Strand-Invasion of Duplex DNA by Peptide Nucleic Acid Oligomers

• Published in: Proceedings of the National Academy of Sciences - PNAS 1993-11, Vol.90 (22), p.10648-10652
• Main Authors: Peffer, Nancy J., Hanvey, Jeffrey C., Bisi, John E., Thomson, Stephen A., Hassman, C. Fred, Noble, Stewart A., Babiss, Lee E.
• Format: Article
• Language: English
• Subjects: Analytical, structural and metabolic biochemistry; Base Sequence; Bending; Biochemistry; Biological and medical sciences; Biological Assay; Deoxyribonucleic acid; DNA; DNA - chemistry; Dna, deoxyribonucleoproteins; Fundamental and applied biological sciences. Psychology; Gels; Hydrogen Bonding; Molecular Sequence Data; Molecules; Nucleic Acid Conformation; Nucleic acids; Nucleic Acids - chemistry; Oligodeoxyribonucleotides - chemistry; Oligomers; Peptide nucleic acids; Plasmids; RNA; Salts; Sodium Chloride - chemistry; Structure-Activity Relationship; Transcription, Genetic
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.90.22.10648

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.