scholarly journals Pairing properties of bromouracil and repair of bromouracil-containing DNA. Possible utilization of bromodeoxyuridine triphosphate for site-directed mutagenesis

1988 ◽  
Vol 253 (3) ◽  
pp. 637-643 ◽  
Author(s):  
M Muller ◽  
J Martial ◽  
W G Verly
Keyword(s):  
Dna Polymerase ◽  
Site Directed Mutagenesis ◽  
Klenow Fragment ◽  
Single Experiment ◽  
E Coli ◽  
Partial Repair ◽  
Before And After ◽  
Polymerase I

5-Bromo-2′-deoxyuridine triphosphate (Br-dUTP) and dTTP are used interchangeably for DNA synthesis in vitro by the Klenow fragment of Escherichia coli DNA polymerase I. When DNA containing Br-dUMP instead of dTMP at a few preselected sites is transfected into competent bacteria, no mutation occurs, indicating that in vivo E. coli DNA polymerase always places a dAMP residue in front of any unrepaired Br-dUMP residue. On the other hand, in vitro Br-dUTP can also replace dCTP, but only with difficulty: when dCTP is absent, Br-dUMP can be forced in front of a dGMP residue, but the Klenow polymerase pauses before and after addition of Br-dUMP. Transfection into E. coli of the substituted DNA leads to the expected G→A transitions. These mutations can easily be targeted by using a suitable primer and the correctly chosen mix of deoxynucleoside triphosphates containing Br-dUTP. When Br-dUMP has been placed in front of a dGMP residue, the mutation yield is not 100%, showing a partial repair of the transfected DNA before it is replicated. Advantage can be taken of this partial repair to prepare a set of different mutations within a target region in a single experiment.

scholarly journals Catalytically inactive T7 DNA polymerase imposes a lethal replication roadblock

2020 ◽  
Vol 295 (28) ◽  
pp. 9542-9550
Author(s):  
Alfredo J. Hernandez ◽  
Seung-Joo Lee ◽  
Seungwoo Chang ◽  
Jaehun A. Lee ◽  
Joseph J. Loparo ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Metal Binding ◽  
Polymerase Activity ◽  
Stable Complex ◽  
Klenow Fragment ◽  
Dna Polymerase I ◽  
E Coli ◽  
Growth System ◽  
Polymerase I

Bacteriophage T7 encodes its own DNA polymerase, the product of gene 5 (gp5). In isolation, gp5 is a DNA polymerase of low processivity. However, gp5 becomes highly processive upon formation of a complex with Escherichia coli thioredoxin, the product of the trxA gene. Expression of a gp5 variant in which aspartate residues in the metal-binding site of the polymerase domain were replaced by alanine is highly toxic to E. coli cells. This toxicity depends on the presence of a functional E. coli trxA allele and T7 RNA polymerase-driven expression but is independent of the exonuclease activity of gp5. In vitro, the purified gp5 variant is devoid of any detectable polymerase activity and inhibited DNA synthesis by the replisomes of E. coli and T7 in the presence of thioredoxin by forming a stable complex with DNA that prevents replication. On the other hand, the highly homologous Klenow fragment of DNA polymerase I containing an engineered gp5 thioredoxin-binding domain did not exhibit toxicity. We conclude that gp5 alleles encoding inactive polymerases, in combination with thioredoxin, could be useful as a shutoff mechanism in the design of a bacterial cell-growth system.

scholarly journals Exonuclease III (XthA) EnforcesIn VivoDNA Cloning ofEscherichia coliTo Create Cohesive Ends

2018 ◽  
Vol 201 (5) ◽  
Author(s):  
Shingo Nozaki ◽  
Hironori Niki
Keyword(s):  
Dna Polymerase ◽  
Dna Fragments ◽  
Dna Polymerase I ◽  
Dna Cloning ◽  
Content Type ◽  
E Coli ◽  
Polymerase I ◽  
Cloning Technology

