Steric inhibition of human immunodeficiency virus type-1 Tat-dependent trans-activation in vitro and in cells by oligonucleotides containing 2'-O-methyl G-clamp ribonucleoside analogues

Nucleic Acids Res. 2003 Jun 1;31(11):2759-68. doi: 10.1093/nar/gkg384.

Abstract

We report the synthesis of a novel 2'-O-methyl (OMe) riboside phosphoramidite derivative of the G-clamp tricyclic base and incorporation into a series of small steric blocking OMe oligonucleotides targeting the apical stem-loop region of human immunodeficiency virus type 1 (HIV-1) trans- activation-responsive (TAR) RNA. Binding to TAR RNA is substantially enhanced for certain single site substitutions in the centre of the oligonucleotide, and doubly substituted anti-TAR OMe 9mers or 12mers exhibit remarkably low binding constants of <0.1 nM. G-clamp-containing oligomers achieved 50% inhibition of Tat-dependent in vitro transcription at approximately 25 nM, 4-fold lower than for a TAR 12mer OMe oligonucleotide and better than found for any other oligonucleotide tested to date. Addition of one or two OMe G-clamps did not impart cellular trans-activation inhibition activity to cellularly inactive OMe oligonucleotides. Addition of an OMe G-clamp to a 12mer OMe-locked nucleic acid chimera maintained, but did not enhance, inhibition of Tat-dependent in vitro transcription and cellular trans-activation in HeLa cells. The results demonstrate clearly that an OMe G-clamp has remarkable RNA-binding enhancement ability, but that oligonucleotide effectiveness in steric block inhibition of Tat-dependent trans-activation both in vitro and in cells is governed by factors more complex than RNA-binding strength alone.

MeSH terms

  • Anti-HIV Agents / chemistry
  • Anti-HIV Agents / metabolism
  • Anti-HIV Agents / pharmacology*
  • Base Sequence
  • Binding Sites
  • DNA / metabolism
  • Gene Products, tat / antagonists & inhibitors*
  • Gene Products, tat / genetics
  • HIV-1* / genetics
  • HeLa Cells
  • Humans
  • Methylation
  • Oligoribonucleotides / chemistry
  • Oligoribonucleotides / metabolism
  • Oligoribonucleotides / pharmacology*
  • Organophosphorus Compounds / chemistry
  • RNA, Viral / chemistry
  • RNA, Viral / metabolism
  • Ribonucleosides / chemical synthesis
  • Ribonucleosides / chemistry
  • Transcriptional Activation / drug effects*
  • tat Gene Products, Human Immunodeficiency Virus

Substances

  • Anti-HIV Agents
  • Gene Products, tat
  • Oligoribonucleotides
  • Organophosphorus Compounds
  • RNA, Viral
  • Ribonucleosides
  • phosphoramidite
  • tat Gene Products, Human Immunodeficiency Virus
  • DNA