DNA triplex formation by base, backbone, and sugar-ring modified oligonucleotides with HIV targets

Triplex forming oligonucleotides (TFOs) bind to polypurine tracts in the major groove of DNA. This thesis describes studies on TFOs that target the env- and gag-genes of HIV-1 proviral DNA. Interactions between nuclease resistant, 5′-psoralen conjugated, chimeric methylphosphonate oligodeoxyribo- or oligo-2′ -O-methylribo-triplex forming oligomers (psTFOs), and the purine tract of env-DNA were investigated by gel mobility shift assays. A pyrimidine, chimeric methylphosphonate psTFO composed of thymidine and 5-methyl-2 ′-deoxycytidine, formed a stable triplex with env-DNA (apparent Kd = 1.3 μM). The apparent Kd of another chimeric psTFO decreased to 400 nM when four thymidines were replaced with 5-propynyl-2′ -deoxyuridines. The apparent Kd of the all-phosphodiester counterpart TFOs decreased to 50 nM. A chimeric oligo-2′-O-methylribopyrimidine formed a stable triplex (apparent Kd = 1.4 μM). Antiparallel A/G oligomers and parallel or antiparallel T/G oligomers did not form triplexes.; Thermal denaturation experiments were used to investigate interactions of psTFOs with env-DNA or gag-DNA targets. Triplex stability of a deoxy-env-psTFO containing 5-methylcytosines and thymines decreased with increasing pH. Replacement of 5-methylcytosines with 8-oxo-adenines reduced pH dependence but lowered triplex stability. A 2′-O-methyl-env-psTFO containing uracil and cytosine did not form a triplex at pH 7.5. Replacement of cytosines with 5-methylcytosines increased triplex stability, and greater stability was achieved by selective replacement of uracils with thymines. Substitution of contiguous 5-methylcytosines in a deoxy-gag-psTFO with 8-oxo-adenines reduced pH dependence and increased triplex stability. Triplexes formed by 2′-O-methyl-gag-psTFOs did not show enhanced stability. Replacement of the TFO 3′-terminal phosphodiester with a methylphosphonate increased nuclease resistance of deoxy- and 2′-O-methyl-TFOs.; In vitro transcription experiments were performed to determine the effect of psTFOs on transcription of pGEM®-3Z plasmids containing the env-DNA insert. Two env-specific and two gag-specific psTFOs were investigated. Non-specific inhibition of transcription was observed in the presence all psTFOs, with and without UV irradiation. Upon irradiation, specific inhibition of synthesis of the full length transcript was observed in the presence of env-specific psTFOs. Thus, all four psTFOs demonstrated non-specific inhibition of transcription of the env-DNA target. Specific inhibition of transcription was only observed when the env-specific psTFOs were covalently crosslinked to env-DNA.