3 entities in total)
• 機能のキーワード: right handed dna, double helix, complexed with drug, modified, dna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 3210.30

構造登録者

Peek, M.E.,Lipscomb, L.A.,Bertrand, J.A.,Gao, Q.,Roques, B.P.,Garbay-Jaureguiberry, C.,Williams, L.D. (登録日: 1993-12-14, 公開日: 1994-08-31, 最終更新日: 2024-02-07)

主引用文献

Peek, M.E.,Lipscomb, L.A.,Bertrand, J.A.,Gao, Q.,Roques, B.P.,Garbay-Jaureguiberry, C.,Williams, L.D.
DNA distortion in bis-intercalated complexes.
Biochemistry, 33:3794-3800, 1994

PubMed Abstract: The bis-intercalators Flexi-Di and ditercalinium are synthetic dimers that bis-intercalate into DNA and cause cell death in prokaryotes from futile and abortive repair of DNA. Each is composed of two 7H-pyridocarbazole units and a linker. Flexi-Di has a flexible spermine-like linker while ditercalinium has a rigid bis(ethylpiperidinium) linker. This report, describing the 2.5-A X-ray structure of Flexi-Di complexed with [d(BrCGCG)]2, appears to be the first report of a three-dimensional structure of a DNA complex with a bis-intercalator with a flexible linker. DNA complex formation with a ditercalinium analog having a flexible linker was not anticipated to yield unstacked and bent DNA as was observed in the previously reported ditercalinium.[d(CGCG)]2 complex. Surprisingly, the DNA in the Flexi-Di complex is bent to a degree exceeding that of the ditercalinium complex. A comparison of the DNA complexes of Flexi-Di and ditercalinium has allowed us to propose a mechanism by which these bis-intercalators distort DNA. We propose that this class of bis-intercalators pulls the internal base pairs into the major groove and pushes the external base pairs into the minor groove. The result is a bend toward the minor groove. It appears that hydrogen bonds between the linker and the internal guanines effectively pull the central base pairs of the complex out into the major groove. At the external regions of the complex, stacking interactions between the chromophores and terminal base pairs effectively push the terminal base pairs into the minor groove. The result of this push/pull combination is to bend the DNA.

PubMed: 8142381
DOI: 10.1021/bi00179a002

実験手法

X-RAY DIFFRACTION (2.5 Å)