Biochemical Evidence That a D-Loop Is Part of a Four-Stranded PNA−DNA Bundle. Nickel-Mediated Cleavage of Duplex DNA by a Gly-Gly-His Bis-PNA
- 1 January 1996
- journal article
- Published by American Chemical Society (ACS) in Biochemistry
- Vol. 35 (33) , 10673-10679
- https://doi.org/10.1021/bi960486p
Abstract
A peptide nucleic acid (PNA) with improved strand-displacement capability and a site-specific DNA cleavage function is a novel reagent for probing the structure of PNA−DNA complexes in solution. By linking two PNAs in tandem with an aliphatic linker, the bis-PNA forms a bis-PNA−DNA triple-stranded complex having a higher stability to thermal denaturation than conventional monomeric PNAs. When a Gly-Gly-His tripeptide is placed on either the Watson−Crick or Hoogsteen bis-PNA strand, nickel-mediated cleavage is detected at specific sites on the displaced and hybridized DNA strands. Because the displaced strand is cleaved when GGH is placed on either PNA strand, the D-loop must be close to the backbone of the bis-PNA−DNA triplex. Furthermore, the pattern of cleavage on the displaced strand suggests the nickel−tripeptide complex lies in a groove formed by the displaced DNA strand and both PNA strands. These observations suggest that the D-loop is a part of a four-stranded bis-PNA−DNA2 bundle.Keywords
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