Recognition and cleavage of single-stranded DNA containing hairpin structures by oligonucleotides forming both Watson-Crick and Hoogsteen hydrogen bonds.
A new approach is described to design antisense oligonucleotides targeted against single-stranded nucleic acids containing hairpin structures by use of both Watson-Crick and Hoogsteen hydrogen bond interactions for recognition. The oligonucleotide has two different domains, one allowing double helix formation involving Watson-Crick base pairs and the other one forming a triple helix involving Hoogsteen-type base triplets in the major groove of a hairpin stem. Spectroscopic and gel retardation experiments provided evidence for such Watson-Crick/Hoogsteen (WC/H) recognition of hairpin structures in single-stranded DNA. An antisense oligonucleotide designed to form only Watson-Crick base pairs was unable to disrupt the stable stem structure of the target under conditions where the oligonucleotide designed with the Watson-Crick/Hoogsteen interactions could bind efficiently to the hairpin-containing target. The addition of one nucleotide to the oligonucleotide at the junction between the double helix and triple helix regions in WC/H complexes had an effect on stability which was dependent on the relative orientation of the Watson-Crick and Hoogsteen domains in the target. An oligodeoxynucleotide-phenanthroline conjugate targeted against such a hairpin-containing DNA fragment induced specific cleavage in the double-stranded stem. This WC/H approach may be useful in designing artificial regulators of gene expression.
François
J C
JC
Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, INSERM U 201, CNRS UA 481, Paris, France.
Hélène
C
C
D001483:Base Sequence; D004277:DNA, Single-Stranded / Q000378:metabolism*; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016376:Oligonucleotides, Antisense / Q000378:metabolism*; D013816:Thermodynamics
D004277:DNA, Single-Stranded; D016376:Oligonucleotides, Antisense