Methods and compositions for amplifying DNA clone copy number

Title: Methods and compositions for amplifying DNA clone copy number

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.

Inventors:: Jendrisak, Jerome J.; Hoffman, Leslie M.; Fiandt, Michael J.; Haskins, Darin

Issue Date:: 2006-11-21

Research Org.:: Epicentre Technologies Corp., Madison, WI (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1531519

Patent Number(s):: 7138267

Application Number:: 10/116,886

Assignee:: Epicentre Technologies Corporation (Madison, WI)

Patent Classifications (CPCs):: C - CHEMISTRY C12 - BIOCHEMISTRY C12N - MICROORGANISMS OR ENZYMES

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C - CHEMISTRY C12 - BIOCHEMISTRY C12N - MICROORGANISMS OR ENZYMES
C12N15/70 - Vectors or expression systems specially adapted for E. coli
C12N15/69 - Increasing the copy number of the vector

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DOE Contract Number:: FG02-00ER83003

Resource Type:: Patent

Resource Relation:: Patent File Date: 2002-04-04

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Jendrisak, Jerome J., Hoffman, Leslie M., Fiandt, Michael J., and Haskins, Darin. Methods and compositions for amplifying DNA clone copy number.  United States: N. p., 2006. 
        Web.

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                    Jendrisak, Jerome J., Hoffman, Leslie M., Fiandt, Michael J., & Haskins, Darin. Methods and compositions for amplifying DNA clone copy number.  United States.

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                    Jendrisak, Jerome J., Hoffman, Leslie M., Fiandt, Michael J., and Haskins, Darin. Tue .  
        "Methods and compositions for amplifying DNA clone copy number".  United States.  https://www.osti.gov/servlets/purl/1531519.

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@article{osti_1531519,

  title        = {Methods and compositions for amplifying DNA clone copy number},

  author       = {Jendrisak, Jerome J. and Hoffman, Leslie M. and Fiandt, Michael J. and Haskins, Darin},

  abstractNote = {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.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {2006},

  month        = {11}

}

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Title: Methods and compositions for amplifying DNA clone copy number

Abstract

Citation Formats

Nucleotide sequence of the trfA gene of broad host-range plasmid RK2 journal, May 1984

Method for making insertional mutations using a Tn5 synaptic complex patent, December 2000

Tightly controlled two-stage expression vectors employing the Flp/FRT-mediated inversion of cloned genes journal, February 1998

High throughput DNA sequencing vector patent, July 2001

Libraries of green fluorescent protein fusions generated by transposition in vitro journal, November 1998

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 journal, November 1999

Replication Origin of the Broad Host Range Plasmid RK2: POSITIONING OF VARIOUS MOTIFS IS CRITICAL FOR INITIATION OF REPLICATION journal, April 1998

AraB promoters and method of producing polypeptides, including cecropins, by microbiological techniques patent, July 1991

Cloning and assembly strategies in microbial genome projects journal, October 1999

Mutations in the gene encoding the replication-initiation protein of plasmid RK2 produce elevated copy numbers of RK2 derivatives in Escherichia coli and distantly related bacteria journal, October 1993

Cloning and stable maintenance of DNA fragments over 300 kb in Escherichia coli with conventional plasmid-based vectors journal, November 1998

Towards Single-Copy Gene Expression Systems Making Gene Cloning Physiologically Relevant: Lambda InCh, a Simple Escherichia coli Plasmid-Chromosome Shuttle System journal, February 2000

Copy-up mutants of the plasmid RK2 replication initiation protein are defective in coupling RK2 replication origins. journal, April 1996

Direct sequencing of bacterial and P1 artificial chromosome-nested deletions for identifying position-specific single-nucleotide polymorphisms journal, November 1999

High throughput DNA sequencing vector patent, February 2000

Transferrin receptor subunit proteins of Neisseria meningitidis patent, December 2001

Binary BAC vector patent, November 1999

Binary BAC vector patent, March 1998

Highly regulable promoter for heterologous gene expression patent, February 2000

Efficient Insertion Mutagenesis Strategy for Bacterial Genomes Involving Electroporation of In Vitro-Assembled DNA Transposition Complexes of Bacteriophage Mu journal, February 2002

