149d

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SOLUTION STRUCTURE OF A PYRIMIDINE(DOT)PURINE(DOT) PYRIMIDINE DNA TRIPLEX CONTAINING T(DOT)AT, C+(DOT)GC AND G(DOT)TA TRIPLES

Overview

BACKGROUND: Under certain conditions, homopyrimidine oligonucleotides can, bind to complementary homopurine sequences in homopurine-homopyrimidine, segments of duplex DNA to form triple helical structures. Besides having, biological implications in vivo, this property has been exploited in, molecular biology applications. This approach is limited by a lack of, knowledge about the recognition by the third strand of pyrimidine residues, in Watson-Crick base pairs. RESULTS: We have therefore determined the, solution structure of a pyrimidine.purine.pyrimidine (Y.RY) DNA triple, helix containing a guanine residue in the third strand which was, postulated to specifically recognize a thymine residue in a Watson-Crick, TA base pair. The structure was solved by combining NMR-derived restraints, with molecular dynamics simulations conducted in the presence of explicit, solvent and counter ions. The guanine of the G-TA triple is tilted out of, the plane of its target TA base pair towards the 3'-direction, to avoid a, steric clash with the thymine methyl group. This allows the guanine amino, protons to participate in hydrogen bonds with separate carbonyls, forming, one strong bond within the G-TA triple and a weak bond to an adjacent T.AT, triple. Dramatic variations in helical twist around the guanine residue, lead to a novel stacking interaction. At the global level, the Y.RY DNA, triplex shares several structural features with the recently solved, solution structure of the R.RY DNA triplex. CONCLUSIONS: The formation of, a G.TA triple within an otherwise pyrimidine.purine.pyrimidine DNA triplex, causes conformational realignments in and around the G.TA triple. These, highlight new aspects of molecular recognition that could be useful in, triplex-based approaches to inhibition of gene expression and, site-specific cleavage of genomic DNA.

About this Structure

149D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

Solution structure of a pyrimidine.purine.pyrimidine DNA triplex containing T.AT, C+.GC and G.TA triples., Radhakrishnan I, Patel DJ, Structure. 1994 Jan 15;2(1):17-32. PMID:8075980

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