Satoru Tsukahara

The influence of oligodeoxyribonucleotide phosphorothioate pyrimidine strands on triplex formation

Analogues of the homopyrimidine oligonucleotide dT15 that contained phosphorothioate bonds of a mixture of diastereoisomers or one of the two stereoisomers (either Rp or Sp) were synthesized. The analogues were mixed under conditions conducive to the formation of triple‐stranded assemblies. The mixtures were characterized by their thermal stabilities (T m values), CD spectra, and gel electrophoresis pattern. The 34‐mer duplexes containing 15 central purines on one strand and 15 complementary pyrimidines on the other strand gave no detectable triple helix upon combination with dT15S14. On the other hand, 34‐bp duplexes with dT15S1, having Rp or Sp, formed triple helixes. This suggests that a steric factor plays an important role in triple helix formation.

Inhibition of HIV-1 replication by a two-strand system (FTFOs) targeted to the polypurine tract

Reverse transcription of HIV‐1 vRNA into the double‐stranded DNA provirus involves initiation of plus‐strand DNA synthesis at the polypurine tract (PPT) by reverse transcriptase (RT). The PPT is highly conserved among the known human immunodeficiency virus (HIV‐1) strains and is a possible target for triplex formation. We show the effects of triple‐helix formation by assays of primer extension inhibition in vitro, using a two‐strand system (foldback triplex‐forming oligonucleotides (FTFOs)) targeted to the PPT of HIV‐1. The two‐stranded composition of a triple‐helix is thermodynamically and kinetically superior to the three‐strand system. The FTFOs inhibited the RT activity in a sequence‐specific manner, i.e. the triplex actually formed at the PPT and blocked the RT. The FTFOs containing the phosphorothioate groups at the antisense sequences showed greater 3′‐exonuclease resistance. In HIV‐1‐infected MOLT‐4 cells, the FTFOs containing the phosphorothioate groups at the antisense sequence sites and guanosine rich parts within the third Hoogsteen base‐pairing sequence inhibit the replication of HIV‐1 more effectively than the antisense oligonucleotides, indicating sequence‐specific inhibition of HIV‐1 replication.

PH-INDEPENDENT INHIBITION OF RESTRICTION ENDONUCLEASE CLEAVAGE VIA TRIPLE HELIX FORMATION BY OLIGONUCLEOTIDES CONTAINING 8-OXO-2'-DEOXYADENOSINE

The ability of homopyrimidine oligonucleotides containing 8‐oxo‐2′‐deoxyadenosine to form stable, triple helical structures with the sequence containing the recognition site for the class II‐S restriction enzyme, Ksp632‐I, was studied as a function of pH. The 8‐oxo‐2′‐deoxyadenosine‐substituted oligomers were shown to inhibit enzymatic cleavage and to bind within the physiological pH range in a pH‐independent fashion without compromising specificity.

Anti-HIV-1 Activity by a Triple-Helix Forming Oligonucleotides Targeted to Polypurine Tract on Viral RNA

Abstract Reverse transcription of HIV-1 into double-stranded DNA involves initiation of plus-strand DNA synthesis at the polypurine tract, PPT, by reverse transcriptase (RT). The PPT is a possible target for triple-helix formation. We show the effects of triple-helix formation by assays of RNase H cleavage inhibition in vitro using two systems (two-strand-system (FTFOs) or three-strand-system (TFOs)) targeted to the polypurine tract (PPT) of HIV-1. The two-stranded composition of a triple-helix is thermodynamically and kinetically superior to the three-strand-system. The FTFOs inhibited the RNase H activity in a sequence-specific manner, i.e., the triplex actually formed at the PPT and blocked the RNase H. The FTFOs containing the phosphorothioate groups at the antisense strand showed greater 3′-exonuclease resistance. In HIV-1 infected MT-4 cells, the FTFOs containing the phosphorothioate groups at the antisense strand and guanosine rich parts within the third Hoogsteen base pairing sequence inhibit the replication of HIV-1 more effectively than the antisense phosphorothioate oligonucleotides, indicating sequence-specific inhibition of HIV-1 replication.

Inhibition of Restriction Enzyme Ksp 632-I Via Triple Helix Formation by Phosphorothioate Oligonucleotides

Abstract The ability of pyrimidine-rich oligonucleotide phosphorothioate to form stable triple helical structures with the sequence containing the recognition site for the class II-S restriction enzyme Ksp 632-I was examined. First, we prepared double strand oligonucleotides corresponding to the major groove of SV40 DNA at 17 base pair homopurine-homopyrimidine sequences, and studied their interaction with homopyrimidine oligodeoxyribonucleotides including replacement of the PS group in the second nucleotide position from the 5′-terminus (SO-ODNs) and of the PS group at both the 3′- and 5′-ends (S2O-ODNs). The resulting perfect DNA triplexes were detected by the gel-mobility shift. The phosphorothioate oligonucleotide analogues (SO-ODNs) and (S2O-ODNs) were shown to inhibit enzymatic cleavage under conditions that allow for triple helix formation. Inhibition is sequence-specific and occurs in the micromolar concentration range. Of particular interest is the Sp-phosphorothioate analogue (Sp-SO-ODNs) which ...