title: Strand-invasion of duplex DNA by peptide nucleic acid oligomers.
abstract: Polyamide oligomers, termed peptide nucleic acids (PNAs), bind with high affinity to both DNA and RNA and offer both antisense and antigene approaches for regulating gene expression. When a PNA binds to a complementary sequence in a double-stranded DNA, one strand of the duplex is displaced, and a stable D-loop is formed. Unlike oligodeoxynucleotides for which binding polarity is determined by the deoxyribose sugar, the unrestrained polyamide backbone of the PNA could permit binding to a DNA target in an orientation-independent manner. We now provide evidence that PNAs can, in fact, bind to their complementary sequence in DNA independent of the DNA-strand polarity--that is, a PNA binds to DNA in both "parallel" and "antiparallel" fashion. With a mixed-sequence 15-mer PNA, kinetic studies of PNA.DNA interactions revealed that D-loop formation was rapid and the complex was stable for several hours. However, when measured either by gel-mobility-shift analysis or RNA polymerase II-elongation termination, D-loop formation was salt dependent, but PNA-strand dissociation was not salt dependent. We observed that D-loop-containing DNA fragments had anomalous gel mobilities that varied as a function of the position of the D-loop relative to the DNA termini. On the basis of permutation analysis, the decreased mobility of the PNA.DNA complex was attributed to a bend in the DNA at or near the D-loop.
authors.affiliation: Department of Cell Biology, Glaxo, Inc., Research Triangle Park, NC 27709.
authors.forename: N J
authors.initials: NJ
authors.lastname: Peffer
authors.forename: J C
authors.initials: JC
authors.lastname: Hanvey
authors.forename: J E
authors.initials: JE
authors.lastname: Bisi
authors.forename: S A
authors.initials: SA
authors.lastname: Thomson
authors.forename: C F
authors.initials: CF
authors.lastname: Hassman
authors.forename: S A
authors.initials: SA
authors.lastname: Noble
authors.forename: L E
authors.initials: LE
authors.lastname: Babiss
mesh_terms: D001483:Base Sequence; D001681:Biological Assay; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D012965:Sodium Chloride / Q000737:chemistry; D013329:Structure-Activity Relationship; D014158:Transcription, Genetic
chemical_list: D009696:Nucleic Acids; D009838:Oligodeoxyribonucleotides; D012965:Sodium Chloride; D004247:DNA