title: 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.
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.
authors.affiliation: Whitehead Institute for Biomedical Research, Nine Cambridge Center, Massachusetts, USA.
authors.forename: M
authors.initials: M
authors.lastname: Footer
authors.forename: M
authors.initials: M
authors.lastname: Egholm
authors.forename: S
authors.initials: S
authors.lastname: Kron
authors.forename: J M
authors.initials: JM
authors.lastname: Coull
authors.forename: P
authors.initials: P
authors.lastname: Matsudaira
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D006868:Hydrolysis; D008969:Molecular Sequence Data; D009532:Nickel / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D015345:Oligonucleotide Probes; D009842:Oligopeptides / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*
chemical_list: C101083:Gly-Gly-His-bis(4-nitroanilide); D009696:Nucleic Acids; D015345:Oligonucleotide Probes; D009842:Oligopeptides; D010455:Peptides; C051802:triplex DNA; D009532:Nickel; D004247:DNA