Slide into Action: Dynamic Shuttling of HIV Reverse Transcriptase on Nucleic Acid Substrates

Shixin Liu,1 Elio A. Abbondanzieri,1 Jason W. Rausch,4 Stuart F. J. Le Grice,4 Xiaowei Zhuang1,2,3*

The reverse transcriptase (RT) of human immunodeficiency virus (HIV) catalyzes a series of reactions to convert single-stranded viral RNA into double-stranded DNA for host cell integration. This process requires a variety of enzymatic activities, including DNA polymerization, RNA cleavage, strand transfer, and strand displacement synthesis. We used single-molecule fluorescence resonance energy transfer to probe the interactions between RT and nucleic acid substrates in real time. RT was observed to slide on nucleic acid duplexes, rapidly shuttling between opposite termini of the duplex. Upon reaching the DNA 3' terminus, RT can spontaneously flip into a polymerization orientation. Sliding kinetics were regulated by cognate nucleotides and anti-HIV drugs, which stabilized and destabilized the polymerization mode, respectively. These long-range translocation activities facilitate multiple stages of the reverse transcription pathway, including normal DNA polymerization and strand displacement synthesis.

1 Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
2 Department of Physics, Harvard University, Cambridge, MA 02138, USA.
3 Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
4 HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA.