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Selection of primer-template sequences that bind human immunodeficiency virus reverse transcriptase with high

Jeffrey J DeStefano1, Jason V Cristofaro

  • 1Department of Cell Biology and Molecular Genetics, University of Maryland, Building 231, College Park, MD 20742, USA. jdestefa@umd.edu

Nucleic Acids Research
|January 7, 2006
PubMed
Summary

Researchers used systematic evolution of ligands by exponential enrichment (SELEX) to find HIV-RT primer-template preferences. They discovered HIV-RT strongly binds sequences with a G-rich run at the primer terminus.

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Area of Science:

  • Molecular Biology
  • Virology
  • Biochemistry

Background:

  • Human immunodeficiency virus reverse transcriptase (HIV-RT) is a key enzyme in viral replication.
  • Understanding primer-template sequence preferences of HIV-RT is crucial for developing antiviral therapies.
  • Previous studies have not fully elucidated specific sequence requirements for optimal HIV-RT binding.

Purpose of the Study:

  • To investigate primer-template sequence specificity for HIV-RT using a SELEX approach.
  • To identify DNA sequences that exhibit high affinity for HIV-RT.
  • To determine the structural features of preferred primer-template sequences.

Main Methods:

  • Systematic evolution of ligands by exponential enrichment (SELEX) was employed.
  • A DNA substrate with fixed flanking sequences and a randomized internal region was designed.

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  • HIV-RT binding was assessed using gel-shift assays, followed by PCR amplification and selection over 12 rounds.

    • Main Results:

    • SELEX identified primer-template sequences with significantly enhanced binding affinity (approx. 10-fold) after 12 rounds.
    • Selected sequences consistently featured a 6-8 base guanine (G) run at the 3' primer terminus.
    • Further modifications confirmed the necessity and sufficiency of G-runs for strong HIV-RT binding.

    Conclusions:

    • HIV-RT exhibits a strong preference for primer-template sequences containing a G-rich run at the 3' primer terminus.
    • This G-rich motif resembles the HIV polypurine tract, suggesting functional relevance.
    • The findings provide insights into HIV-RT substrate recognition and can inform the design of inhibitors.