title: Structure of HIV-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer.
abstract: 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.
authors: Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854.
authors: Matthew T
authors: MT
authors: Miller
authors: Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854.
authors: Steve
authors: S
authors: Tuske
authors: Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854.
authors: Kalyan
authors: K
authors: Das
authors: Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, Maryland, 20742.
authors: Jeffrey J
authors: JJ
authors: DeStefano
authors: Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854.
authors: Eddy
authors: E
authors: Arnold
mesh_terms: D019380:Anti-HIV Agents / Q000737:chemistry; D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites; D017931:DNA Primers / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D054303:HIV Reverse Transcriptase / Q000737:chemistry* / Q000378:metabolism; D015497:HIV-1 / Q000201:enzymology; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D018894:Reverse Transcriptase Inhibitors / Q000737:chemistry; D013329:Structure-Activity Relationship; D013698:Templates, Genetic
chemical_list: D019380:Anti-HIV Agents; D052157:Aptamers, Nucleotide; D017931:DNA Primers; D018894:Reverse Transcriptase Inhibitors; C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase
keywords: 2′-O-methylcytidine; DNA aptamer; HIV; SELEX; p66/p51; reverse transcriptase