ABSTRACTEscherichia colihas an ability to assemble DNA fragments with homologous overlapping sequences of 15 to 40 bp at each end. Several modified protocols have already been reported to improve this simple and useful DNA cloning technology. However, the molecular mechanism by whichE. coliaccomplishes such cloning is still unknown. In this study, we provide evidence that thein vivocloning ofE. coliis independent of both RecA and RecET recombinases but is dependent on XthA, a 3′ to 5′ exonuclease. Here,in vivocloning ofE. coliby XthA is referred to asin vivoE. colicloning (iVEC). We also show that iVEC activity is reduced by deletion of the C-terminal domain of DNA polymerase I (PolA). Collectively, these results suggest the following mechanism of iVEC. First, XthA resects the 3′ ends of linear DNA fragments that are introduced intoE. colicells, resulting in exposure of the single-stranded 5′ overhangs. Then, the complementary single-stranded DNA ends hybridize each other, and gaps are filled by DNA polymerase I. Elucidation of the iVEC mechanism at the molecular level would further advance the development ofin vivoDNA cloning technology. Already we have successfully demonstrated multiple-fragment assembly of up to seven fragments in combination with an effortless transformation procedure using a modified host strain for iVEC.IMPORTANCECloning of a DNA fragment into a vector is one of the fundamental techniques in recombinant DNA technology. Recently, anin vitrorecombination system for DNA cloning was shown to enable the joining of multiple DNA fragments at once. Interestingly,E. colipotentially assembles multiple linear DNA fragments that are introduced into the cell. Improved protocols for thisin vivocloning have realized a high level of usability, comparable to that byin vitrorecombination reactions. However, the mechanism ofin vivocloning is highly controversial. Here, we clarified the fundamental mechanism underlyingin vivocloning and also constructed a strain that was optimized forin vivocloning. Additionally, we streamlined the procedure ofin vivocloning by using a single microcentrifuge tube.

scholarly journals Exonuclease III (XthA) enforcesin vivoDNA cloning ofEscherichia colito create cohesive ends

2018 ◽  
Author(s):  
Shingo Nozaki ◽  
Hironori Niki
Keyword(s):  
Dna Polymerase ◽  
Recombination Reaction ◽  
Dna Fragments ◽  
Dna Polymerase I ◽  
Dna Cloning ◽  
E Coli ◽  
Polymerase I ◽  
Cloning Technology

AbstractEscherichia colihas an ability to assemble DNA fragments with homologous overlapping sequences of 15-40 bp at each end. Several modified protocols have already been reported to improve this simple and useful DNA-cloning technology. However, the molecular mechanism by whichE. coliaccomplishes such cloning is still unknown. In this study, we provide evidence that thein vivocloning ofE. coliis independent of both RecA and RecET recombinase, but is dependent on XthA, a 3’ to 5’ exonuclease. Here, in vivocloning ofE. coliby XthA is referred to as iVEC (in vivo E. colicloning). Next, we show that the iVEC activity is reduced by deletion of the C-terminal domain of DNA polymerase I (PolA). Collectively, these results suggest the following mechanism of iVEC. First, XthA resects the 3′ ends of linear DNA fragments that are introduced intoE. colicells, resulting in exposure of the single-stranded 5′ overhangs. Then, the complementary single-stranded DNA ends hybridize each other, and gaps are filled by DNA polymerase I. Elucidation of the iVEC mechanism at the molecular level would further advance the development ofin vivoDNA-cloning technology. Already we have successfully demonstrated multiple-fragment assembly of up to seven fragments in combination with an effortless transformation procedure using a modified host strain for iVEC.ImportanceCloning of a DNA fragment into a vector is one of the fundamental techniques in recombinant DNA technology. Recently,in vitrorecombination of DNA fragments effectively joins multiple DNA fragments in place of the canonical method. Interestingly,E. colican take up linear double-stranded vectors, insert DNA fragments and assemble themin vivo.Thein vivocloning have realized a high level of usability comparable to that byin vitrorecombination reaction, since now it is only necessary to introduce PCR products intoE. colifor thein vivocloning. However, the mechanism ofin vivocloning is highly controversial. Here we clarified the fundamental mechanism underlyingin vivocloning of E. coli and also constructed anE. colistrain that was optimized forin vivocloning.

