STRAND-INVASION OF DUPLEX DNA BY PEPTIDE NUCLEIC-ACID OLIGOMERS

Polyamide oligomers, termed peptide nucleic acids (PNAs), bind with hi gh affinity to both DNA and RNA and offer both antisense and antigene approaches for regulating gene expression. When a PNA binds to a compl ementary sequence in a double-stranded DNA, one strand of the duplex i s displaced, and a stable D-loop is formed. Unlike oligodeoxynucleotid es 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 evi dence 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-seque nce 15-mer PNA, kinetic studies of PNA-DNA interactions revealed that D-loop formation was rapid and the complex was stable for several hour s. However, when measured either by gel-mobility-shift analysis or RNA polymerase II-elongation termination, D-loop formation was salt depen dent, 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 DN A termini. On the basis of permutation analysis, the decreased mobilit y of the PNA.DNA complex was attributed to a bend in the DNA at or nea r the D-loop.