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Journal of Virology, February 2002, p. 980-989, Vol. 76, No. 3
0022-538X/01/$04.00+0     DOI: 10.1128/JVI.76.3.980-989.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Small DNA Hairpin Negatively Regulates In Situ Priming during Duck Hepatitis B Virus Reverse Transcription

Jeffrey W. Habig and Daniel D. Loeb*

McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison, Wisconsin 53706

Received 13 August 2001/ Accepted 19 October 2001

There are two mutually exclusive pathways for plus-strand DNA synthesis in hepadnavirus reverse transcription. The predominant pathway gives rise to relaxed circular DNA, while the other pathway yields duplex linear DNA. Both pathways use the same RNA primer, which is capped and 18 or 19 nucleotides in length. At the completion of minus-strand DNA synthesis, the final RNase H cleavage generates the plus-strand primer. To make relaxed circular DNA, primer translocation must occur, resulting in the transfer of the primer generated at DR1 to the acceptor site (DR2) near the opposite end of the minus-strand DNA. A small fraction of viruses instead make duplex linear DNA after initiating plus-strand DNA synthesis from DR1, a process called in situ priming. We are interested in understanding the mechanism of discrimination between these two pathways. Some variants of duck hepatitis B virus exhibit high levels of in situ priming due to cis-acting mutations. The mechanism by which these mutations act has been obscure. Sequence inspection predicted formation of a small DNA hairpin in the region overlapping these mutations. We have shown that substitutions disrupting base pairing potential in this hairpin led to increased levels of in situ priming. The introduction of compensatory changes to restore base pairing potential led to reduced levels of in situ priming. Thus, formation of the small DNA hairpin overlapping the 5' end of DR1 in the minus strand contributes to the regulation of primer translocation, at least, through inhibition of in situ priming by making the 3' end of the minus-strand DNA a poor template for initiation.

* Corresponding author. Mailing address: McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, 1400 University Ave., Madison, WI 53706. Phone: (608) 262-1260. Fax: (608) 262-2824. E-mail: loeb{at}oncology.wisc.edu.

Journal of Virology, February 2002, p. 980-989, Vol. 76, No. 3
0022-538X/01/$04.00+0     DOI: 10.1128/JVI.76.3.980-989.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Lewellyn, E. B., Loeb, D. D. (2007). Base Pairing between cis-Acting Sequences Contributes to Template Switching during Plus-Strand DNA Synthesis in Human Hepatitis B Virus. J. Virol. 81: 6207-6215 [Abstract] [Full Text]  
  • Abraham, T. M., Loeb, D. D. (2006). Base Pairing between the 5' Half of {varepsilon} and a cis-Acting Sequence, {Phi}, Makes a Contribution to the Synthesis of Minus-Strand DNA for Human Hepatitis B Virus. J. Virol. 80: 4380-4387 [Abstract] [Full Text]  
  • Ostrow, K. M., Loeb, D. D. (2004). Chimeras of Duck and Heron Hepatitis B Viruses Provide Evidence for Functional Interactions between Viral Components of Pregenomic RNA Encapsidation. J. Virol. 78: 8780-8787 [Abstract] [Full Text]  
  • Habig, J. W., Loeb, D. D. (2003). The Conformation of the 3' End of the Minus-Strand DNA Makes Multiple Contributions to Template Switches during Plus-Strand DNA Synthesis of Duck Hepatitis B Virus. J. Virol. 77: 12401-12411 [Abstract] [Full Text]  
  • Habig, J. W., Loeb, D. D. (2003). Template Switches during Plus-Strand DNA Synthesis of Duck Hepatitis B Virus Are Influenced by the Base Composition of the Minus-Strand Terminal Redundancy. J. Virol. 77: 12412-12420 [Abstract] [Full Text]  
  • Liu, N., Tian, R., Loeb, D. D. (2003). Base pairing among three cis-acting sequences contributes to template switching during hepadnavirus reverse transcription. Proc. Natl. Acad. Sci. USA 100: 1984-1989 [Abstract] [Full Text]  


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