Native molecular state of adeno-associated viral vectors revealed by single-molecule sequencing

Human Gene Therapy

Volumn 23, Issue 1, 2012, Pages 46-55

  Kapranov, Philipp ^a   Chen, Lingxia ^b   Dederich, Debra ^a   Dong, Biao ^b   He, Jie ^a   Steinmann, Kathleen E ^a   Moore, Andrea R ^b   Thompson, John F ^a   Milos, Patrice M ^a   Xiao, Weidong ^b  

^a Building 700 ^*  (United States)

^b TEMPLE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; PARVOVIRUS VECTOR; PLASMID DNA;

ARTICLE; CONTROLLED STUDY; GENE SEQUENCE; INVERTED TERMINAL REPEAT; MOLECULAR CLONING; NONHUMAN; SINGLE MOLECULE SEQUENCING; VIRUS GENOME;

BASE SEQUENCE; DEPENDOVIRUS; DNA, VIRAL; GENETIC VECTORS; GENOME, VIRAL; HEK293 CELLS; HUMANS; PLASMIDS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TERMINAL REPEAT SEQUENCES; TRANSFECTION; VIRUS ASSEMBLY;

MIRIDAE;

EID: 84862969739     PISSN: 10430342     EISSN: 15577422     Source Type: Journal    
DOI: 10.1089/hum.2011.160     Document Type: Article

References (36)

