Targeting peptide nucleic acid-protein conjugates to structural features within duplex DNA.
A convenient small scale synthesis has been developed for obtaining peptide nucleic acid oligomers (PNAs). PNAs have been conjugated to a protein, staphylococcal nuclease, through disulfide exchange between a cysteine at the 3'-(carboxy) end of the PNA and an introduced cysteine on the surface of the nuclease. Site specific DNA cleavage by the attached nuclease has been used to examine the Watson-Crick hybridization of the PNAs to duplex DNA. Substantial affinity cleavage occurred when target sites contained inverted repeats which have the potential to form non B-DNA structures such as cruciforms. No affinity cleavage was observed at a site lacking apparent potential for non B-DNA structures. These results indicate that the Watson-Crick hybridization of PNAs to duplex DNA by strand displacement is favored by the presence of potential alternative secondary structures within the target sequence.
Norton
J C
JC
Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas 75235, USA.
Waggenspack
J H
JH
Varnum
E
E
Corey
D R
DR
D001483:Base Sequence; D017403:In Situ Hybridization; D008836:Micrococcal Nuclease / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry* / Q000378:metabolism; D009696:Nucleic Acids / Q000138:chemical synthesis* / Q000302:isolation & purification; D010455:Peptides / Q000138:chemical synthesis* / Q000302:isolation & purification / Q000378:metabolism; D010957:Plasmids / Q000378:metabolism; D013210:Staphylococcus / Q000201:enzymology
D009692:Nucleic Acid Heteroduplexes; D009696:Nucleic Acids; D010455:Peptides; D008836:Micrococcal Nuclease