Methods and compositions for amplifying DNA clone copy number

Details Methods and compositions for amplifying DNA clone copy number Methods and compositions for amplifying DNA clone copy number

2006-11-21

2006-11-21

Sullivan, Daniel M. (Department: 1636)

Chemistry: molecular biology and microbiology

Micro-organism, per se ; compositions thereof; proces of...

Bacteria or actinomycetales; media therefor

C435S471000

Reexamination Certificate

active

07138267

ABSTRACT:
A method for retrofitting DNA in a single-copy or high-copy vector, such as a fosmid or BAC, whereby an artificial transposon is used to introduce a conditional multi-copy origin of replication (“ori”) into the DNA in said vector. Following random in vitro or in vivo transposition of the ori-containing transposon into DNA in the single-copy or low-copy vector, the resulting insertion clones are introduced into a special host strain that contains a gene which encodes a polypeptide required for replication from the multi-copy ori. However, since the gene for this polypeptide is expressed from a tightly-regulated inducible promoter, the polypeptide is not expressed in the absence of inducer. On addition of inducer to the culture medium, the host cell synthesizes the polypeptide, which in turn activates replication from the multi-copy ori, thereby increasing the amount of clone DNA synthesized by the cell.

REFERENCES:
patent: 5028530 (1991-07-01), Lai et al.
patent: 5733744 (1998-03-01), Hamilton
patent: 5874259 (1999-02-01), Szybalski
patent: 5948622 (1999-09-01), Reznikoff et al.
patent: 5977439 (1999-11-01), Hamilton
patent: 6022716 (2000-02-01), Chumakov et al.
patent: 6030807 (2000-02-01), De Lencastre et al.
patent: 6143530 (2000-11-01), Crouzet et al.
patent: 6159736 (2000-12-01), Reznikoff et al.
patent: 6258565 (2001-07-01), Blatny et al.
patent: 6258571 (2001-07-01), Chumakov et al.
patent: 6274369 (2001-08-01), Donahue, Jr. et al.
patent: 6294385 (2001-09-01), Goryshin et al.
patent: 6326350 (2001-12-01), Jacobs et al.
patent: 6346655 (2002-02-01), Hohn et al.
patent: 2001/0046698 (2001-11-01), Donahue, Jr., et al.
patent: 2002/0094575 (2002-07-01), Suzuki
patent: WO99/61034 (1999-12-01), None
patent: WO00/55346 (2000-09-01), None
patent: WO02/08431 (2002-01-01), None
Griffin, T.J., Parsons, L., Leschziner, DeVost, J., Derbyshire, K.M. and Grindley, N.D.F. In vitro tranposition of Tn552: tool for DNA sequencing and mutagenesis. Nucleic Acids Research, 27(19), 3859-3865 (1999).
Merkulov, G.V. and Boeke, J.D. Libraries of green fluorescent protein fusions generated by transposition in vitro. Gene, 222, 213-222 (1998).
U.S. Appl. No. 60/232,979.
GeneJumper™ oriV Transposon Kit, For retrofitting BAC DNA with an oriV transposon and primer binding sites to generate high DNA yields for sequencing, Invitrogen Life Technologies, pp. 1-22, 2001. (Advertisement).
Retrofit BACs with oriV and generate high DNA yields for sequencing, Expressions 8.6, 8(6):12, 2001. (Advertisement).
M. Better, “AraB Expression System inEscherichia coli,” Gene Expression Systems Using Nature for the Art of Expression, pp. 95-107, Academic Press, 1999.
B. Birren, et al., “Bacterial Artificial Chromosomes,” Genome Analysis: A Laboratory Manual vol. 3 Cloning Systems, Cold Spring Harbor Laboratory Press, Chapter 4, pp. 241-245, 1999.
A. Blasina, et al., “Copy-up Mutants of the Plasmid RK2 Replication Initiation Protein are Defective in Coupling RK2 Replication Origins,” Proc. Natl. Acad. Sci. USA 93:3559-3564, 1996.
J. M. Blatny, et al., “Improved Broad-Host-Range RK2 Vectors Useful for High and Low Regulated Gene Expression Levels in Gram-Negative Bacteria,” Plasmid 38:35-51, 1997.
D. Boyd, et al., “Towards Single-Copy Gene Expression Systems making Gene Cloning Physiologically Relevant: Lambda InCh, a SimpleEscherichia coliPlasmid-Chromosome Shuttle System,” J. Bacter. 182(3):842-847, 2000.
