Literature DB >> 19386556

Construction of a circular single-stranded DNA template containing a defined lesion.

Kiyonobu Karata1, Antonio E Vidal, Roger Woodgate.   

Abstract

We report a concise and efficient method to make a circular single-stranded DNA containing a defined DNA lesion. In this protocol, phagemid DNA containing Uracil is used as a template to synthesize a complementary DNA strand using T7 DNA polymerase and an oligonucleotide primer including a site-specific DNA lesion. The ligated lesion-containing strand can be recovered after the phage-derived template DNA is degraded by treatment with E. coli Uracil DNA glycosylase and Exonucleases I and III. The resulting product is a circular single-stranded DNA containing a defined DNA lesion suitable for in vitro translesion replication assays.

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Year:  2009        PMID： 19386556      PMCID： PMC2700212          DOI： 10.1016/j.dnarep.2009.03.006

Source DB:  PubMed          Journal:  DNA Repair (Amst)        ISSN： 1568-7856


  16 in total

Review 1.  Switching from high-fidelity replicases to low-fidelity lesion-bypass polymerases.

Authors:  Brian S Plosky; Roger Woodgate
Journal:  Curr Opin Genet Dev       Date:  2004-04       Impact factor: 5.578

2.  Defining the position of the switches between replicative and bypass DNA polymerases.

Authors:  Shingo Fujii; Robert P Fuchs
Journal:  EMBO J       Date:  2004-10-07       Impact factor: 11.598

3.  The use of native T7 DNA polymerase for site-directed mutagenesis.

Authors:  K Bebenek; T A Kunkel
Journal:  Nucleic Acids Res       Date:  1989-07-11       Impact factor: 16.971

Review 4.  Efficient site-directed mutagenesis using uracil-containing DNA.

Authors:  T A Kunkel; K Bebenek; J McClary
Journal:  Methods Enzymol       Date:  1991       Impact factor: 1.600

5.  Frequency and spectrum of mutations produced by a single cis-syn thymine-thymine cyclobutane dimer in a single-stranded vector.

Authors:  S K Banerjee; R B Christensen; C W Lawrence; J E LeClerc
Journal:  Proc Natl Acad Sci U S A       Date:  1988-11       Impact factor: 11.205

6.  Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis.

Authors:  M Tang; P Pham; X Shen; J S Taylor; M O'Donnell; R Woodgate; M F Goodman
Journal:  Nature       Date:  2000-04-27       Impact factor: 49.962

7.  Selective inactivation of the exonuclease activity of bacteriophage T7 DNA polymerase by in vitro mutagenesis.

Authors:  S Tabor; C C Richardson
Journal:  J Biol Chem       Date:  1989-04-15       Impact factor: 5.157

8.  Isolation and characterization of mutants of Escherichia coli deficient in induction of mutations by ultraviolet light.

Authors:  T Kato; Y Shinoura
Journal:  Mol Gen Genet       Date:  1977-11-14

9.  Rapid and efficient site-specific mutagenesis without phenotypic selection.

Authors:  T A Kunkel
Journal:  Proc Natl Acad Sci U S A       Date:  1985-01       Impact factor: 11.205

10.  Polymer-stimulated ligation: enhanced blunt- or cohesive-end ligation of DNA or deoxyribooligonucleotides by T4 DNA ligase in polymer solutions.

Authors:  B H Pheiffer; S B Zimmerman
Journal:  Nucleic Acids Res       Date:  1983-11-25       Impact factor: 16.971
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  4 in total

1.  Simple and efficient purification of Escherichia coli DNA polymerase V: cofactor requirements for optimal activity and processivity in vitro.

Authors:  Kiyonobu Karata; Alexandra Vaisman; Myron F Goodman; Roger Woodgate
Journal:  DNA Repair (Amst)       Date:  2012-02-15

2.  Escherichia coli UmuC active site mutants: effects on translesion DNA synthesis, mutagenesis and cell survival.

Authors:  Wojciech Kuban; Alexandra Vaisman; John P McDonald; Kiyonobu Karata; Wei Yang; Myron F Goodman; Roger Woodgate
Journal:  DNA Repair (Amst)       Date:  2012-07-10

3.  Critical amino acids in Escherichia coli UmuC responsible for sugar discrimination and base-substitution fidelity.

Authors:  Alexandra Vaisman; Wojciech Kuban; John P McDonald; Kiyonobu Karata; Wei Yang; Myron F Goodman; Roger Woodgate
Journal:  Nucleic Acids Res       Date:  2012-03-15       Impact factor: 16.971

4.  Mechanisms employed by Escherichia coli to prevent ribonucleotide incorporation into genomic DNA by Pol V.

Authors:  John P McDonald; Alexandra Vaisman; Wojciech Kuban; Myron F Goodman; Roger Woodgate
Journal:  PLoS Genet       Date:  2012-11-08       Impact factor: 5.917
  4 in total

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