1994年4月
CORRELATIONS OF CRYSTAL-STRUCTURES OF DNA OLIGONUCLEOTIDES WITH ENANTIOSELECTIVE RECOGNITION BY RH(PHEN)(2)PHI(3+) - PROBES OF DNA PROPELLER TWISTING IN SOLUTION
BIOCHEMISTRY
- ,
- ,
- 巻
- 33
- 号
- 14
- 開始ページ
- 4130
- 終了ページ
- 4139
- 記述言語
- 英語
- 掲載種別
- 研究論文(学術雑誌)
- DOI
- 10.1021/bi00180a005
- 出版者・発行元
- AMER CHEMICAL SOC
Rh(phen)2phi3+(phen = 1,10-phenanthroline; phi = 9,10-phenanthrenequinone diimine) avidly binds to DNA via intercalation from the major groove and upon photoactivation produces strand scission with single base 5' asymmetry. Enantiomers of Rh(phen)2phi3+, which lack hydrogen-bonding substituents in ancillary positions, distinguish a DNA site through shape-selection; site recognition depends upon the local variations in structure at a binding site. Here, we examine the application of DELTA-Rh(phen)2phi3+ as a sequence-dependent structural probe and, in particular, as a probe of DNA propeller twisting in solution, by comparing directly cleavage results using DELTA- and LAMBDA-Rh(phen)2phi3+ on crystallographically characterized oligonucleotides with several sequence-dependent crystallographic parameters. The three oligonucleotides examined in this study are the Dickerson-Drew dodecamer, 5'-CGCGAATTCGCG-3', the Nar I dodecamer, 5'-ACCGGCGCCACA-3', and the CG decamer, 5'-CCAACGTTGG-3', all of which have been crystallized in the B-form. Enantioselective cleavage and reaction favored by the DELTA-isomer is found to be governed locally by the opening of the site in the major groove. A correlation is demonstrated between cleavage by DELTA-Rh(phen)2phi3+ and the opening in the major groove that results from the change in propeller twist (differential propeller twist) at a base step. When the major groove is closed as a result of a change in propeller twist, there is little cleavage evident by either enantiomer; at sites which are indicated crystallographically to be open in the major groove, a direct correlation is observed between enantioselective cleavage and the degree of opening. A trend of higher enantioselectivity at sites possessing higher twist angles is also observed. The roll angle of a site in isolation, the rise per base step, and the groove width show no correlation with cleavage. The distribution of reaction products at a site, as a result of partitioning along oxygen-dependent or oxygen-independent pathways, also provides a sensitive measure of the shape-complementarity between metal complex and binding site. These results provide evidence for site-recognition by the metal complex which correlates directly with DNA propeller twisting in oligonucleotide crystals. Importantly, these results indicate that Rh(phen)2phi3+ may be uniquely applied as a chemical probe for sequence-dependent changes in the propeller twisting of DNA.
- リンク情報
- ID情報
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- DOI : 10.1021/bi00180a005
- ISSN : 0006-2960
- Web of Science ID : WOS:A1994NF70100005