334D

DEFINING GC-SPECIFICITY IN THE MINOR GROOVE: SIDE-BY-SIDE BINDING OF THE DI-IMIDAZOLE LEXITROPSIN TO C-A-T-G-G-C-C-A-T-G

Summary for 334D

• Entry DOI: 10.2210/pdb334d/pdb
• Descriptor: DNA (5'-D(*CP*AP*TP*GP*GP*CP*CP*AP*TP*G)-3'), DIIMIDAZOLE LEXITROPSIN, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: b-dna, double helix, dna
• Total number of polymer chains: 2
• Total formula weight: 6854.82

Authors

Kopka, M.L.,Goodsell, D.S.,Dickerson, R.E. (deposition date: 1997-05-22, release date: 1997-08-29, Last modification date: 2024-04-03)

Primary citation

Kopka, M.L.,Goodsell, D.S.,Han, G.W.,Chiu, T.K.,Lown, J.W.,Dickerson, R.E.
Defining GC-specificity in the minor groove: side-by-side binding of the di-imidazole lexitropsin to C-A-T-G-G-C-C-A-T-G.
Structure, 5:1033-1046, 1997

PubMed Abstract: Polyamide drugs, such as netropsin, distamycin and their lexitropsin derivatives, can be inserted into a narrow B-DNA minor groove to form 1:1 complexes that can distinguish AT base pairs from GC, but cannot detect end-for-end base-pair reversals such as TA for AT. In contrast, 2:1 side-by-side polyamide drug complexes potentially are capable of such discrimination. Imidazole (Im) and pyrrole (Py) rings side-by-side read a GC base pair with the Im ring recognizing the guanine side. But the reason for this specific G-Im association is unclear because the guanine NH2 group sits in the center of the groove. A 2:1 drug:DNA complex that presents Im at both ends of a GC base pair should help unscramble the issue of imidazole reading specificity.

PubMed: 9309219
DOI: 10.1016/S0969-2126(97)00255-4

Experimental method

X-RAY DIFFRACTION (1.8 Å)