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Solution structure and hydration patterns of a pyrimidine.purine.pyrimidine DNA triplex containing a novel T.CG
1Department 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.