Topoisomerase linker-mediated amplification methods

Organic compounds -- part of the class 532-570 series – Organic compounds – Carbohydrates or derivatives

Reexamination Certificate

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C536S023200, C536S023500, C536S024100, C536S024300, C536S024200, C435S006120, C435S091100, C435S091200

Reexamination Certificate

active

07078501

ABSTRACT:
A Vaccinia topoisomerase-adapted linker, which contains an oligonucleotide primer binding site of known sequence, useful for specifically joining the linker to the end of a polynucleotide of unknown sequence and allowing subsequent PCR amplification of the polynucleotide or DNA is provided. Kits containing the invention Vaccinia topoisomerase-adapted linker and one or more linker-specific oligonucleotides for annealing to the linker in PCR are also provided. In addition, the invention provides methods for using the invention linkers in linker-mediated PCR amplification procedures for isolation and optional sequencing of isolated PCR amplification products.

REFERENCES:
patent: 4661450 (1987-04-01), Kempe
patent: 4800159 (1989-01-01), Mullis
patent: 5162209 (1992-11-01), Scheele
patent: 5624826 (1997-04-01), Kato et al.
patent: 5746997 (1998-05-01), Reed
patent: 5766891 (1998-06-01), Shuman
patent: 5851808 (1998-12-01), Elledge et al.
patent: 5958681 (1999-09-01), Wetmur et al.
patent: 5981182 (1999-11-01), Jacobs, Jr. et al.
patent: 6013440 (2000-01-01), Lipshutz et al.
patent: 6140086 (2000-10-01), Fox et al.
patent: 6174669 (2001-01-01), Hayashizaki et al.
patent: 6238884 (2001-05-01), Short
patent: 6277632 (2001-08-01), Harney
patent: 6280977 (2001-08-01), Liang
patent: 6291213 (2001-09-01), Rothstein
patent: 6340595 (2002-01-01), Vogels et al.
patent: 6537776 (2003-03-01), Short
patent: 6548277 (2003-04-01), Shuman
patent: 6653106 (2003-11-01), Shuman et al.
patent: 2002/0025561 (2002-02-01), Hodgson
patent: 2002/0028444 (2002-03-01), Harney et al.
patent: 2002/0068290 (2002-06-01), Yarovinsky
patent: 2002/0182731 (2002-12-01), Ji et al.
patent: 0 373 914 (1989-12-01), None
patent: 0 625 572 (1993-09-01), None
patent: 1 018 549 (2000-07-01), None
patent: 85/04898 (1985-11-01), None
patent: 94/29443 (1994-12-01), None
patent: 96/19497 (1996-06-01), None
patent: 96/34981 (1996-11-01), None
patent: 97/24455 (1997-07-01), None
patent: WO 97/48716 (1997-12-01), None
patent: 98/20122 (1998-05-01), None
patent: 98/55502 (1998-12-01), None
patent: 98/56943 (1998-12-01), None
patent: WO 00/12687 (2000-03-01), None
patent: 00/56878 (2000-09-01), None
patent: 01/62892 (2001-08-01), None
patent: WO 02/16594 (2002-02-01), None
patent: 02/061034 (2002-08-01), None
(J. of Biol. Chem. (1997) 272(42): 26441-47).
Sigma Catalog (1996).
Carninci, et al. “High-Efficiency Full-Length cDNA Cloning by Biotinylated CAP Trapper,”Genomics, 37(3):327-36 (1996) Academic Press, Inc.
Carninci, et al. “High Efficiency Selection of full-length cDNA by Improved Biotinylated Cap Trapper,”DNA Research, 4:61-66 (1997). Universal Academy Press.
Cheng and Shuman, “DNA strand transfer catalyzed by vaccinia topoisomerase: ligation of DNAs containing a 3′mononucleotide overhang,”Nucleic Acids Res., 28(9):1893-8. (2000). Oxford University Press.
Cheng and Shuman, “Recombinogenic flap ligation pathway for intrinsic repair of topoisomerase IB-induced double-strand breaks,”Mol. Cell. Biol. 20(21):8059-8068 (2000) American Society for Microbiology.
Cheng and Shuman, “Site-specific DNA transesterification by vaccinia topoisomerase: Role of specific phosphates and nucleosides,”Biochemistry38(50):16599-612 (1999) American Chemical Society.
Cheng and Shuman, “A catalytic domain of eukaryotic DNA topoisomerase I,”J. Biol. Chem. 273(19):11589-95 (1998) The American Society for Biochemistry and Molecular Biology, Inc.
Cheng, et al., “Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases,”Cell. 92(6):841-50 (1998) Cell Press.
