Topoisomerase-based reagents and methods for molecular cloning

Details Topoisomerase-based reagents and methods for molecular cloning Topoisomerase-based reagents and methods for molecular cloning

2006-04-11

2006-04-11

Vogel, Nancy (Department: 1636)

Chemistry: molecular biology and microbiology

Micro-organism, tissue cell culture or enzyme using process...

Preparing compound containing saccharide radical

C435S091100, C536S023100

Reexamination Certificate

active

07026141

ABSTRACT:
This invention provides a modified vaccinia topoisomerase enzyme containing an affinity tag which is capable of facilitating purification of protein-DNA complexes away from unbound DNA. This invention further provides a modified sequence specific topoisomerase enzyme.This invention provides a method of ligating duplex DNAs, a method of molecular cloning of DNA, a method of synthesizing polynucleotides, and a method of gene targeting.Lastly, this invention provides a recombinant DNA molecule composed of segments of DNA which have been joined ex vivo by the use of a sequence specific topoisomerase and which has the capacity to transform a suitable host cell comprising a DNA sequence encoding polypeptide activity.

REFERENCES:
patent: 4661450 (1987-04-01), Kempe et al.
patent: 4800159 (1989-01-01), Mullis et al.
patent: 5624826 (1997-04-01), Kato et al.
patent: 5766891 (1998-06-01), Shuman et al.
patent: 6238884 (2001-05-01), Short et al.
patent: 6280977 (2001-08-01), Liang et al.
patent: 6291213 (2001-09-01), Rothstein
patent: 6548277 (2003-04-01), Shuman et al.
patent: 0373914 (1994-07-01), None
patent: 0625572 (2001-04-01), None
patent: WO8504898 (1985-11-01), None
patent: WO9429443 (1994-12-01), None
patent: WO9619497 (1996-06-01), None
patent: WO9634981 (1996-11-01), None
patent: WO9724455 (1997-07-01), None
patent: WO9820122 (1998-05-01), None
patent: WO9855502 (1998-12-01), None
patent: WO9856943 (1998-12-01), None
patent: WO0012687 (2000-03-01), None
patent: WO0056878 (2000-09-01), None
patent: WO0162943 (2001-08-01), None
patent: WO0262892 (2001-08-01), None
patent: WO0216594 (2002-02-01), None
Carninci et al. “High efficiency selection of full-length cDNA by improved biotinylated cap trapper,” DNA Research 4:61-66 (1997).
Carninci et al. “High-efficiency full-length cDNA cloning by biotinylated CAP trapper,” Genomics 37(3):327-36(1996).
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).
Cheng and Shuman, “Site-specific DNA transestification by vaccinia topoisomerase: Role of specific phosphates and nucleosides,” Biochemistry 38(50):16599-612 (1999).
Cheng et al. “Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases,” Cell 92(6):841-50 (1998).
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).
DiGate and Marians, “Molecular cloning and DNA sequence analysis ofEscherichia colitopoB, the gene encoding topoisomerase III,” J. Biol. Chem. 264(30);17924-17930 (1989).
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).
Ericsson et al. “Characterization of ts16, a temperature-sensitive mutant of vaccinia virus,” J. Virol. 69(11):7072-86 (1995).
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).
Haghighat and Sonenberg, “eIF4G dramatically enhances the binding of eIF4E to the mRNA 5'- cap structure,” J. Biol. Chem. 272(35):21677-21680 (1997).
Haghighat et al. “The eIF4G-eIF4E complex is the target for direct cleavage by the rhinovirus 2A proteinase,” J. Virol. 70:8444-8450 (1996).
Henningfeld and Hecht, “A model for topoisomerase I-mediated insertions and deletions with duplex DNA substrates containing branches, nicks, gaps,” Biochemistry 34(18):6120-9 (1995).
Invitrogen Corporation, Carlsbad, California, catalog pages 18, 29, 43, 44, 49-52 (1998).
