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Solution structure of a pyrimidine-purine-pyrimidine triplex containing the sequence-specific intercalating non-natural base D_3

Wang, Edmond and Koshlap, Karl M. and Gillespie, Paul and Dervan, Peter B. and Feigon, Juli (1996) Solution structure of a pyrimidine-purine-pyrimidine triplex containing the sequence-specific intercalating non-natural base D_3. Journal of Molecular Biology, 257 (5). pp. 1052-1069. ISSN 0022-2836. doi:10.1006/jmbi.1996.0223.

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We have used NMR spectroscopy to study a pyrimidine·purine·pyrimidine DNA triplex containing a non-natural base, 1-(2-deoxy-β-D-ribofuranosyl)- 4-(3-benzamido)phenylimidazole (D_3), in the third strand. The D_3base 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 D_3base 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 D_3base stack on the bases of all three strands and mimic a triplet. The conformation of the D_3base and its sequence specificity are discussed.

Item Type:Article
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Dervan, Peter B.0000-0001-8852-7306
Additional Information:© 1996 Academic Press. (Received 21 November 1995; received in revised form 17 January 1996; accepted 22 January 1996) This work was supported by NIH grant R01 GM37254 to J.F., and an Office of Naval Research grant to P.B.D. The coordinates for the structures have been deposited with the Brookhaven Protein Data Base (accession no. 1WAN).
Funding AgencyGrant Number
NIHR01 GM37254
Office of Naval Research (ONR)UNSPECIFIED
Subject Keywords:DNA; triplex; NMR; 2DNMR; triple helix; triple strand; intercalator
Issue or Number:5
Record Number:CaltechAUTHORS:20160510-110519457
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Official Citation:Edmond Wang, Karl M. Koshlap, Paul Gillespie, Peter B. Dervan, Juli Feigon, Solution Structure of a Pyrimidine·Purine·Pyrimidine Triplex Containing the Sequence-specific Intercalating Non-natural Base D3, Journal of Molecular Biology, Volume 257, Issue 5, 19 April 1996, Pages 1052-1069, ISSN 0022-2836, (
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66902
Deposited By: Victoria Brennan
Deposited On:18 May 2016 21:55
Last Modified:11 Nov 2021 00:23

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