The Mechanism of Replication of Single-Stranded DNA. VI. Requirements for Ribonucleoside Triphosphates and DNA Polymerase III

1973 ◽  
Vol 51 (12) ◽  
pp. 1588-1597 ◽  
Author(s):  
David T. Denhardt ◽  
Makoto Iwaya ◽  
Grant McFadden ◽  
Gerald Schochetman
Keyword(s):  
Dna Polymerase ◽  
Dna Polymerases ◽  
Temperature Sensitive ◽  
Restrictive Temperature ◽  
Dna Polymerase Iii ◽  
Single Stranded Dna ◽  
E Coli ◽  
Polymerase Iii

Evidence is presented that in Escherichia coli made permeable to nucleotides by exposure to toluene, the synthesis of a DNA chain complementary to the infecting single-stranded DNA of bacteriophage [Formula: see text] requires ATP as well as the four deoxyribonucleoside triphosphates. This synthesis results in the formation of the parental double-stranded replicative-form (RF) molecule. The ATP is not required simply to prevent degradation of the ribonucleoside or deoxyribonucleoside triphosphates; it can be partially substituted for by other ribonucleoside triphosphates.No single one of the known E. coli DNA polymerases appears to be uniquely responsible in vivo for the formation of the parental RF. Since [Formula: see text] replicates well in strains lacking all, or almost all, of the in-vitro activities of DNA polymerases I and II, neither of these two enzymes would seem essential; and in a temperature-sensitive E. coli mutant (dnaEts) deficient in DNA polmerase-I activity and possessing a temperature-sensitive DNA polymerase III, the viral single-stranded DNA is efficiently incorporated into an RF molecule at the restrictive temperature. In contrast, both RF replication and progeny single-stranded DNA synthesis are dependent upon DNA polymerase III activity.

DNA polymerase I proofreading exonuclease activity is required for endonuclease V repair pathway both in vitro and in vivo

DNA Repair ◽  
2018 ◽  
Vol 64 ◽  
pp. 59-67 ◽  
Author(s):  
Kang-Yi Su ◽  
Liang-In Lin ◽  
Steven D. Goodman ◽  
Rong-Syuan Yen ◽  
Cho-Yuan Wu ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Exonuclease Activity ◽  
Repair Pathway ◽  
Dna Polymerase I ◽  
Endonuclease V ◽  
Polymerase I

How E. coli DNA polymerase I (klenow fragment) distinguishes between deoxy- and dideoxynucleotides

1998 ◽  
Vol 278 (1) ◽  
pp. 147-165 ◽  
Author(s):  
Mekbib Astatke ◽  
Nigel D.F Grindley ◽  
Catherine M Joyce
Keyword(s):  
Dna Polymerase ◽  
Klenow Fragment ◽  
Dna Polymerase I ◽  
E Coli ◽  
Polymerase I

scholarly journals DNA polymerase X from Deinococcus radiodurans implicated in bacterial tolerance to DNA damage is characterized as a short patch base excision repair polymerase

Microbiology ◽  
2009 ◽  
Vol 155 (9) ◽  
pp. 3005-3014 ◽  
Author(s):  
Nivedita P. Khairnar ◽  
Hari S. Misra
Keyword(s):  
Dna Damage ◽  
Dna Polymerase ◽  
Base Excision Repair ◽  
Deinococcus Radiodurans ◽  
Excision Repair ◽  
Strand Break ◽  
Klenow Fragment ◽  
E Coli ◽  
Base Excision

The Deinococcus radiodurans R1 genome encodes an X-family DNA repair polymerase homologous to eukaryotic DNA polymerase β. The recombinant deinococcal polymerase X (PolX) purified from transgenic Escherichia coli showed deoxynucleotidyltransferase activity. Unlike the Klenow fragment of E. coli, this enzyme showed short patch DNA synthesis activity on heteropolymeric DNA substrate. The recombinant enzyme showed 5′-deoxyribose phosphate (5′-dRP) lyase activity and base excision repair function in vitro, with the help of externally supplied glycosylase and AP endonuclease functions. A polX disruption mutant of D. radiodurans expressing 5′-dRP lyase and a truncated polymerase domain was comparatively less sensitive to γ-radiation than a polX deletion mutant. Both mutants showed higher sensitivity to hydrogen peroxide. Excision repair mutants of E. coli expressing this polymerase showed functional complementation of UV sensitivity. These results suggest the involvement of deinococcal polymerase X in DNA-damage tolerance of D. radiodurans, possibly by contributing to DNA double-strand break repair and base excision repair.

