Solution structure and hydration patterns of a Pyrimidine·Purine·Pyrimidine DNA triplex containing a novel T·CG base-triple

Ishwar Radhakrishnan*, Dinshaw J. Patel

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

80 Scopus citations

Abstract

The solution structure of a pyrimidine purine pyrimidine DNA triplex containing a novel T·CG base-triple has been determined via two and three-dimensional NMR spectroscopy and restrained molecular dynamics simulations incorporating explicit solvent and counter-ions. The T·CG triple, which expands the triplex code, is stabilized by a single hydrogen bond between the O-2 atom of thymine and the free amino proton of cytosine in the Watson-Crick C·G base-pair. This hydrogen bonding alignment produces large variations in helical twist at the dinucleotide steps involving the thymine residue. Localized structural perturbations in the purine-rich strand of the molecule are observed around the cytosine residue in the T·CG triple. Globally, the triplex resembles the solution structure of a previously solved pyrimidine-purine-pyrimidine DNA triplex containing an unusual G·TA triple. Also conserved are the sites and patterns of hydration in the two triplexes.

Original languageEnglish (US)
Pages (from-to)600-619
Number of pages20
JournalJournal of Molecular Biology
Volume241
Issue number4
DOIs
StatePublished - Jan 1 1994

Keywords

  • DNA
  • Molecular dynamics
  • NMR spectroscopy
  • Pyrimidine·purine·pyrimidine triplexes
  • T·CG triple

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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