STABLE TRIPLE HELICES FORMED BY OLIGONUCLEOTIDE N3'-]P5' PHOSPHORAMIDATES INHIBIT TRANSCRIPTION ELONGATION

Oligonucleotide analogs with N3' --> P5' phosphoramidate linkages bind to the major groove of double-helical DNA at specific oligopurine oli gopyrimidine sequences. These triple-helical complexes are much more s table than those formed by oligonucleotides with natural phosphodieste r linkages. Oligonucleotide phosphoramidates containing thymine and cy tosine or thymine, cytosine, and guanine bind strongly to the polypuri ne tract of human immunodeficiency virus proviral DNA under physiologi cal conditions. Site-specific cleavage by the Dra I restriction enzyme at the 5' end of the polypurine sequence was inhibited by tripler for mation. A eukaryotic transcription assay was used to investigate the e ffect of oligophosphoramidate binding to the polypurine tract sequence on transcription of the type 1 human immunodeficiency virus nef gene under the control of a cytomegalovirus promoter. An efficient arrest o f RNA polymerase II was observed at the specific tripler site at submi cromolar concentrations.