Rapid characterization of HIV-1 sequence diversity using denaturing gradient gel electrophoresis and direct automated DNA sequencing of PCR products

Björn Andersson, Ying Jia-Hsu, Dorothy E. Lewis, Richard A. Gibbs

Research output: Contribution to journalArticle

8 Scopus citations

Abstract

A direct method for visualization and isolation of sequence variants of human immunodeficiency virus type 1 (HIV-1) utilizing denaturing gradient gel electrophoresis (DGGE) combined with automated direct DNA sequencing was developed. Two fragments from the env gene and one from the nef gene of HIV-1, which together constitute approximately 1.0 kb of sequence, were amplified by PCR and analyzed. HIV-1 variants from each region were resolved and excised from the gel; this was followed by direct sequencing of different viral variants. In 9 infected patients, a limited number of dominant sequence variants could be seen in the three regions, together with a faint background of minor variants. The use of DGGE makes it possible to obtain a direct estimate of overall HIV-1 sequence diversity within patient samples without an intermediate DNA cloning step.

Original languageEnglish (US)
Pages (from-to)293-300
Number of pages8
JournalGenome Research
Volume2
Issue number4
DOIs
StatePublished - 1993

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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