J Mol Biol. 1994 Aug 26;241(4):600-19.

Solution structure and hydration patterns of a pyrimidine.purine.pyrimidine DNA triplex containing a novel T.CG base-triple.

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Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons of Columbia University, New York, NY 10032.

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.

PMID:: 8057381; [PubMed - indexed for MEDLINE]

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GM 34504/GM/NIGMS NIH HHS/United States

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Structures reported by this article

Solution Structure And Hydration Patterns Of A Pyrimidine(Dot)purine(Dot)pyrimidine Dna Triplex Containing A Novel T(Dot)cg Triple

PDB: 177D

Source: synthetic construct

Method: Solution Nmr

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