DSSR-PyMOL cartoon-block schematics: PDB entry 177d

PDB-id

177d; SNAP-derived features in text and JSON formats

Class

DNA

Method

NMR

Summary

Solution structure and hydration patterns of a pyrimidine(dot)purine(dot)pyrimidine DNA triplex containing a novel t(dot)cg triple

Reference

Radhakrishnan I, Patel DJ (1994): "Solution structure and hydration patterns of a pyrimidine.purine.pyrimidine DNA triplex containing a novel T.CG base-triple." J.Mol.Biol., 241, 600-619. doi: 10.1006/jmbi.1994.1534.

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.