1WAN

DNA DTA TRIPLEX, NMR, 7 STRUCTURES

Summary for 1WAN

• Entry DOI: 10.2210/pdb1wan/pdb
• Descriptor: DNA (5'-D(*AP*GP*AP*TP*AP*GP*AP*AP*CP*CP*CP*CP*TP*TP*CP*TP*AP*TP*CP*TP*TP*AP*TP*AP*TP*CP*TP*(D3)P*TP*CP*TP*T)-3') (1 entity in total)
• Functional Keywords: triplex, intercalator, deoxyribonucleic acid, dna
• Total number of polymer chains: 1
• Total formula weight: 9828.44

Authors

Wang, E.,Koshlap, K.M.,Gillespie, P.,Dervan, P.B.,Feigon, J. (deposition date: 1996-01-14, release date: 1996-07-11, Last modification date: 2024-05-22)

Primary citation

Wang, E.,Koshlap, K.M.,Gillespie, P.,Dervan, P.B.,Feigon, J.
Solution structure of a pyrimidine-purine-pyrimidine triplex containing the sequence-specific intercalating non-natural base D3.
J.Mol.Biol., 257:1052-1069, 1996

PubMed Abstract: We have used NMR spectroscopy to study a pyrimidine-purine-pyrimidine DNA triplex containing a non-natural base, 1-(2-deoxy-beta-D-ribofuranosyl)-4-(3-benzamido)phenylimidazole (D3), in the third strand. The D3 base has been previously shown to specifically recognize T-A and C-G base-pairs via intercalation on the 3' side (with respect to the purine strand) of the target base pair, instead of forming sequence-specific hydrogen bonds. 1H resonance assignments have been made for the D3 base and most of the non-loop portion of the triplex. The solution structure of the triplex was calculated using restrained molecular dynamics and complete relaxation matrix refinement. The duplex portion of the triplex has an over-all helical structure that is more similar to B-DNA than to A-DNA. The three aromatic rings of the D3 base stack on the bases of all three strands and mimic a triplet. The conformation of the D3 base and its sequence specificity are discussed.

PubMed: 8632468
DOI: 10.1006/jmbi.1996.0223

Experimental method

SOLUTION NMR