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

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 tripler 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 lar recognition that could be useful in tripler-based approaches to inhibition of gene expression and site-specific cleavage of genomic DNA.