Cheng, et al., “Mutational analysis of 39 residues of vaccinia DNA topoisomerase identifies Lys-220, Arg-223, and Asn-228 as important for covalent catalysis,”J. Biol. Chem. 272(13):8263-9 (1997) The American society for Biochemistry and Molecular Biology, Inc.
DiGate and Marians, “Molecular Cloning and DNA Sequence Analysis ofEscherichia Coli topB, the Gene Encoding Topoisomerase III,”J. Biol. Chem. 264(30):17924-17930 (1989). The American society for Biochemistry and Molecular Biology, Inc.
Edery, et al., “An Efficient Strategy to Isolate Full-Length cDNAs Based on an mRNA Cap Retention Procedure (CAPture),”Mol Cell. Biol., 15(6):3363-3371 (1995). American Society for Microbiology.
Ericsson, et al., “Characterization of ts 16, a temperature-sensitive mutant of vaccinia virus,”J. Virol.. 69(11):7072-86 (1995) American Society for Microbiology.
Gross and Shuman, “Vaccinia virions lacking the RNA helicase nucleoside triphosphate phosphohydrolase II are defective in early transcription,”J. Virol. 70(12):8549-5 (1996) American Society for Microbiology.
Haghighat and Sonenberg. “eIF4G Dramatically Enhances the Binding of eIF4E to the mRNA 5′-Cap Structure,”J. Biol. Chem., 272(35):21677-21680 (1997). The American society for Biochemistry and Molecular Biology, Inc.
Haghighat et al., “The eIF4G-eIF4E Complex is the Target for Direct Cleavage by the Rhinovirus 2A Proteinase,”J. Virol. 70:8444-8450 (1996). American Society for Microbiology.
Henningfeld and Hecht, “A model for topoisomerase I-mediated insertions and deletions with duplex DNA substrates containing branches, nicks, and gaps,”Biochemistry34(18):6120-9. (1995) American Chemical Society.
Invitrogen Corporation.Invitrogen Catalog, Carlsbad, California, pp. 18, 29, 43, 44, 49-52 (1998).
Janknecht, et al., “Rapid and efficient purification of native histidine-tagged protein expressed by recombinant vaccinia virus,”Proc. Natl. Acad. Sci., U S A88:8972-8976(1991) National Academic of Sciences.
Kane and Shuman, “Vaccinia virus morphogenesis is blocked by a temperature-sensitive mutation in the I7 gene that encodes a virion component,”J. Virol. 67(5):2689-98 (1993) American Society for Microbiology.
Kato, et al., “Construction of a Human Full-Length cDNA Bank,”Gene. 150: 243-250 (1994) Elsevier Science.
Klemm, et al., “Peptide inhibitors of DNA cleavage by tyrosine recombinases and topoisomerases,”J. Mol. Biol. 299(5):1203-16. (2000) Academic Press, Inc.
Klemperer, et al., “Identification and characterization of the orf virus type I topoisomerase,”Virology206:203-215 (1995) Academic Press, Inc.
Krogh and Shuman, “Vaccinia topoisomerase mutants illuminate conformational changes during closure of the protein clamp and assembly of a functional active site,”J. Biol. Chem. Jul. 5, 2001 [Manuscript]The American Society for Biochemistry and Molecular Biology, Inc.
Krogh and Shuman, “Catalytic mechanism of DNA topoisomerase IB,”Mol. Cell.. 5(6):1035-41 (2000) Cell Press.
Krogh and Shuman, “DNA strand transfer catalyzed by vaccinia topoisomerase: peroxidolysis and hydroxylaminolysis of the covalent protein-DNA intermediate,”Biochemistry39(21):6422-32. (2000) American Chemical Society.
Krogh, et al., “Effect of 2′-5′phosphodiesters on DNA transesterification by vaccinia topoisomerase,”J. Biol. Chem. 276(24):20907-20912. (2001) The American Society for Biochemistry and Molecular Biology, Inc.
Krogh, et al., Melanoplus sanguinipes entomopoxvirus DNA topoisomerase: site-specific DNA transesterification and effects of 5′-bridging phosphorothiolates,Virology264(2):441-51. (1999) Academic Press, Inc.
Maruyama and Sugano, “Oligo-Capping: A Simple Method to Replace the Cap Structure of Eukaryotic mRNAs with Oligoribonucleotides,”Gene. 138:171-174 (1994).
Morham and Shuman, “Covalent and Noncovalent DNA Binding by Mutants of Vaccinia DNA Topoisomerase I,”J. Biol. Chem. 267:15984-15992 (1992) The American Society for Biochemistry and Molecular Biology, Inc.
Morham and Shuman, “Phenotypic selection and characterization of mutant alleles of a eukaryotic DNA topoisomerase I,”Genes. Dev. 4(4):515-24 (1990) Cold Spring Harbor L

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