Methods for obtaining directionally truncated polypeptides

Chemistry: molecular biology and microbiology – Micro-organism – tissue cell culture or enzyme using process... – Using tissue cell culture to make a protein or polypeptide

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C435S069100, C435S091410, C435S455000

Reexamination Certificate

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07727744

ABSTRACT:
Methods, compositions and kits are disclosed for obtaining directionally truncated polypeptides by inserting a transposon. Preferably the transposon comprises a selectable marker and an ori, and optionally a promoter, a ribosome binding site and a translation start codon, into a target sequence in vitro or in vivo. Amplification products, varying in length depending on the transposon insertion site, are obtained using one primer that anneals to the target sequence and a second primer that anneals to the transposon. Amplification products are ligated to circular dsDNA, transformed into host cells, and individual colonies, each containing a directionally truncated clone of the target sequence, are obtained by plating on medium for which the selectable marker encodes resistance. Directionally truncated polypeptides encoded by the target sequence are obtained in vivo by inducing an RNAP in the host cells that uses the promoter or, in vitro by cell-free transcription and translation.

REFERENCES:
patent: 4843003 (1989-06-01), Henikoff et al.
patent: 5356773 (1994-10-01), Shen et al.
patent: 5677170 (1997-10-01), Devine et al.
patent: 5728551 (1998-03-01), Devine et al.
patent: 5733753 (1998-03-01), Jørgensen
patent: 5928908 (1999-07-01), Dunn et al.
patent: 5948622 (1999-09-01), Reznikoff et al.
patent: 5968768 (1999-10-01), Haynes et al.
patent: 5968785 (1999-10-01), Devine et al.
patent: 6159736 (2000-12-01), Reznikoff et al.
patent: 6248569 (2001-06-01), Dunn et al.
patent: 6265159 (2001-07-01), Sugino et al.
patent: 6294385 (2001-09-01), Goryshin et al.
patent: 6504081 (2003-01-01), Westphal et al.
patent: 6593113 (2003-07-01), Tenkanen et al.
patent: 2003/0096349 (2003-05-01), Kazmierczak et al.
patent: WO 95/23875 (1995-09-01), None
patent: WO 97/29202 (1997-08-01), None
patent: WO98/10077 (1998-03-01), None
patent: WO98/37205 (1998-08-01), None
patent: WO98/40510 (1998-09-01), None
patent: WO 03/087370 (2003-10-01), None
Brune et al (Rapid Identification of essential and non-essential herpesvirus genes by direct transposon mutagenesis. Nature Biotechnology, 1999. 17:360-364).
Hobom et al (Fast Screening Procedure for Random Transposon Libraries of Cloned Herpesvirus Genomes: Mutational Analysis of Human Cytomegalovirus Envelope Glycoprotein Genes. Journal of Virology, 2000. 74(17)7720-7729).
Costa et al (Cloning and analysis of PCR-generated fragments. PCR Methods and Applications, 1994. 3(6): 338-345).
Yohda et al., Solid-Phase Nested Deletion: A New Subcloning-less Method for Generating Nested Deletions; DNA Research, 2:175-181, (1995).
Zhu and Clarke, Rapid construction of nested deletions of recombinant plasmid DNA for dideoxy sequencing.; BioTechniques, 18:222-224, (1995).
Henikoff et al., Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing.; Gene, 28:351-359, (1984).
Pues et al., Construction of a deletion library using a mixture of 5′-truncated primers for inverse PCR (IPCR); Nucleic Acids Res. 25:1303-1304, (1997).
Strathmann et al., Transposon-Facilitated DNA Sequencing; Proc. Nat. Acad. Sci. USA 88:1247-1250, (1991).
Phadnis et al., Tn5supF, a 264-Base-Pair Transposon Derived from Tn5 for Insertion Mutagenesis and Sequencing DNAs Cloned in Phage lambda; Proc. Nat. Acad. Sci. USA 86:5908-.
Way et al., New Tn10 derivatives for transposon mutagenesis and for construction of lacZ operon fusions by transposition.; Gene 32:369-279, (1984).
Kleckner et al., Uses of transposons with emphasis on Tn10.; Method. Enzymol. 204:139-180, (1991).
Lee et al., Efficient Tn 10 Transposition into a DNA Insertion Hot Spot in vivo Requires the 5-methyl Groups of Symmetrically Disposed Thymines within the Hot-Spot Consensus Sequence: Proc. Nat. Acad. Sci. USA 84:7876, (1987).
Brown et al., Correct integration of retroviral DNA in vitro.; Cell, 49:347-356, (1987).
