Creating a novel origin of replication through modulating DNA-protein interfaces

PLoS ONE

Volumn 5, Issue 1, 2010, Pages

  Curtis Hewitt, F ^b   Jude Samulski, R ^b  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS DNA; VIRUS PROTEIN;

ADENO ASSOCIATED VIRUS; ARTICLE; DNA REPLICATION; GENE TARGETING; NONHUMAN; PROTEIN DNA INTERACTION; STRUCTURE ACTIVITY RELATION; VIRUS REPLICATION;

BASE SEQUENCE; BINDING SITES; DEPENDOVIRUS; DNA, VIRAL; DNA-BINDING PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; REPLICATION ORIGIN; STRUCTURE-ACTIVITY RELATIONSHIP;

ADENO-ASSOCIATED VIRUS; DNA VIRUSES; EUKARYOTA; VERTEBRATA;

EID: 77749321137     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008850     Document Type: Article

References (30)

1. Im DS, Muzyczka N (1990) The AAV origin binding protein Rep68 is an ATP-dependent site-specific endonuclease with DNA helicase activity. Cell 61: 447-457.
2. Hauswirth WW, Berns KI (1977) Origin and termination of adeno-associated virus DNA replication. Virology 78: 488-499.
3. Ryan JH, Zolotukhin S, Muzyczka N (1996) Sequence requirements for binding of Rep68 to the adeno-associated virus terminal repeats. J Virol 70: 1542-1553. 4. Brister JR, Muzyczka N (2000) Mechanism of Rep-mediated adeno-associated virus origin nicking. J Virol 74: 7762-71.
4. Hermonat PL, Batchu RB (1997) The adeno-associated virus Rep78 major regulatory protein forms multimeric complexes and the domain for this activity is contained within the carboxy-half of the molecule. FEBS Lett 20: 180-184.
5. Brister JR, Muzyczka N (1999) Rep-mediated nicking of the adeno-associated virus origin requires two biochemical activities, DNA helicase activity and transesterification. J Virol 73: 9325-9336.
6. King JA, Dubielzig R, Grimm D, Kleinschmidt JA (2001) DNA helicase-mediated packaging of adeno-associated virus type 2 genomes into preformed capsids. EMBO J 20: 3282-3291.
7. Hewitt FC, Li C, Gray SJ, Cockrell S, Washburn M, Samulski RJ (2009) Reducing the Risk of AAV Vector Mobilization with AAV5 Vectors. J Virol 83: 3919-3929.
8. Grimm D, Pandey K, Nakai H, Storm TA, Kay MA (2006) Liver transduction with recombinant adeno-associated virus is primarily restricted by capsid serotype not vector genotype. J Virol 80: 426-439.
9. Chiorini JA, Afione S, Kotin RM (1999) Adeno-associated virus (AAV) type 5 Rep protein cleaves a unique terminal resolution site compared with other AAV serotypes. J Virol 73: 4293-4298.
10. Chiorini JA, Kim F, Yang L, Kotin RM (1999) Cloning and characterization of adeno-associated virus type 5. J Virol 73: 1309-1319.
11. Wu J, Davis MD, Owens RA (2001) A Rep recognition sequence is necessary but not sufficient for nicking of DNA by adeno-associated virus type-2 Rep proteins. Arch Biochem Biophys 389: 271-277.
12. Young SM Jr, McCarty DM, Degtyareva N, Samulski RJ (2000) Roles of adeno-associated virus Rep protein and human chromosome 19 in site-specific recombination. J Virol 74: 3953-3966.
13. Samulski RJ, Srivastava A, Berns KI, Muzyczka N (1983) Rescue of Adeno-Associated Virus from Recombinant Plasmids: Gene Correction within the Terminal Repeats of AAV. Cell 33: 135-143.
14. Xiao X, Xiao W, Li J, Samulski RJ (1997) A novel 165-base-pair terminal repeat sequence is the sole cis requirement for the adeno-associated virus life cycle. J Virol 71: 941-948.
15. Hickman AB, Ronning DR, Perez ZN, Kotin RM, Dyda F (2004) The nuclease domain of adeno-associated virus rep coordinates replication initiation using two distinct DNA recognition interfaces. Mol Cell 13: 403-414.
16. Yoon M, Smith DH, Ward P, Medrano FJ, Aggarwal AK, et al. (2001) Amino-terminal domain exchange redirects origin-specific interactions of adeno-associated virus rep78 in vitro. J Virol 75: 3230-3239.
17. Hickman AB, Ronning DR, Kotin RM, Dyda F (2002) Structural unity among viral origin binding proteins: crystal structure of the nuclease domain of adenoassociated virus Rep. Mol Cell 10: 327-337.
18. Farkas SL, Zadori Z, Benko M, Essbauer S, Harrach B, et al. (2004) A parvovirus isolated from royal python (Python regius) is a member of the genus Dependovirus. J Gen Virol 85: 555-561.
19. Deiss V, Tratschin JD, Weitz M, Siegl G (1990) Cloning of the human parvovirus B19 genome and structural analysis of its palindromic termini. Virology 175: 247-254.
20. Samulski RJ, Zhu X, Xiao X, Brook JD, Housman DE, et al. (1991) Targeted integration of adeno-associated virus (AAV) into human chromosome 19. EMBO J 10: 3941-3950.
21. Young SM Jr, Xiao W, Samulski RJ (2000) Site-specific targeting of DNA plasmids to chromosome 19 using AAV cis and trans sequences. Methods Mol Biol 133: 111-126.
22. Vos JC, van Luenen HGAM, Plasterk RHA (1993) Characterization of the Caenorhabditis elegans Tc1 transposase in vivo and in vitro. Genes Dev 7: 1244-1253.
23. Ilyina TV, Koonin EV (1992) Conserved sequence motifs in binding domain of the Epstein-Barr virus origin-binding protein, the initiator proteins for rolling circle DNA replication encoded by EBNA1, bound to DNA. Cell 84: 791-800.
24. Xiao X, Li J, Samulski RJ (1998) Production of high-titer recombinant adeno-associated virus vectors in the absence of helper adenovirus. J Virol 72: 2224-2232.
25. Higuchi R, Krummel B, Saiki RK (1988) A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions. Nucleic Acids Res 16: 7351-7367.
26. Hirt B (1967) Selective extraction of polyoma DNA from infected mouse cell cultures. J Mol Biol 26: 365-369.
27. Chomczynski P (1992) One-hour downward alkaline capillary transfer for blotting of DNA and RNA. Anal Biochem 201: 134.
28. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
29. SantaLucia J Jr (1998) A unified view of polymer, dumbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci 95: 1460-1465.
30. Prasad KM, Trempe JP (1995) The adeno-associated virus Rep78 protein is covalently linked to viral DNA in a preformed virion. Virology 214: 360-70.