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

Background: Under certain conditions, homopyrimidine oligonucleotides can bind to complementary homopurine sequences in homopurine-homopyrim idine segments of duplex DNA to form triple helical structures. Beside s having biological implications in vivo, this property has been explo ited in molecular biology applications. This approach is limited by a lack of knowledge about the recognition by the third strand of pyrimid ine residues in Watson-Crick base pairs. Results: We have therefore de termined the solution structure of a pyrimidine purine pyrimidine (Y.R Y) DNA triple helix containing a guanine residue in the third strand w hich was postulated to specifically recognize a thymine residue in a W atson-Crick TA base pair. The structure was solved by combining NMR-de rived 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 grou p. This allows the guanine amino protons to participate in hydrogen bo nds with separate carbonyls, forming one strong bond within the G.TA t riple and a weak bond to an adjacent T.AT triple. Dramatic variations in helical twist around the guanine residue lead to a novel stacking i nteraction. At the global level, the Y.RY DNA tripler shares several s tructural features with the recently solved solution structure of the R.RY DNA triplex. Conclusions: The formation of a G.TA triple within a n otherwise pyrimidine purine pyrimidine DNA triplex causes conformati onal realignments in and around the G.TA triple. These highlight new a spects of molecular lar recognition that could be useful in tripler-ba sed approaches to inhibition of gene expression and site-specific clea vage of genomic DNA.