Labeling of Synthetic Oligonucleotides Using the Klenow Fragment of E. coli DNA Polymerase I

2021 ◽  
Vol 2021 (10) ◽  
pp. pdb.prot100693
Author(s):  
Michael R. Green ◽  
Joseph Sambrook
Keyword(s):  
Dna Polymerase ◽  
Oligonucleotide Probes ◽  
Klenow Fragment ◽  
Dna Polymerase I ◽  
E Coli ◽  
Specific Activities ◽  
Radiolabeled Probe ◽  
Polymerase I ◽  
Synthetic Oligonucleotides ◽  
Radioactive Atoms

In this method, a short primer is hybridized to an oligonucleotide template whose sequence is the complement of the desired radiolabeled probe. The primer is then extended using the Klenow fragment to incorporate [α-32P]dNTPs in a template-directed manner. After the reaction, the template and product are separated by denaturation followed by electrophoresis through a polyacrylamide gel under denaturing conditions. With this method, it is possible to generate oligonucleotide probes that contain several radioactive atoms per molecule of oligonucleotide and to achieve specific activities as high as 2 × 1010 cpm/µg of probe. Because the end product of the reaction is dsDNA, whose strands must be separated and the labeled product isolated, this method is generally not used to prepare nonradiolabeled oligonucleotides.

Eucaryotic transcription complexes are specifically associated in large sedimentable structures: rapid isolation of polymerase I, II, and III transcription factors

1985 ◽  
Vol 5 (7) ◽  
pp. 1582-1590
Author(s):  
V C Culotta ◽  
R J Wides ◽  
B Sollner-Webb
Keyword(s):  
Transcription Factors ◽  
Dna Polymerase ◽  
In Vitro Transcription ◽  
Cell Extracts ◽  
S 100 ◽  
Major Late Promoter ◽  
Transcription Complexes ◽  
Polymerase I

RNA synthesis in eucaryotes takes place on template molecules that are activated by stably associating with limiting transcription factors. In this paper we demonstrate that such stable transcription complexes can be specifically sedimented from in vitro transcription reaction mixtures by mild centrifugation. This occurs with stable complexes of genes transcribed by all three classes of eucaryotic RNA polymerase and with S-100 as well as whole-cell extracts. However, the transcriptional capacity of the isolated complex differs for the three polymerase classes. The pelleted ribosomal DNA (polymerase I) complex contains all the factors necessary for transcription, each purified 25- to 50-fold, whereas the pelleted adenovirus major late promoter (polymerase II) complex lacks a factor that remains in the supernatant. In the case of 5S DNA (polymerase III), a necessary factor associates slowly with the sedimentable complex. Notably, the interactions responsible for this rapid sedimentation are specific for DNA molecules in stable complexes, suggesting that the in vitro sedimentable complex mirrors the in vivo structural organization of active genes.

Biochemical characterization of human DNA polymerase i provides clues to its biological function

2001 ◽  
Vol 29 (2) ◽  
pp. 183-187 ◽  
Author(s):  
A. Tissier ◽  
E. G. Frank ◽  
J. P. McDonald ◽  
A. Vaisman ◽  
A. R. Fernàndez deHenestrosa Henestrosa ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Biochemical Characterization ◽  
Short Review ◽  
Biochemical Properties ◽  
Dna Polymerase I ◽  
Polymerase I

The human RAD30B gene has recently been shown to encode a novel DNA polymerase, DNA polymerase i (poli). The role of poli within the cell is presently unknown, and the only clues to its cellular function come from its biochemical characterization in vitro. The aim of this short review is, therefore, to summarize the known enzymic activities of poli and to speculate as to how these biochemical properties might relate to its in vivo function.

Sign in / Sign up

Export Citation Format

Share Document