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Updated: Apr 18, 2026
13:07
Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells
Published on: January 30, 2019
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Structural Basis of Polypurine Track Strand Displacement by HIV-1 Reverse Transcriptase
Xin Wen1, Rachel Lee1, Sri Dhanya Muppalla2
1Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA.
Biorxiv : the Preprint Server for Biology
|April 17, 2026
Summary
HIV-1 reverse transcriptase (RT) uses a unique template flip mechanism to displace polypurine tract (PPT) primers during reverse transcription. This discovery reveals a new vulnerability for designing next-generation antiretrovirals.
Area of Science:
- Structural Biology
- Virology
- Biochemistry
Background:
- Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is essential for viral replication.
- RT must displace polypurine tract (PPT) primers to complete reverse transcription and form viral DNA.
- The molecular mechanism of PPT strand displacement (SD) by RT was previously unknown.
Purpose of the Study:
- To elucidate the structural mechanism of PPT strand displacement by HIV-1 RT.
- To provide the first structural insights into how retroviral polymerases perform PPT SD.
Main Methods:
- Cryo-electron microscopy (cryo-EM) to determine structures of HIV-1 RT bound to nucleic acid substrates.
- Biochemical and virological mutagenesis experiments to validate structural findings.
Main Results:
- First cryo-EM structures of HIV-1 RT with PPT RNA or DNA displacement strands.
- Identified a novel binding mode involving a 90° template nucleotide flip.
- Key RT residues (F61, R78, W24) identified at the strand displacement interface.
- Mutagenesis confirmed essential roles for F61/R78 in polymerization and SD, and W24 exclusively in SD.
Conclusions:
- The study reveals the molecular mechanism of PPT strand displacement by HIV-1 RT.
- Identified specific RT-nucleic acid interactions driving PPT SD.
- These findings highlight a potential mechanistic vulnerability for antiretroviral drug design.
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