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Journal of Virology, June 2005, p. 6801-6807, Vol. 79, No. 11
0022-538X/05/$08.00+0     doi:10.1128/JVI.79.11.6801-6807.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Effects of Adeno-Associated Virus DNA Hairpin Structure on Recombination{ddagger}

Vivian W. Choi,1,2 R. Jude Samulski,1,2* and Douglas M. McCarty2,3,{dagger}

Department of Pharmacology,1 Gene Therapy Center,2 Department of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 275993

Received 12 November 2004/ Accepted 28 December 2004

Hairpin DNA ends are evolutionarily conserved intermediates in DNA recombination. The hairpin structures present on the ends of the adeno-associated virus (AAV) genome are substrates for recombination that give rise to persistent circular and concatemeric DNA episomes through intramolecular and intermolecular recombination, respectively. We have developed circularization-dependent and orientation-specific self-complementary AAV (scAAV) vectors as a reporter system to examine recombination events involving distinct hairpin structures, i.e., closed versus open hairpins. The results suggest that intramolecular recombination (circularization) is far more efficient than intermolecular recombination (concatemerization). Among all possible combinations of terminal repeats (TRs) involved in intermolecular recombination, the closed-closed TR structures are twice as efficient as the open-open TR substrates for recombination. In addition, both intramolecular recombination and intermolecular recombination exhibit the common dependency on specific DNA polymerases and topoisomerases. The circularization-dependent and orientation-specific scAAV vectors can serve as an efficient and controlled system for the delivery of DNA structures that mimic mammalian recombination intermediates and should be useful in assaying recombination in different experimental settings as well as elucidating the molecular mechanism of recombinant AAV genome persistence.

* Corresponding author. Mailing address: 7119 Thurston Bowles, CB 7352, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599. Phone: (919) 962-3285. Fax: (919) 966-0907. E-mail: rjs{at}med.unc.edu.

{ddagger} Supplemental material for this article may be found at http://jvi.asm.org/.

{dagger} Present address: 700 Children's Drive, Children's hospital, Columbus, Ohio 43205.

Journal of Virology, June 2005, p. 6801-6807, Vol. 79, No. 11
0022-538X/05/$08.00+0     doi:10.1128/JVI.79.11.6801-6807.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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