3'-Hairpin oligonucleotides containing phosphodiester or phosphorothioate backbone in the loop portion of the oligonucleotides were synthesized and their binding to Moloney murine leukemia virus (MMLV) Reverse transcriptase (RT) was evaluated using Polyacrylamide gel electrophoresis (PAGE) band mobility shift assay. The dissociation constants were in the micro molar range. The inhibitory activity of the RNase H activity of MMLV reverse transcriptase was studied in vitro using ³H-UTP-labeled RNA: RNA-DNA hybrid. The oligonucleotide containing phosphorothioates linkage at 3'-loop portion showed inhibition of RNase H activity with IC₅₀ falling in the range of 140-150 nM which is lower than tenofovir a nucleotide drug used for curing Acquired immuno deficiency syndrome (AIDS).

Retroviruses are the etiological agents of several forms of cancer and Acquired immuno deficiency syndrome (AIDS) (Brre-Sinoussi et al., 1983; and Popovic et al., 1984). The viral replication cycle requires conversion of single stranded RNA genome into double-stranded DNA. Reverse transcriptase (RT), the enzyme responsible for viral genome replication is multifunctional and bears an RNA and a DNA dependent DNA polymerase activity and also RNase H activity (Varmus and Swanstrom, 1984; Di Marzo Veronase et al., 1986; and Starnes et al., 1988). RNase H is required for: (1) degradation of viral genome RNA after RNA directed first strand DNA synthesis has occurred; (2) generating primers for second strand synthesis; and (3) eliminating the tRNA primer (Champoux et al., 1993). Therefore, any ligand able to block the RNase H activity would prevent the development of retroviruses. Moloney murine leukemia virus (MMLV) RT is 80 Kda monomer protein and possesses all the above three activities (Verma, 1975). Up to now very few molecules have shown RNase H inhibitory activity (Hostomsky et al., 1993). Although the catalytic activity of RNase H is restricted to RNA-DNA hybrids, these enzymes can bind to different duplexes as well as single-stranded nucleic acids, dumbbell oligonucleotides and 3'-hairpin oligonucleotides. 3'-hairpin oligonucleotides display significant nuclease resistance, therefore they should be considered as good candidates to design RNase H inhibitors (Khan and Coulson, 1993). Recently, it has been shown that hairpin, dumbbell, and single-stranded phosphodiester oligonucleotides exhibit identical uptake in T lymphocyte cell lines (Aguilar et al., 2009). The paper describes the binding studies of the hairpin oligonucleotides to RT of MMLV and inhibition of RNase H activity.

Biotechnology Journal, Hairpin Oligonucleotides, Moloney Murine Leukemia Virus, MMLV, Reverse Transcriptase, RT, RNase H Activity, IC₅₀ , Polyacrylamide Gel Electrophoresis, PAGE, Acquired Immuno Deficiency Syndrome, AIDS, Viral Replication Cycle, Antisense Oligonucleotides, Oligonucleotide Concentration.