Watson-Crick Hoogsteen Research Articles

Molecular dynamics simulations and coupled nucleotide substitution experiments indicate the nature of A{middle dot}A base pairing and a putative structure of the coralyne-induced homo-adenine duplex.

Coralyne is an alkaloid drug that binds homo-adenine DNA (and RNA) oligonucleotides more tightly than it does Watson–Crick DNA. Hud’s laboratory has shown that poly(dA) in the presence of coralyne forms an anti-parallel duplex, however attempts to determine the structure by NMR spectroscopy and X-ray crystallography have been unsuccessful. Assuming adenine–adenine hydrogen bonding between the two poly(dA) strands, we constructed 40 hypothetical homo-(dA) anti-parallel duplexes and docked coralyne into the six most favorable duplex structures. The two most stable structures had trans glycosidic bonds, but distinct pairing geometries, i.e. either Watson–Crick Hoogsteen (transWH) or Watson–Crick Watson–Crick (transWW) with stability of transWH > transWW. To narrow down the possibilities, 7-deaza adenine base substitutions (dA→7) were engineered into homo-(dA) sequences. These substitutions significantly reduced the thermal stability of the coralyne-induced homo-(dA) structure. These experiments strongly suggest the involvement of N7 in the coralyne-induced A·A base pairs. Moreover, due to the differential effect on melting as a function of the location of the dA→7 mutations, these results are consistent with the N1–N7 base pairing of the transWH pairs. Together, the simulation and base substitution experiments predict that the coralyne-induced homo-(dA) duplex structure adopts the transWH geometry.

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.