Staying straight with A-tracts: a DNA analog of the HIV-1 polypurine tract

J Mol Biol. 2003 Jun 27;330(1):57-74. doi: 10.1016/s0022-2836(03)00554-0.


The polypurine tract (PPT) from the HIV-1 genome is resistant to digestion by reverse transcriptase following (-)-strand synthesis and is used to prime (+)-strand synthesis during retroviral replication. We have determined the crystal structure of the asymmetric DNA/DNA analog16-mer duplex (CTTTTTAAAAGAAAAG/CTTTTCTTTTAAAAAG) comprising most of the "visible" portion of the RNA:DNA hybrid from the polypurine tract of HIV-1, which was previously reported in a complex with HIV-1 reverse transcriptase. Our 16-mer completely encompasses a 10-mer DNA duplex analog of the HIV-1 PPT. We report here a detailed analysis of our B' form 16-mer DNA structure, including three full pure A-tracts, as well as a comparative structural analysis with polypurine tract and other A-tract-containing nucleic acid structures. Our analysis reveals that the polypurine tract structures share structural features despite being different nucleic acid forms (i.e. DNA:DNA versus RNA:DNA). In addition, the previously reported A-tract-containing DNA molecules bound to topoisomerase I are remarkably similar to our polypurine tract 16-mer structure. On the basis of our analysis, we suggest that the specific topology of long pure A-tracts is remarkably comparable across a wide array of biological environments.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • DNA Topoisomerases, Type I / chemistry
  • DNA Topoisomerases, Type I / metabolism
  • DNA, Viral / chemistry*
  • DNA, Viral / metabolism
  • HIV-1 / genetics*
  • Moloney murine leukemia virus / enzymology
  • Nucleic Acid Conformation
  • Nucleic Acid Hybridization
  • Poly A / chemistry*
  • Poly A / metabolism
  • Purines / chemistry*
  • RNA, Viral / chemistry
  • RNA-Directed DNA Polymerase / chemistry
  • RNA-Directed DNA Polymerase / metabolism


  • DNA, Viral
  • Purines
  • RNA, Viral
  • Poly A
  • RNA-Directed DNA Polymerase
  • DNA Topoisomerases, Type I

Associated data

  • PDB/1N4L