Kane and Shuman, “Vaccinia virus morphogenesis is blocked by a temperature-sensitive mutation in the 17 gene that encodes a virion component,” J. Virol. 67(5):2689-98 (1993).
Kato et al. “Construction of a human full-length cDNA bank,” Gene 150:243-250 (1994).
Klemm et al. “Peptide inhibitors of DNA cleavage by tyrosine recombinases and topoisomerases,” J. Mol. Biol. 299(5):1203-16 (2000).
Klemperer et al. “Identification and characterization of the orf virus type I topoisomerase,” Virology 206:203-215 (1995).
Krogh and Shuman, “Catalytic mechanism of DNA topoisomerase IB,” Mol. Cell 5(6):1035-41 (2000).
Krogh and Shuman, “DNA strand transfer catalyzed by vaccinia topoisomerase: peroxidolysis and hydroxylaminolysis of the covalent protein-DNA intermediate,” Biochemistry 39(21):6422-32 (2000).
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. (2001).
Krogh et al. “Effect of 2′-5′ phosphodiesters on DNA transesterification by vaccinia topoisomerase,” J. Biol. Chem. 276(24):20907-20912 (2001).
Krogh et al. “Melanoplus sanguinipes entomopoxvirus DNA topoisomerase: site-specific DNA transesterification and effects of 5′-bridging phosphorothiolates,” Virology 264(2):441-51 (1999).
Liu et al. “Mapping the 5' and 3' ends of tetrahymena thermophila mRNAs using ligase mediated amplification of cDNA ends (RLM-Race),” Nucleic Acids Res. 21(21):4954-4960 (1993).
Krogh and Shuman, “DNA strand transfer catalyzed by vaccinia topoisomerase: peroxidolysis and hydroxylaminolysis of the covalent protein-DNA intermediate,” Biochemistry 39(21):6422-32 (2000).
Lockard et al. “Labeling of eukaryotic messenger RNA 52terminus with phosphorus-32: Use of tobacco acid pyrophosphatase for removal of cap structure,” Gene Amp. Anal. 2:229-251 (1981).
Maruyama et al. “Oligo-Capping: A simple method to replace the cap structure fo eukaryotic mRNAs with oligonucleotides,” Gene 138:171-174 (1994).
Matthews et al. “Analytical strategies for the use of DNA probes,” Anal. Biochem. 169:1-25 (1988).
Morham and Shuman, “Covalent and noncovalent DNA binding by mutants of vaccinia DNA topoisomerase I,” J. Biol. Chem. 267:15984-15992 (1992).
Morham and Shuman, “Phenotypic selection and characterization of mutant alleles of a eukaryotic DNA topoisomerase I,” Genes. Dev. 4(4):515-24 (1990).
Palaniyar et al. “SFV topoisomerase: sequence specificity in a genetically mapped interval,” Virology 221:351-354 (1996).
Petersen and Shuman, “DNA strand transfer reactions catalyzed by vaccinia topoisomerase: hydrolysis and glycerololysis of the covalent protein-DNA intermediate,” Nucleic Acids Res. 25(11):2091-7 (1997).
Petersen and Shuman, “Histidine 265 is important for covalent catalysis by vaccinia topoisomerase and is conserved in all eukaryotic type I enzymes,” J. Biol. Chem. 272(7):3891-6 (1997).
Petersen et al. “Characterization of a DNA topoisomerase encoded by Amsacta moore entomopoxvirus,” Virology 230(2):197-206 (1997).
Petersen et al. “Mutations within a conserved region of vaccinia topoisomerase affect the DNA cleavage-religation equilibrium,” J. Mol. Biol. 1263(2):181-95 (1996).
Salazar et al. “The DNA strand in DNA:RNA hybrid duplexes is neither B-form nor A-form in solution,” Biochemistry 32(16);4207-15 (1993).
Sekiguchi and Shuman, “Covalent DNA binding by vaccinia topoisomerase results in unpairing of the thymine base 5′ of the scissile bond,” J. Biol. Chem. 271(32):19436-42 (1996).
Sekiguchi and Shuman, “Domain structure of vaccinia DNA ligase,” Nucleic Acids Res. 25(4):727-43(1997).
Sekiguchi and Shuman, “Identification of contacts between topoisomerase I and its target DNA by site-specific photocrosslinking,” EMBO J. 15(13):3448-57 (1996).
Sekiguchi and Shum

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