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

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

Protein Sci

Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854.

Published: January 2016

AI Article Synopsis

  • - A new DNA aptamer that binds to HIV-1 reverse transcriptase (RT) has been created, allowing researchers to determine the X-ray structure of the RT-DNA complex at a resolution of 2.3 Å without using antibodies or cross-linking methods.
  • - The aptamer is a 38-nucleotide hairpin structure that effectively positions itself at the RT's polymerase active site, featuring specific modifications that enhance its interaction with the enzyme.
  • - This high-resolution structure not only provides insights into the mechanics of RT but also serves as a potential platform for developing new anti-HIV drugs and understanding the aptamer's unique design and high affinity for RT.

Article 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.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815302PMC
http://dx.doi.org/10.1002/pro.2776DOI Listing

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