Derivation of primary sequences and secondary structures of rev responsive element from HIV-1 infected mothers and infants following vertical transmission

Rajesh Ramakrishnan, Nafees Ahmad

Research output: Contribution to journalArticle

4 Scopus citations

Abstract

We have characterized the primary RRE sequences of HIV-1, including in vivo genetic variation and functional motifs required for Rev-RRE interactions as well as evaluated the RNA secondary structures of RRE derived from five mother-infant pairs following vertical transmission. Multiple (157) RRE sequences derived from mother-infant pairs showed that primary nucleotide sequences of RRE were highly conserved with a low degree of viral heterogeneity following vertical transmission. We found that the RRE sequences from mothers and infants folded and retained all the essential stem-loop formation required for Rev-RRE interactions. More importantly, a primary 9-nucleotide (5′-CACTATGGG-3′) RRE sequence in the stem-loop B that is required for optimal Rev recognition and must be presented as a stem-bulge-stem structure was highly conserved in most of the sequences. The domains required for RRE-host protein interactions were also conserved in most of the RRE sequences. Taken together, the primary RRE sequences in the context of secondary structures were maintained and the Rev-RRE interaction domains were conserved following vertical transmission, which is consistent with a crucial role of RRE in HIV-1 pathogenesis.

Original languageEnglish (US)
Pages (from-to)201-211
Number of pages11
JournalVirology
Volume359
Issue number1
DOIs
StatePublished - Mar 1 2007

Keywords

  • HIV-1
  • HIV-1 vertical transmission
  • RRE
  • RRE secondary structures
  • RRE variation
  • Rev-RRE

ASJC Scopus subject areas

  • Virology

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