Structure of HIV-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer

Protein Sci. 2016 Jan;25(1):46-55. doi: 10.1002/pro.2776. Epub 2015 Sep 18.


The development of a modified DNA aptamer that binds HIV-1 reverse transcriptase (RT) with ultra-high affinity has enabled the X-ray structure determination of an HIV-1 RT-DNA complex to 2.3 Å resolution without the need for an antibody Fab fragment or RT-DNA cross-linking. The 38-mer hairpin-DNA aptamer has a 15 base-pair duplex, a three-deoxythymidine hairpin loop, and a five-nucleotide 5'-overhang. The aptamer binds RT in a template-primer configuration with the 3'-end positioned at the polymerase active site and has 2'-O-methyl modifications at the second and fourth duplex template nucleotides that interact with the p66 fingers and palm subdomains. This structure represents the highest resolution RT-nucleic acid structure to date. The RT-aptamer complex is catalytically active and can serve as a platform for studying fundamental RT mechanisms and for development of anti-HIV inhibitors through fragment screening and other approaches. Additionally, the structure allows for a detailed look at a unique aptamer design and provides the molecular basis for its remarkably high affinity for RT.

Keywords: 2′-O-methylcytidine; DNA aptamer; HIV; SELEX; p66/p51; reverse transcriptase.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Anti-HIV Agents / chemistry
  • Aptamers, Nucleotide / chemistry*
  • Aptamers, Nucleotide / genetics*
  • Aptamers, Nucleotide / metabolism
  • Binding Sites
  • DNA Primers / chemistry*
  • DNA Primers / genetics
  • DNA Primers / metabolism
  • HIV Reverse Transcriptase / chemistry*
  • HIV Reverse Transcriptase / metabolism
  • HIV-1 / enzymology
  • Models, Molecular
  • Nucleic Acid Conformation*
  • Protein Conformation
  • Reverse Transcriptase Inhibitors / chemistry
  • Structure-Activity Relationship
  • Templates, Genetic


  • Anti-HIV Agents
  • Aptamers, Nucleotide
  • DNA Primers
  • Reverse Transcriptase Inhibitors
  • reverse transcriptase, Human immunodeficiency virus 1
  • HIV Reverse Transcriptase