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Nucleic Acids Research, Vol 25, Issue 13 2574-2581, Copyright © 1997 by Oxford University Press

ARTICLES

A macrocyclic bis-acridine shifts the equilibrium from duplexes towards DNA hairpins

A Slama-Schwok, F Peronnet, E Hantz-Brachet, E Taillandier, MP Teulade-Fichou, JP Vigneron, M Best-Belpomme and JM Lehn
Laboratoire de Spectroscopie Biomoleculaire, URA CNRS 1430, UFR de Sante, Medecine et Biologie Humaine, Universite Paris XIII, Bobigny, France. schwok@ibpc.fr

Nucleic acids can undergo dynamic conformational changes associated with the regulation of biological processes. A molecule presenting larger affinities for alternative structures relative to a duplex is expected to modify such conformational equilibria. We have previously reported that macrocyclic bis-acridine binds preferentially to single- stranded regions, especially DNA hairpins, due to steric effects. Here, we show, using gel electrophoresis, fluorescence and melting temperature experiments, that the macrocycle bis-acridine shifts an equilibrium from a duplex towards the corresponding hairpins. Competition experiments enlighten the higher affinity of the macrocycle for hairpins compared with double-stranded DNA. The macrocycle bis- acridine destabilizes a synthetic polynucleotide, by the formation of premelted areas. By extrapolation, the macrocycle bis-acridine should be able to disrupt, at least locally, genomic DNA duplexes and to stabilize unpaired areas, especially palindromic ones forming hairpins. Such macrocyclic compounds may have potential applications in the therapy of diseases involving hairpins.
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