Chemistry: molecular biology and microbiology – Process of mutation – cell fusion – or genetic modification – Introduction of a polynucleotide molecule into or...
Reexamination Certificate
2004-07-09
2009-10-20
Burkhart, Michael (Department: 1633)
Chemistry: molecular biology and microbiology
Process of mutation, cell fusion, or genetic modification
Introduction of a polynucleotide molecule into or...
C435S455000, C435S091400, C435S091100
Reexamination Certificate
active
07604995
ABSTRACT:
A method of stimulating homologous recombination by creating at least one nick in a targeted polynucleotide sequence. Wherein nonhomologous recombination is suppressed resulting in increasing the ratio of targeted to nontargeted events. A method of increasing double strand break-initiated gene targeting by inducing a nick in a targeted polynucleotide sequence, wherein overall recombination levels are increased. A method of increasing homologous recombination employing a recombinase that releases the ends in living cells by stimulating homolgous recombination to higher levels than those attainable with standard nucleases. A composition for stimulating homologous recombination including a nicking mechanism for creating nicks in a polynucleotide, wherein the nicking mechanism stimulates homologous recombination. A composition for stimulating homologous recombination including a nicking endonucleases. Various kits for stimulating homologous recombination. A method for modulating and channeling site-specific DNA stand breaks by shepherding the DNA strand breaks to particular recombination pathways.
REFERENCES:
patent: 5756323 (1998-05-01), Kallenbach et al.
Neiditch, M. et al., “The V(D)J Recombinase Efficiently Cleaves and Transposes Signal Joints”, Mol. Cell, Apr. 2002, vol. 9: pp. 871-878.
Babinet, C. et al., “Genome engineering via homologous recombination in mouse embryonic stem cells: ana amzingly versatile tool for the study of mammalian biology”, 2001, An. Acad. Bras. Cienc., vol. 73: pp. 365-383.
Shibata, T. et al., “Homologous genetic recombination as an intrinsic dynamic property of a DNA structure induced by RecA/Rad51-family proteins: A possible advantage of DNA over RNA as genomic material”, 2001, PNAS, vol. 98: pp. 8425-8432.
Weterings, E. et al., “The endless tale of non-homologous end-joining”, 2008, Cell Res., vol. 18: pp. 114-124.
Roth, D., “Restraining the V(D)J Recombinase”, 2003, Nat. Rev. Immunol., vol. 3: pp. 656-666.
Declaration of Dr. David Roth, May 21, 2009, 2 pages.
Gonda, D. et al., “By Searching Processively RecA Protein Pairs DNA Molecules That Share a Limited Stretch of Homology”, 1983, Cell., vol. 34: pp. 647-654.
Agrawal, A., and Schatz, D. G. (1997). RAG1 and RAG2 form a stable postcleavage synaptic complex with DNA containing signal ends in V(D)J recombination. Cell 89, 43-53.
Agrawal, A., Eastman, Q. M., and Schatz, D. G. (1998). Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 394, 744-751.
Arcangioli, B. (1998). A site- and strand-specific DNA break confers asymmetric switching potential in fission yeast. Embo J 17, 4503-4510.
Arcangioli, B., and de Lahondes, R. (2000). Fission yeast switched mating type by a replication-recombination coupled process. Embo J 19, 1389-1396.
Baumann, P., and West, S. C. (1998). DNA End-joining catalyzed by human cell-free extracts. Proc Natl Acad Sci USA 95, 14066-14070.
Brandt, V. L., and Roth, D. B. (2002). A recombinase diversified: new functions of the RAG proteins. Curr Opin Immunol 14, 224-229.
Chen, H. T., Bhandoola, A., Difilippantonio, M. J., Zhu, J., Brown, M. J., Tai, X., Rogakou, E. P., Brotz, T. M., Bonner, W. M., Ried, T., and Nussenzweig, A. (2000). Response to RAG-mediated VDJ cleavage by NBS1 and gamma-H2AX. Science 290, 1962-1965.
Cuomo, C. A., Mundy, C. L., and Oettinger, M. A. (1996). DNA sequence and structure requirements for cleavage of V(D)J recombination signal sequences. Molecular and Cellular Biology 16, 5683-5690.
Ferguson, D. O., and Alt, F. W. (2001). DNA double strand break repair and chromosomal translocation: lessons from animal models. Oncogene 20, 5572-5579.
Ferguson, D. O., Sekiguchi, J. M., Chang, S., Frank, K. M., Gao, Y., DePinho, R. A., and Alt, F. W. (2000). The nonhomologous end-joining pathway of DNA repair is required for genomic stability and the suppression of translocations. Proc Natl Acad Sci U S A 97, 6630-6633.
Frank-Vaillant, M., and Marcand, S. (2002). Transient stability of DNA ends allows nonhomologous end joining to precede homologous recombination. Mol Cell 10, 1189-1199.
