Long sequence duplications, repeats, and palindromes in HIV-1 gp120: Length variation in V4 as the product of misalignment mechanism

Silvia Guglietta, Giuseppe Pantaleo, Cecilia Graziosi

Research output: Contribution to journalArticlepeer-review

Abstract

We have shown that indels in gp120 V4 are associated to the presence of duplicated and palindromic sequences, suggesting that they may be produced by strand-slippage misalignment mechanism. Indels in V4 involved region-specific duplications 9 to 15 bp long, and repeats of various lengths, associated to trinucleotides AAT. No duplications were found in V3 and C3. The frequency of palindromic sequences in individual genes was found to be significantly higher in gp120 (p ≤ 3.00E-7), and significantly lower in Tat (p ≤ 9.00E-7) than the average frequency calculated over the full genome. The finding of elements of misalignment in association with indels in V4 suggests that these mutations may occur in proviral DNA after integration of HIV into the host genome. It also implies that occurrence of large indels in gp120 is not random but is directed by the presence and distribution of elements of misalignment in the HIV genome.

Original languageEnglish
Pages (from-to)167-175
Number of pages9
JournalVirology
Volume399
Issue number1
DOIs
Publication statusPublished - Mar 30 2010

Keywords

  • gp120
  • HIV
  • Indels
  • Misalignment
  • Mutation
  • V4

ASJC Scopus subject areas

  • Virology

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