Analysis of the trfA region of broad host-range plasmid RK2 by transposon mutagenesis and identification of polypeptide products journal, May 1984

Mutations in the trfA replication gene of the broad-host-range plasmid RK2 result in elevated plasmid copy numbers. journal, January 1990

Chromosomal insertion of the entire Escherichia coli lactose operon, into two strains of Pseudomonas, using a modified mini-Tn5 delivery system journal, February 1997

Circular DNA expression cassettes for in vivo gene transfer patent, November 2000

The Host Range of RK2 Minimal Replicon Copy-Up Mutants Is Limited by Species-Specific Differences in the Maximum Tolerable Copy Number journal, January 1995

A Modular, Positive Selection Bacterial Artificial Chromosome Vector with Multiple Cloning Sites journal, June 1999

System for in vitro transposition patent, September 1999

Improved Broad-Host-Range RK2 Vectors Useful for High and Low Regulated Gene Expression Levels in Gram-Negative Bacteria journal, July 1997

Method capable of increasing competency of bacterial cell transformation patent, August 2001

Trichothecne-Resistant transgenic plants patent, February 2002

Compositions and methods for stable transformation using Mu bacteriophage cleaved donor complex patent-application, July 2002

Expression vectors based on RK2 and TOL plasmids patent, July 2001

Method capable of increasing competency of bacterial cell transformatio patent-application, November 2001

Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. journal, September 1992

Method for making insertional mutations using a Tn5 synaptic complex patent, September 2001

Conditionally amplifiable BAC vector patent, February 1999

In vitro transposition of Tn552: a tool for DNA sequencing and mutagenesis journal, October 1999

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 journal, January 1996

The development and applications of the bacterial artificial chromosome cloning system. journal, January 2001

Linking sequence reads using paired code tags patent, September 2014

Partitioning and processing of analytes and other species patent, December 2018

Partitioning and processing of analytes and other species patent, December 2018

Compositions and methods for sample processing patent, March 2019

Methods and systems for processing polynucleotides patent, February 2019

Sample preparation on a solid support patent, June 2017

Methods and systems for processing polynucleotides patent, August 2018

Processes and systems for preparation of nucleic acid sequencing libraries and libraries prepared using same patent, March 2019

Transposition of native chromatin for personal epigenomics patent, December 2018

Fluidic devices, systems, and methods for encapsulating and partitioning reagents, and applications of same patent, December 2018

Sample preparation on a solid support patent, August 2018

Fluidic devices, systems, and methods for encapsulating and partitioning reagents, and applications of same patent, September 2018

Capsule array devices and methods of use patent, August 2018

Methods and systems for processing polynucleotides patent, March 2019

Transposition of native chromatin for personal epigenomics patent, August 2018

Methods and systems for processing polynucleotides patent, July 2018

Linking sequence reads using paired code tags patent, July 2015

Nucleotide sequence of the trfA gene of broad host-range plasmid RK2
journal, May 1984

Method for making insertional mutations using a Tn5 synaptic complex
patent, December 2000

Tightly controlled two-stage expression vectors employing the Flp/FRT-mediated inversion of cloned genes
journal, February 1998

High throughput DNA sequencing vector
patent, July 2001

Libraries of green fluorescent protein fusions generated by transposition in vitro
journal, November 1998

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
journal, November 1999

Replication Origin of the Broad Host Range Plasmid RK2: POSITIONING OF VARIOUS MOTIFS IS CRITICAL FOR INITIATION OF REPLICATION
journal, April 1998

AraB promoters and method of producing polypeptides, including cecropins, by microbiological techniques
patent, July 1991

Cloning and assembly strategies in microbial genome projects
journal, October 1999

Mutations in the gene encoding the replication-initiation protein of plasmid RK2 produce elevated copy numbers of RK2 derivatives in Escherichia coli and distantly related bacteria
journal, October 1993