1. Bowers, J., Mitchell, J., Beer, E., et al. (2009). Virtual terminator nucleotides for next-generation DNA sequencing. Nat. Methods 6, 593-595.
2. Dong, B., Nakai, H., and Xiao, W. (2010). Characterization of genome integrity for oversized recombinant AAV vector. Mol. Ther. 18, 87-92.
3. Ferrari, F.K., Samulski, T., Shenk, T., and Samulski, R.J. (1996). Second-strand synthesis is a rate-limiting step for efficient transduction by recombinant adeno-associated virus vectors. J. Virol. 70, 3227-3234. (Pubitemid 26121941)
4. Fisher, K.J., Gao, G.P., Weitzman, M.D., et al. (1996). Transduction with recombinant adeno-associated virus for gene therapy is limited by leading-strand synthesis. J. Virol. 70, 520-532. (Pubitemid 126508820)
5. Fisher, K.J., Jooss, K., Alston, J., et al. (1997). Recombinant adeno-associated virus for muscle directed gene therapy. Nat. Med. 3, 306-312. (Pubitemid 27112928)
6. Giladi, E., Healy, J., Myers, G., et al. (2010). Error tolerant indexing and alignment of short reads with covering template families. J. Comput. Biol. 17, 1397-1411.
7. Harris, T.D., Buzby, P.R., Babcock, H., et al. (2008). Single-molecule DNA sequencing of a viral genome. Science 320, 106-109. (Pubitemid 351490765)
8. Hart, C., Lipson, D., Ozsolak, F., et al. (2010). Single-molecule sequencing: Sequence methods to enable accurate quantita-tion. Methods Enzymol. 472, 407-430.
9. Hauswirth, W.W., and Berns, K.I. (1977). Origin and termination of adeno-associated virus DNA replication. Virology 78, 488-499. (Pubitemid 8115897)
10. Hauswirth, W.W., and Berns, K.I. (1979). Adeno-associated virus DNA replication: Nonunit-length molecules. Virology 93, 57-68. (Pubitemid 9142518)
11. Hong, G., Ward, P., and Berns, K.I. (1992). In vitro replication of adeno-associated virus DNA. Proc. Natl. Acad. Sci. U.S.A. 89, 4673-4677.
12. King, J.A., Dubielzig, R., Grimm, D., and Kleinschmidt, J.A. (2001). DNA helicase-mediated packaging of adeno-associated virus type 2 genomes into preformed capsids. EMBO J. 20, 3282-3291. (Pubitemid 32612015)
13. Kotin, R.M., Linden, R.M., and Berns, K.I. (1992). Characterization of a preferred site on human chromosome 19q for integration of adeno-associated virus DNA by non-homologous recombination. EMBO J. 11, 5071-5078. (Pubitemid 23023451)
14. Lai, Y., Yue, Y., and Duan, D. (2010). Evidence for the failure of adeno-associated virus serotype 5 to package a viral genome ‡ 8.2 kb. Mol. Ther. 18, 75-79.
15. Laughlin, C.A., Myers, M.W., Risin, D.L., and Carter, B.J. (1979). Defective-interfering particles of the human parvovirus adeno-associated virus. Virology 94, 162-174. (Pubitemid 9164791)
16. Lipson, D., Raz, T., Kieu, A., et al. (2009). Quantification of the yeast transcriptome by single-molecule sequencing. Nat. Bio-technol. 27, 652-658.
17. Maguire, A.M., Simonelli, F., Pierce, E.A., et al. (2008). Safety and efficacy of gene transfer for Leber's congenital amaurosis. N. Engl. J. Med. 358, 2240-2248. (Pubitemid 351724453)
18. Maguire, A.M., High, K.A., Auricchio, A., et al. (2009). Age-dependent effects of RPE65 gene therapy for Leber's congenital amaurosis: A phase 1 dose-escalation trial. Lancet 374, 1597-1605.
19. Manno, C.S., Pierce, G.F., Arruda, V.R., et al. (2006). Successful transduction of liver in hemophilia by AAV-Factor IX and limitations imposed by the host immune response. Nat. Med. 12, 342-347. (Pubitemid 43355084)
20. Mayor, H.D., Torikai, K., Melnick, J.L., and Mandel, M. (1969). Plus and minus single-stranded DNA separately encapsidated in adeno-associated satellite virions. Science 166, 1280-1282.
21. Muzyczka, N. (1992). Use of adeno-associated virus as a general transduction vector for mammalian cells. Curr. Top. Micro-biol. Immunol. 158, 97-129.
22. Muzyczka, N., and Berns, K.I. (2002). Parvoviridae: The viruses and their replication. In Fields Virology. D.M. Knipe, P.M. Howley, D.E. Griffin, et al., eds. (Lippincott Williams & Wilkins, Philadelphia).
23. Nakai, H., Storm, T.A., and Kay, M.A. (2000). Recruitment of single-stranded recombinant adeno-associated virus vector genomes and intermolecular recombination are responsible for stable transduction of liver in vivo. J. Virol. 74, 9451-9463.
24. Ozsolak, F., Platt, A.R., Jones, D.R., et al. (2009). Direct RNA sequencing. Nature 461, 814-818.
25. Ozsolak, F., Kapranov, P., Foissac, S., et al. (2010). Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 143, 1018-1029.
26. Powell, J.S. (2009). Recombinant factor VIII in the management of hemophilia A: Current use and future promise. Ther. Clin. Risk Manag. 5, 391-402.
27. Samulski, R.J., Berns, K.I., Tan, M., and Muzyczka, N. (1982). Cloning of adeno-associated virus into pBR322: Rescue of intact virus from the recombinant plasmid in human cells. Proc. Natl. Acad. Sci. U.S.A. 79, 2077-2081. (Pubitemid 12120800)
28. Samulski, R.J., Srivastava, A., Berns, K.I., and Muzyczka, N. (1983). Rescue of adeno-associated virus from recombinant plasmids: Gene correction within the terminal repeats of AAV. Cell 33, 135-143. (Pubitemid 13096442)
29. Samulski, R.J., Chang, L.S., and Shenk, T. (1989). Helper-free stocks of recombinant adeno-associated viruses: Normal integration does not require viral gene expression. J. Virol. 63, 3822-3828. (Pubitemid 19205454)
30. Snyder, R.O., Im, D.S., and Muzyczka, N. (1990a). Evidence for covalent attachment of the adeno-associated virus (AAV) Rep protein to the ends of the AAV genome. J. Virol. 64, 6204-6213.
31. Snyder, R.O., Samulski, R.J., and Muzyczka, N. (1990b). In vitro resolution of covalently joined AAV chromosome ends. Cell 60, 105-113.
32. Srivastava, A., Lusby, E.W., and Berns, K.I. (1983). Nucleotide sequence and organization of the adeno-associated virus 2 genome. J. Virol. 45, 555-564. (Pubitemid 13225420)
33. Wang, J., Xie, J., Lu, H., et al. (2007). Existence of transient functional double-stranded DNA intermediates during re-combinant AAV transduction. Proc. Natl. Acad. Sci. U.S.A. 104, 13104-13109. (Pubitemid 351737600)
34. Ward, P., and Berns, K.I. (1991). In vitro rescue of an integrated hybrid adeno-associated virus/simian virus 40 genome. J. Mol. Biol. 218, 791-804. (Pubitemid 121003376)
35. Ward, P., and Berns, K.I. (1995). Minimum origin requirements for linear duplex AAV DNA replication in vitro. Virology 209, 692-695.
36. Wu, Z., Yang, H., and Colosi, P. (2010). Effect of genome size on AAV vector packaging. Mol. Ther. 18, 80-86.