Mutations in the U5 region adjacent to the primer binding site affect tRNA cleavage by human immunodeficiency virus type 1 reverse transcriptase in vivo

J Virol. 2008 Jan;82(2):719-27. doi: 10.1128/JVI.02611-06. Epub 2007 Nov 7.


In retroviruses, the first nucleotide added to the tRNA primer defines the end of the U5 region in the right long terminal repeat, and the subsequent removal of this tRNA primer by RNase H exactly defines the U5 end of the linear double-stranded DNA. In most retroviruses, the entire tRNA is removed by RNase H cleavage at the RNA/DNA junction. However, the RNase H domain of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase cleaves the tRNA 1 nucleotide from the RNA/DNA junction at the U5/primer binding site (PBS) junction, which leaves an rA residue at the U5 terminus. We made sequence changes at the end of the U5 region adjacent to the PBS in HIV-1 to determine whether such changes affect the specificity of tRNA primer cleavage by RNase H. In some of the mutants, RNase H usually removed the entire tRNA, showing that the cleavage specificity was shifted by 1 nucleotide. This result suggests that the tRNA cleavage specificity of the HIV-1 RNase domain H depends on sequences in U5.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Binding Sites
  • Cell Line
  • HIV Reverse Transcriptase / chemistry
  • HIV Reverse Transcriptase / genetics
  • HIV Reverse Transcriptase / metabolism*
  • HIV-1 / genetics
  • HIV-1 / physiology*
  • Humans
  • Mutant Proteins / genetics
  • Mutant Proteins / metabolism*
  • RNA, Transfer / metabolism*
  • Substrate Specificity / genetics*


  • Mutant Proteins
  • RNA, Transfer
  • reverse transcriptase, Human immunodeficiency virus 1
  • HIV Reverse Transcriptase