Mechanistic studies of early pausing events during initiation of HIV-1 reverse transcription

J Biol Chem. 1998 Aug 14;273(33):21309-15. doi: 10.1074/jbc.273.33.21309.


We have investigated the role of sequences that surround the primer binding site (PBS) in the reverse transcriptase-mediated initiation of (-) strand DNA synthesis in human immunodeficiency virus type 1. In comparisons of reverse transcription initiated from either the cognate primer tRNALys.3 or a DNA primer D-Lys.3, bound to PBS sequences, we observed that a +3 pausing site occurred in both circumstances. However, the initiation reaction with tRNALys.3 was also characterized by a pausing event after incorporation of the first nucleotide. Alteration of sequences at the 5'-end instead of the 3'-end of the PBS resulted in elimination of the +3 pausing site, suggesting that this site was template sequence-dependent. In contrast, the pausing event at the +1 nucleotide position was still present in experiments that employed either of these mutated RNA templates. The mutations at the 5'-end of the PBS also caused a severely diminished rate of initiation and the strong arrest of reactions at the +1 stage when tRNALys.3 was used as primer. Therefore, we propose that the +1 pausing event is an initiation-specific event in regard to reactions primed by tRNALys.3 and that sequences at the 5'-end of the PBS may facilitate the release of reverse transcription from initiation to elongation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • DNA Primers
  • DNA Replication
  • DNA, Viral / biosynthesis
  • HIV Reverse Transcriptase / metabolism
  • HIV-1 / genetics*
  • Mutagenesis
  • Nucleic Acid Conformation
  • RNA, Transfer, Lys / chemistry
  • RNA, Transfer, Lys / metabolism
  • RNA, Viral / chemistry
  • RNA, Viral / metabolism
  • Transcription, Genetic*


  • DNA Primers
  • DNA, Viral
  • RNA, Transfer, Lys
  • RNA, Viral
  • HIV Reverse Transcriptase