Inhibition of Replication of Fresh HIV Type 1 Patient Isolates by a Polypurine Tract-Specific Self-Complementary Oligodeoxynucleotide

Abstract

A previously described self-complementary oligodeoxynucleotide termed triplex-forming oligodeoxynucleotide (TFO A), 54 bases in length, designed against the polypurine tract of HIV-1 RNA, inhibited viral replication at a 1 to 3 microM concentration in acutely infected cells, whereas antisense and scrambled sequence oligodeoxynucleotides were ineffective. Three HIV-1 viral isolates from patients of clinical categories A1, B, and C3 were transmitted to peripheral blood mononuclear cells and tested for production of p24 antigen and syncytium formation in the absence and in the presence of either TFO A or a control oligodeoxynucleotide of randomized sequence. No p24 antigen or syncytia were detected for up to 30 days when TFO A was added to the cells. Viability of the cells was found not to be affected by the drugs compared to controls within 2 weeks. Analysis of viral DNA synthesis by PCR for the LTR and gag gene indicated no DNA signal, suggesting that TFO A affects viral replication before formation of a DNA provirus. Measurements of the stability of TFO A indicate a half-life of about 2 hr. A two-dimensional computer fold analysis of TFO A suggested a self-complementary hairpin-loop configuration with GC-rich stems and single-stranded 5' and 3' ends. Since intracellular triplex formation may not be an efficient process, the observed inhibitory effect may be due to a direct inhibition of the RT and RNase H enzyme activities by the oligodeoxynucleotide. However, a triple-helix effect on the incoming RNA may play a role as well.

A Short Hairpin DNA Analogous to miR-125b Inhibits C-Raf Expression, Proliferation, and Survival of Breast Cancer Cells

“…Inhibition of translation has also been described for asDNA as secondary effect (14,15). ODNs are a special class of short hairpin-looped DNAs that can induce cleavage of viral RNAs via a retroviral or cellular RNase H and therefore are active as antiviral agents (16)(17)(18)(19)(20).…”

“…Thus, ODNRaf is a multifunctional molecule that reduces proliferation by inhibition of oncogene expression and induces cell death. (1,8,17,19,20,31,32). The 3′UTRs of mRNAs are preferred target sites for miRs and play an essential role in translational control and in the stability of transcripts (13,33).…”

Is antisense an appropriate nomenclature or design for oligodeoxynucleotides aimed at the inhibition of HIV-1 replication?

“…PS-ODNs are polyanions and, as a consequence, they are able to bind to various cellular proteins on the basis of charge interaction and base sequence (aptamer approach). 27,34 The presence of a Gquartet, along with particular sequences flanking the Gquartet, may also enhance non-specific effects. 28 Furthermore, CpG motifs have been found to be highly immunostimulatory in mice.…”

Relationship between Retroviral Replication and RNA Interference Machineries

“…A linker of four nucleotides connected the strands. The PPT is the site that resists RNase H digestion during reverse transcription of the first cDNA copy, then the RT initiates at this local hybrid the second cDNA strand including cleavage by the RNase H at the ACU site, where two non-purines interrupt the PPT (Jendis et al 1996(Jendis et al , 1998see Coffin et al 1997).…”

“…This resulted in inhibition of viral replication for 20 days without viral breakthrough (Jendis et al 1996). Patient isolates including resistant isolates against azidothymidin (AZT) were also inhibited.…”