Ligand-induced formation of hoogsteen-paired parallel DNA.

Abstract

INTRODUCTION Based on molecular modeling studies, a model has been proposed for intercalation of triple-helix-specific ligands (benzopyridoindole (BPI) derivatives) into triple helices, in which the intercalating compounds interact mainly with the Hoogsteen-paired strands of the triple helix. We set out to test this model experimentally using DNA duplexes capable of forming parallel Hoogsteen base-paired structures. RESULTS We have investigated the possible formation of a parallel DNA structure involving Hoogsteen hydrogen bonds by thermal denaturation, FTIR spectroscopy and gel-shift experiments. We show that BPI derivatives bind to Hoogsteen base-paired duplexes and stabilize them. The compounds induce a reorganization from a non-perfectly matched antiparallel Watson- Crick duplex into a perfectly matched parallel Hoogsteen-paired duplex. CONCLUSIONS These results suggest that preferential intercalation of BPI derivatives in triple helices is due to their ability to interact specifically with the Hoogsteen-paired bases. The results are consistent with a model proposed on the basis of molecular modeling studies using energy minimization, and they open a new field of investigations regarding the biological relevance of Hoogsteen base-pairing.

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@article{Escud1996LigandinducedFO, title={Ligand-induced formation of hoogsteen-paired parallel DNA.}, author={C Escud{\'e} and S Mohammadi and J S Sun and C H Nguyen and E Bisagni and J Liquier and E Taillandier and T Garestier and C H{\'e}l{\`e}ne}, journal={Chemistry & biology}, year={1996}, volume={3 1}, pages={57-65} }