Comparison of interactions of 5?-derivatives of deoxyoctathymidylate with human DNA polymerize ? and HIV reverse transcriptase

Abstract

Km and Vmax values for d(pT8) and its derivatives containing various 5'-end groups were estimated in the reaction of DNA polymerization alpha catalyzed by DNA polymerase alpha and HIV-RT. The effect of 5'-end modification of primer is more pronounced in the case of HIV-RT. Strong influence is observed for an intercalating (ethidium) group. The affinity of EtpT8 is 200-fold higher than that of d(pT8). Attachment of Phn-, Dnm- and Hem-groups results in the increase of affinity of modified primer from 10 up to 20 times. For DNA polymerase alpha the influence of modifiers on primer affinity is much weaker. The effect of 5'-end residues on the Vmax values is also more pronounced for HIV RT. The way to improve selective interaction of oligonucleotide derivatives with the primer site of HIV RT is suggested.

Interaction of Oligonucleotides Conjugated to Substituted Chromones and Coumarins with HIV-1 Reverse Transcriptase

“…Because such compounds significantly increased the stability of complexes formed by complementary ODNs in solution (Balbi et al, 1994(Balbi et al, , 1997, it was reasonable to suppose that the observed increase in primer affinity was due to the intercalating properties of these compounds. Although we have already shown that the ethidium group had an important effect on the interaction between RT and primer (Khodyreva et al, 1993), its influence was markedly lower than that produced by the two new modifying groups.…”

“…At the same time, it should be noted that the features of DNA interaction with some compounds in solution cannot always be extrapolated to the interaction of nucleic acids in complexes with enzymes, because the latter cause substantial structural changes in the nucleic acid regions situated within the protein globule (for review, see Nevinsky, 1995). For example, ODNs containing the 5'terminal phenazine group demonstrated a comparable affinity for complementary DNA and RNA in solution, while the affinity of the derivative of d(pT)8 was about two orders of magnitude higher for poly(A) than that for poly(dA) template in their complexes with HIV-1 RT (Khodyreva et al, 1993). Such changes in the interaction seem to result from alterations in nucleic acid structure after binding to the enzyme.…”

“…Some additional groups can stabilize DNA duplexes not only in solution, but also in their complexes with enzymes. We have shown that the attachment of phenazine, ethidium, deuteroporphyrin, or daunomycin enhanced the affinity of primers for avian myeloblastosis virus (AMV) (Lokhova et al, 1991) and HIV-1 RTs (Khodyreva et al, 1993) from 10to 20-fold. At the same time, it should be noted that the features of DNA interaction with some compounds in solution cannot always be extrapolated to the interaction of nucleic acids in complexes with enzymes, because the latter cause substantial structural changes in the nucleic acid regions situated within the protein globule (for review, see Nevinsky, 1995).…”

HIV‐1 integrase inhibition by pyrrole/imidazole‐containing polyamides

“…In the interaction of nucleic acid with different compounds including MGBs, there may be significant differences depending on whether they are free or complexed with enzymes (38–40). For example, oligonucleotides containing the phenazinium group at the 5′‐end showed a similar affinity for the complementary DNA or RNA in solution, while the affinity of these derivatives for the nucleic acids was about two orders of magnitude higher in their complexes with HIV‐1 RT (41). Thiazole containing polyamides demonstrated significantly higher affinity to RNA·DNA complexes with HIV‐1 RT than to the same RNA·DNA duplexes in solution (30).…”