P. K. Chatterjee, et al., “Direct Sequencing of Bacterial and P1 Artificial Chromosome-nested Deletions for Identifying Position-specific Single-nucleotide Polymorphisms,” PNAS 96(23):13276-13281, 1999.
S. Choi, et al., Plant & Animal Genome VII Conference, Jan. 17-21, 1999 (Abstract).
K. S. Doran, et al., “Replication Origin of the Broad Host Range Plasmid RK2,” J. Biol. Chem. 273(14):8447-8453, 1998.
R. H. Durland, et al., “Mutations in the trfA Replication Gene of the Broad-Host-Range Plasmid RK2 Result in Elevated Plasmid Copy Numbers,” J. Bacter. 172(7):3859-3867, 1990.
F. C. Fang, et al., “Mutations in the Gene Encoding the Replication-initiation Protein of Plasmid RK2 Produce Elevated Copy Numbers of RK2 Derivatives inEscherichia coliand Distantly Related Bacteria.” Gene 133:1-8. 1993.
E. Frengen, et al., “A Modular, Positive Selection Bacterial Artificial Chromosome Vector with Multiple Cloning Sites,” Genomics 58:250-253, 1999.
L. Frangeul, et al., “Cloning and Assembly Strategies in Microbial Genome Projects,” Microbiology 145:2625-2634, 1999.
L. H. Hansen, et al., “Chromosomal Insertion of the EntireEscherichia coliLactose Operon, into Two Strains ofPsuedomonas, Using a Modified Mini-Tn5 Delivery System,” Gene 186:167-173, 1997.
K. Haugan, et al., “The Host Range of RK2 Minimal Replicon Copy-up Mutants is Limited by Species-specific Differences in the Maximum Tolerable Copy Number,” Plasmid 33:27-39, 1995.
J. J. Jendrisak, et al., “Rapid, Direct Sequencing of Bacterial Artificial Chromosome Clones using Transposomes,” pp. 3-22, 2000.
P. Karunakaran, et al., “A Small Derivative of the Broad-Host-Range Plasmid RK2 which can be Switched from a Replicating to a Non-replicating State as a Response to an Externally Added Inducer,” FEMS Micro. Let. 180:221-227, 1999.
A. Lamberg, et al., “Efficient Insertion Mutagenesis Strategy for Bacterial Genomes Involving Electroporation of In Vitro-assembled DNA Transposition Complexes of Bacteriophase Mu,” App. Env. Micro. 68(2):705-712, 2002.
S. Perri, et al., “Interactions of Plasmid-encoded Replication Initiation Proteins with the Origin of DNA Replication in the Broad Host Range Plasmid RK2,” J. Biol. Chem. 266(19):12536-12543, 1991.
M. Sektas and W. Szybalski, “Tightly Controlled Two-stage Expression Vectors Employing the Flp/FRT-mediated Inversion of Cloned Genes,” Mol. Biotech. 9:17-24, 1998.
V. Shingler and C. M. Thomas, “Analysis of the trfA Region of Broad Host-range Plasmid RK2 by Transposon Mutagenesis and Identification of Polypeptide Products,” J. Mol. Biol. 175:229-249, 1984.
C. A. Smith and C. M. Thomas, “Nucleotide Sequence of the trfA Gene of Broad Host-range Plasmid RK2,” J. Mol. Biol. 175:251-262, 1984.
H. Shizuya, et al., “Cloning and Stable Maintenance of 300-kilobase-pair Fragments of Human DNA inEscherichia coliusing an F-factor-based Vector,” Proc. Natl. Acad. Sci. USA 89:8794-8797, 1992.
H. Shizuya and H. Kouros-Mehr, “Minireview Series for the 50th Volume, The Development and Applications of the Bacterial Artificial Chromosome Cloning System,” Keio J. Med. 50(1): 26-30, 2001.
Q. Tao and H.-B. Zhang, “Cloning and Stable Maintenance of DNA Fragments over 300 kb inEscherichia coliwith Conventional Plasmid-based Vectors,” Nuc. Acids Res. 26(21):4901-4909, 1998.
J. Wild, et al., “A Broad-Host-Range in Vivo Pop-out and Amplification System for Generating Large Quantities of 50- to 100-kb Genomic Fragments for Direct DNA Sequencing,” Gene 179:181-188. 1996.
J. Wild, et al., “Targeting and Retrofitting Pre-existing Libraries of Transposon Insertions with FRT and oriV Elements for In-vivo Generation of Large Quantities of any Genomic Fragment,” Gene 223:55-66, 1998.

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