Cloning and stable maintenance of DNA fragments over 300 kb in Escherichia coli with conventional plasmid-based vectors
journal, November 1998

Towards Single-Copy Gene Expression Systems Making Gene Cloning Physiologically Relevant: Lambda InCh, a Simple Escherichia coli Plasmid-Chromosome Shuttle System
journal, February 2000

Copy-up mutants of the plasmid RK2 replication initiation protein are defective in coupling RK2 replication origins.
journal, April 1996

Direct sequencing of bacterial and P1 artificial chromosome-nested deletions for identifying position-specific single-nucleotide polymorphisms
journal, November 1999

High throughput DNA sequencing vector
patent, February 2000

Transferrin receptor subunit proteins of Neisseria meningitidis
patent, December 2001

Binary BAC vector
patent, November 1999

Binary BAC vector
patent, March 1998

Highly regulable promoter for heterologous gene expression
patent, February 2000

Efficient Insertion Mutagenesis Strategy for Bacterial Genomes Involving Electroporation of In Vitro-Assembled DNA Transposition Complexes of Bacteriophage Mu
journal, February 2002

Analysis of the trfA region of broad host-range plasmid RK2 by transposon mutagenesis and identification of polypeptide products
journal, May 1984

Mutations in the trfA replication gene of the broad-host-range plasmid RK2 result in elevated plasmid copy numbers.
journal, January 1990

Chromosomal insertion of the entire Escherichia coli lactose operon, into two strains of Pseudomonas, using a modified mini-Tn5 delivery system
journal, February 1997

Circular DNA expression cassettes for in vivo gene transfer
patent, November 2000

The Host Range of RK2 Minimal Replicon Copy-Up Mutants Is Limited by Species-Specific Differences in the Maximum Tolerable Copy Number
journal, January 1995

A Modular, Positive Selection Bacterial Artificial Chromosome Vector with Multiple Cloning Sites
journal, June 1999

System for in vitro transposition
patent, September 1999

Improved Broad-Host-Range RK2 Vectors Useful for High and Low Regulated Gene Expression Levels in Gram-Negative Bacteria
journal, July 1997

Method capable of increasing competency of bacterial cell transformation
patent, August 2001

Trichothecne-Resistant transgenic plants
patent, February 2002

Compositions and methods for stable transformation using Mu bacteriophage cleaved donor complex
patent-application, July 2002

Expression vectors based on RK2 and TOL plasmids
patent, July 2001

Method capable of increasing competency of bacterial cell transformatio
patent-application, November 2001

Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector.
journal, September 1992

Method for making insertional mutations using a Tn5 synaptic complex
patent, September 2001

Conditionally amplifiable BAC vector
patent, February 1999

In vitro transposition of Tn552: a tool for DNA sequencing and mutagenesis
journal, October 1999

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
journal, January 1996

The development and applications of the bacterial artificial chromosome cloning system.
journal, January 2001

Linking sequence reads using paired code tags
patent, September 2014

Partitioning and processing of analytes and other species
patent, December 2018

Partitioning and processing of analytes and other species
patent, December 2018

Compositions and methods for sample processing
patent, March 2019

Methods and systems for processing polynucleotides
patent, February 2019

Sample preparation on a solid support
patent, June 2017

Methods and systems for processing polynucleotides
patent, August 2018

Processes and systems for preparation of nucleic acid sequencing libraries and libraries prepared using same
patent, March 2019

Transposition of native chromatin for personal epigenomics
patent, December 2018

Fluidic devices, systems, and methods for encapsulating and partitioning reagents, and applications of same
patent, December 2018

Sample preparation on a solid support
patent, August 2018

Fluidic devices, systems, and methods for encapsulating and partitioning reagents, and applications of same
patent, September 2018

Capsule array devices and methods of use
patent, August 2018

Methods and systems for processing polynucleotides
patent, March 2019

Transposition of native chromatin for personal epigenomics
patent, August 2018

Methods and systems for processing polynucleotides
patent, July 2018

Linking sequence reads using paired code tags
patent, July 2015