Solution conformation of a parallel DNA triple helix with 5 ' and 3 ' triplex-duplex junctions

Background: Polypurine.polypyrimidine sequences of DNA can form parallel tr iple helices via Hoogsteen hydrogen bonds with a third DNA strand that is c omplementary to the purine strand. The tripler prevents transcription and c ould therefore potentially be used to regulate specific genes. The determin ation of the structures of tripler-duplex junctions can help us to understa nd the structural basis of specificity, and aid in the design of optimal an tigene oligonucleotides, Results: The solution structures of the junction triplexes d(<(GAGAGA)under bar>CGTA)-X-(TACG<(TCTCTC)under bar>)-X-(<(CTCTCT)under bar>) and d(<(CTCT CT)under bar>)-X-(<(TCTCTC)under bar>AGTC)-X-(GACT<(GAGAGA)under bar>) (whe re X is bis(octylphosphate) and nucleotides in the tripler regions are unde rlined) have been solved using nuclear magnetic resonance (NMR) spectroscop y. The structure is characterised by significant changes in the conformatio n of the purine residues, asymmetry of the 5' and 3' junctions, and variati ons in groove widths associated with the positive charge of the protonated cytosine residues in the third strand, The thermodynamic stability of tripl exes with either a 5' or a 3' CH+ is higher than those with a terminal thym idine. Conclusions: The observed sequence dependence of the tripler structure, and the distortions of the DNA at the 5' and 3' termini has implications for t he design of optimal tripler-forming sequences, both in terms of the termin al bases and the importance of including positive charges in the third stra nd. Thus, triplex-stabilising ligands might be designed that can discrimina te between TA . T-rich and CG . C+-rich sequences that depend not only on c harge, but also on local groove widths. This could improve the stabilisatio n and specificity of antigene tripler formation.