Eichinger et al., The DNA intermediate in yeast Ty1 element transposition copurifies with virus-like particles: cell-free Ty1 transposition.; Cell, 54:955-966, (1988).
Eichinger et al., A specific terminal structure is required for Ty1 transposition; Genes Dev., 4:324-330, (1990).
Ahmed, Use of transposon-promoted deletions in DNA sequence analysis.; J. Mol. Biol., 178:941-948, (1984).
Hattori et al., A novel method for making nested deletions and its application for sequencing of a 300 kb region of human APP locus; Nucleic Acids Res. 25:1802-1808, (1997).
Jilk et al., Implications of Tn5-associated adjacent deletions.; J. Bacteriology, 175:1264-1271, (1993).
Krishnan et al., Construction of a genomic DNA ‘feature map’ by sequencing from nested deletions: application to the HLA class I region; Nucleic Acids Res. 23:117-122, (1995).
Morita et al., Nested Deletions from a Fixed Site as an Aid to Nucleotide Sequencing: an in vitro System Using Tn3 Transposase; DNA Research, 3:431-433, (1996).
Wang et al., pDUAL: A Transposon-Based Cosmid Cloning Vector for Generating Nested Deletions and DNA Sequencing Templates in vivo; Proc. Natl. Acad. Sci., 90:7874-7878, (1993).
York et al., Simple and efficient generation in vitro of nested deletions and inversions: Tn5 intramolecular transposition; Nucleic Acids Res. 26:1927, (1998).
Goryshin, I. and Reznikoff, Tn5 in Vitro Transposition; W.S., J. Biol. Chem., 273:7367, (1998).
Mizuuchi, K., In vitro transposition of bacteriophage Mu: a biochemical approach to a novel replication reaction.; Cell, 35:785, (1983).
Savilahti, H, et al., The phage Mu transpososome core: DNA requirements for assembly and function.; EMBO J., 14:4893, (1995).
Colegio OR et al., In Vitro Transposition System for Efficient Generation of Random Mutants of Campylobacter jejuni; J Bacteriol., 183:2384-8, (2001).
Kirby C et al., Cryptic plasmids of Mycobacterium avium: Tn552 to the rescue.; Mol Microbiol., 43:173-86, (2002).
Devine SE, and Boeke JD., Efficient integration of artificial transposons into plasmid targets in vitro: a useful tool for DNA mapping, sequencing and genetic analysis; Nucleic Acids Res., 22:3765-72, (1994).
Craig, NL, Update: V(D)J Recombination and Transposition: Closer Than Expected; Science. 271:1512, (1996).
Craig, NL, Transposon Tn7.; Curr Top Microbiol Immunol., 204:27-48, (1996).
Kleckner N, et al., Tn10 and IS10 transposition and chromosome rearrangements: mechanism and regulation in vivo and in vitro.; Curr Top Microbiol Immunol., 204:49-82, (1996).
Lampe DJ, et al., A purified mariner transposase is sufficient to mediate transposition in vitro.; EMBO J., 15:5470-9, (1996).
Plasterk RH, The Tc1/mariner transposon family.; Curr Top Microbiol Immunol, 204:125-43, (1996).
Gloor, Gene targeting inDrosophila.; Methods Mol Biol., 260:97-114, (2004).
Ichikawa H, and Ohtsubo E., In vitro transposition of transposon Tn3; J Biol Chem. 265:18829-32, (1990).
Ohtsubo, F and Sekine, Y, Bacterial insertion sequences.; Curr. Top. Microbiol. Immunol., 204:1-26, (1996).
Brown et al., Retroviral Integration: Structure of the Initial Covalent Product and Its Precursor, and a Role for the Viral IN Protein; Proc Natl Acad Sci USA, 86:2525-9, (1989).
Boeke JD and Corces VG, Transcription and reverse transcription of retrotransposons.; Annu Rev Microbiol., 43:403-34, (1989).
Dennis JJ and Zylstra GJ, Plasposons: Modular Self-Cloning Minitransposon Derivatives for Rapid Genetic Analysis of Gram-Negative Bacterial Genomes; Appl. Environ. Microbiol. 64:2710-2715, (1998.
Zhou and Doetsch, Effects of Abasic Sites and DNA Single-Strand Breaks on Prokaryotic RNA Polymerases; Proc. Nat. Acad. Sci. USA 90:6601-6605, (1993).
Martin, and Coleman, Kinetic analysis of T7 RNA polymerase-promoter interactions with small synthetic promoters.; Biochemistry 26:2690-2696, (1987).
McGraw et al., Sequence and analysis of the gene for bacteriophage T3 RNA polymerase; Nucl. Acid. Res. 13:6753-6766, (1985).
Kazmierczak et al., The phage N4 virion RNA polymerase catalytic domain is related to single-subunit RNA polymerases.; EMBO J., 21:5815-5823, (2002).
Wang et al., “Inversions and deletions generated by a mini-gamma delta (Tn1000) transposon,” Bacteriolog

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