Proton nuclear magnetic resonance assignments and structural characterization of an intramolecular DNA triplex.

Journal Article

Two-dimensional 1H n.m.r. spectroscopy has been used to study the 31-base DNA oligonucleotide 5'-dAGAGAGAACCCCTTCTCTCTTTTTCTCTCTT-3', which folds to form a stable intramolecular triplex in solution at acidic pH. This structure is considerably more difficult to assign than short B-DNA duplexes and requires new assignment methods. The assignment strategy and assignments of almost all of the exchangeable and nonexchangeable resonances are presented. Seven base triplets and one Watson-Crick base-pair form the core of the structure and are connected by a four C and four T loop at either end. The second pyrimidine "strand" (bases 24 to 31) in this intramolecular pyrimidine-purine-pyrimidine triplex binds via Hoogsteen base-pairs in the major groove and is parallel to the purine "strand" (bases 1 to 8). Analysis of the sugar puckers reveals that, contrary to widely accepted belief, the triplex sugars are not predominantly in the N-type (close to C3'-endo) conformation. Except for some of the C nucleotides, all sugars are predominantly S-type (close to C2'-endo). Thus, the duplex DNA does not assume N-type sugar conformations to accommodate a third strand in the major groove. A preliminary model of the triplex structure is presented.

Full Text

Duke Authors

Cited Authors

  • Macaya, R; Wang, E; Schultze, P; Sklenár, V; Feigon, J

Published Date

  • June 5, 1992

Published In

Volume / Issue

  • 225 / 3

Start / End Page

  • 755 - 773

PubMed ID

  • 1318385

International Standard Serial Number (ISSN)

  • 0022-2836

Language

  • eng

Conference Location

  • England