Goedecke, W., Eijpe, M., Offenberg, H. H., van Aalderen, M., and Heyting, C. (1999). Mre11 and Ku70 interact in somatic cells, but are differentially expressed in early meiosis. Nat Genet 23, 194-198.
Grawunder, U., and Lieber, M, R. (1997). A complex of RAG-1 and RAG-2 proteins persists on DNA after single-strand cleavage at V(D)J recombination signal sequences. Nucleic Acids Res 25, 1375-1382.
Haber, J. E. (1999). DNA repair. Gatekeepers of recombination. Nature 398, 665, 667.
Han, J.-O., Erskine, L. A., Purugganan, M. M., Stamato, T. D., and Roth, D. B. (1998). V(D)J recombination intermediates and non-standard products in XRCC4-deficient cells. Nucleic Acids Res 26, 3769-3775.
Han, J.-O., Steen, S. B., and Roth, D. B. (1997). Ku86 is not required for protection of signal ends or for formation of nonstandard V(D)J recombination products. Mol Cell Biol 17, 2226-2234.
Hesse, J. E., Lieber, M. R., Gellert, M., and Mizuuchi, K. (1987). Extrachromosomal DNA substrates in pre-B cells undergo inversion or deletion at immunoglobulin V(D)J joining signals. Cell 49, 775-783.
Hiom, K., and Gellert, M. (1998). Assembly of a 12/23 paired signal complex: A critical control point in V(D)J recombination. Molecular Cell 1, 1011-1019.
Hiom, K., Melek, M., and Gellert, M. (1998). DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell 94, 463-470.
Huye, L. E., Purugganan, M. M., Jiang, M. M., and Roth, D. B. (2002). Mutational analysis of all conserved basic amino acids in RAG-1 reveals catalytic, step arrest, and joining-deficient mutants in the V(D)J recombinase. Mol Cell Biol 22, 3460-3473.
Jasin, M. (1996). Genetic manipulation of genomes with rare-cutting endonucleases. Trends Genet 12, 224-228.
Jones, J. M., and Gellert, M. (2001). Intermediates in V(D)J recombination: a stable RAG1/2 complex sequesters cleaved RSS ends. Proc Natl Acad Sci U S A 98, 12926-12931.
Kabotyanski, E. B., Gomelsky, L., Han, J.-O., Stamato, T. D., and Roth, D. B. (1998). Double-strand break repair in Ku86- and XRCC4-deficient cells. Nucleic Acids Res 26, 5333-5342.
Landree, M. A., Wibbenmeyer, J. A., and Roth, D. B. (1999). Mutational analysis of RAG-1 and RAG-2 identifies three active site amino acids in RAG-1 critical for both cleavage steps of V(D)J recombination. Genes Dev 13, 3059-3069.
Lee, G. S., M.B. Neiditch, S.S. Salus, and D.B. Roth,RAG proteins shepherd double-strand breaks to a specific pathway, suppressing error-prone repair, but RAG nicking initiates homologous recombination. Cell, 2004. 117, 171-84.
Lee, S. S., Fitch, D., Flajnik, M. F., and Hsu, E. (2000). Rearrangement of immunoglobulin genes in shark germ cells. J Exp Med 191, 1637-1648.
Leu, T. M., Eastman, Q. M., and Schatz, D. G. (1997). Coding joint formation in a cell-free V(D)J recombination system. Immunity 7, 303-314.
Lewis, S. M. (1994). The mechanism of V(D)J joining: Lessons from molecular, immunological and comparative analyses. AdvImmunol 56, 27-150.
Lewis, S. M., and Wu, G. E. (2000). The old and the restless. J Exp Med 191, 1631-1636.
Moynahan, M. E., Pierce, A. J., and Jasin, M. (2001). BRCA2 is required for homology-directed repair of chromosomal breaks. Mol Cell 7, 263-272.
Pâques, F., and Haber, J. E. (1999). Multiple pathways of recombination induced by double-strand breaks inSaccharomyces cerevisiae. Microbiol Mol Biol Rev 63, 349-404.
Perkins, E. J., Nair, A., Cowley, D. O., Van Dyke, T., Chang, Y., and Ramsden, D. A. (2002). Sensing of intermediates in V(D)J recombination by ATM. Genes Dev 16, 159-164.
Pierce, A. J., Hu, P., Han, M., Ellis, N., and Jasin, M. (2001). Ku DNA end-binding protein modulates homologous repair of double-strand breaks in mammalian cells. Genes Dev 15, 3237-3242.
Pierce, A. J., Johnson, R. D., Thompson, L. H., and Jasin, M. (1999). XRCC3 promotes homology-directed repair of DNA damage in mammalian cells. Genes Dev 13
Lee Gregory S.
Roth David B.
Burkhart Michael
Kohn Kenneth I.
New York University
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