The structure of an RNA/DNA hybrid: A substrate of the ribonuclease activity of HIV-1 reverse transcriptase

Nancy C. Horton, Barry C. Finzel

Research output: Contribution to journalArticlepeer-review

87 Scopus citations


The structure of a complementary hybrid duplex of RNA and DNA has been determined by X-ray crystallography. A ten residue DNA oligonucleotide of sequence 5'-G-G-C-G-C-C-C-G-A-A-3' was annealed to complementary RNA (5'-u-u-c-g-g-g-c-g-c-c-3') and crystallized, producing tetragonal crystals that diffract to 2.3 Å resolution. The hybrid adopts a geometry that is neither strictly A nor B-form, rather the helix possesses qualities of both, reminiscent of spectroscopic descriptions of a hybrid conformation, or H-form. All of the ribonucleotides maintain the C3'-endo conformation seen in A-form, while both CS'-endo and C2'-endo conformations are found in the deoxyribonucleotides. The minor groove width (8.5 to 10.5 Å) is intermediate between standard values for A (11 Å) and B-form (7.4 Å) DNA. The global parameters rise and base-pairs tilt (or inclination) are like that of A-DNA, however the slide and x: displacement (Dx) are more like that of A-RNA, thus giving the hybrid a unique conformation. In addition, the 10-mer crystallizes in a manner that allows the formation of dimers that stack end-to-end, thereby providing a glimpse of how an extended (20 base-pair) helix of RNA-DNA hybrid might appear. This duplex sequence was selected for study because it is specifically recognized by the ribonuclease H function of HIV reverse transcriptase. A structure of a substrate of this enzyme is of potential value in understanding requirements for the selectivity of this important drug target. The minor groove of the hybrid duplex, lined with the 2-OH of the ribose rings, is the single distinguishing characteristic of the RNA/DNA hybrid, undoubtedly an important structural feature conferring selectivity.

Original languageEnglish (US)
Pages (from-to)521-533
Number of pages13
JournalJournal of Molecular Biology
Issue number3
StatePublished - Dec 6 1996


  • Drug target
  • HIV reverse transcriptase
  • RNA/DNA hybrid
  • RNase H
  • X-ray structure

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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