large klenow fragment  (New England Biolabs)


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    Name:
    Klenow Fragment 3 5 exo
    Description:
    Klenow Fragment 3 5 exo 1 000 units
    Catalog Number:
    m0212l
    Price:
    248
    Size:
    1 000 units
    Category:
    DNA Polymerases
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    New England Biolabs large klenow fragment
    Klenow Fragment 3 5 exo
    Klenow Fragment 3 5 exo 1 000 units
    https://www.bioz.com/result/large klenow fragment/product/New England Biolabs
    Average 90 stars, based on 88 article reviews
    Price from $9.99 to $1999.99
    large klenow fragment - by Bioz Stars, 2020-02
    90/100 stars

    Images

    1) Product Images from "Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment"

    Article Title: Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.67.12.5780-5790.2001

    Quantitative analysis of functional gene arrays. (A) Relationship of hybridization signal intensity to DNA target concentration from a single pure culture. Genomic DNA from nirS -containing P. stutzeri E4-2 was labeled with Cy5 and hybridized to the microarrays at the following target concentrations: 0.5, 1, 2.5, 5, 10, 25, 50, and 100 ng. The plot shows the log-transformed average hybridization intensity versus the log-transformed target DNA concentration. (B) Relationship of hybridization signal intensity to DNA target concentration using a mixture of target DNAs. The PCR products from the following nine strains were mixed together in different quantities (in picograms): E4-2 ( nirS ), 1,000; G179 ( nirK ), 500; wc301–37 ( amoA ), 250; ps-47 ( amoA ), 125; pB49 ( nirS ), 62.5; Y32K ( nirK ), 31.3; wA15 ( nirS ), 15.6; ps-80 ( amoA ), 7.8; wB54 ( nirK ), 3.9. All of these genes are less than 80% identical. The mixed templates were labeled with Cy5. The plot shows the log-transformed average hybridization intensity versus the log-transformed target DNA concentration for each strain. (C) Effects of probe DNA size and composition on hybridization signal intensity. Microarrays contained DNA fragments (200 ng μl −1 ) of different sizes amplified from different regions in the S. oneidensis MR-1 genome. The target DNA was prepared by labeling MR-1 genomic DNA with Cy5 using the Klenow fragment with random hexamer primers. For panels A and B, the data points are mean values derived from three independent microarray slides, with three replicates on each slide (a total of nine data points). Error bars showing the standard deviations are presented.
    Figure Legend Snippet: Quantitative analysis of functional gene arrays. (A) Relationship of hybridization signal intensity to DNA target concentration from a single pure culture. Genomic DNA from nirS -containing P. stutzeri E4-2 was labeled with Cy5 and hybridized to the microarrays at the following target concentrations: 0.5, 1, 2.5, 5, 10, 25, 50, and 100 ng. The plot shows the log-transformed average hybridization intensity versus the log-transformed target DNA concentration. (B) Relationship of hybridization signal intensity to DNA target concentration using a mixture of target DNAs. The PCR products from the following nine strains were mixed together in different quantities (in picograms): E4-2 ( nirS ), 1,000; G179 ( nirK ), 500; wc301–37 ( amoA ), 250; ps-47 ( amoA ), 125; pB49 ( nirS ), 62.5; Y32K ( nirK ), 31.3; wA15 ( nirS ), 15.6; ps-80 ( amoA ), 7.8; wB54 ( nirK ), 3.9. All of these genes are less than 80% identical. The mixed templates were labeled with Cy5. The plot shows the log-transformed average hybridization intensity versus the log-transformed target DNA concentration for each strain. (C) Effects of probe DNA size and composition on hybridization signal intensity. Microarrays contained DNA fragments (200 ng μl −1 ) of different sizes amplified from different regions in the S. oneidensis MR-1 genome. The target DNA was prepared by labeling MR-1 genomic DNA with Cy5 using the Klenow fragment with random hexamer primers. For panels A and B, the data points are mean values derived from three independent microarray slides, with three replicates on each slide (a total of nine data points). Error bars showing the standard deviations are presented.

    Techniques Used: Functional Assay, Hybridization, Concentration Assay, Labeling, Transformation Assay, Polymerase Chain Reaction, Amplification, Random Hexamer Labeling, Derivative Assay, Microarray

    The normalized distribution of signal intensity levels for nirS, nirK , and amoA genes as determined by microarray-based analysis of community DNA from marine sediment (W303) and surface soil (O22) environments. Bulk community DNA isolated from two different environmental samples was directly labeled with Cy5 using Klenow fragment with random hexamer primers and hybridized with the microarrays at 65°C in separate experiments. The hybridization signal intensity for each gene is presented. Shaded bars represent probes from environmental clones, and striped boxes represent pmo A probes from environmental clones. Open bars designate probes from pure cultures. The data represent mean values obtained from nine replicates after subtracting background hybridization to yeast genes. For the nirS graphs, bars 1 to 42 correspond to individual genes S1-S42 (see assigned designation in Table 1 on the web site). Similarly, bars 1 to 18 for nirK correspond to genes K1 to K18, and bars 1 to 22 for amoA and pmoA represent genes M1 to M22 (see our table on the website cited in Materials and Methods). The standard deviation of signal intensity is indicated on the top of each bar.
    Figure Legend Snippet: The normalized distribution of signal intensity levels for nirS, nirK , and amoA genes as determined by microarray-based analysis of community DNA from marine sediment (W303) and surface soil (O22) environments. Bulk community DNA isolated from two different environmental samples was directly labeled with Cy5 using Klenow fragment with random hexamer primers and hybridized with the microarrays at 65°C in separate experiments. The hybridization signal intensity for each gene is presented. Shaded bars represent probes from environmental clones, and striped boxes represent pmo A probes from environmental clones. Open bars designate probes from pure cultures. The data represent mean values obtained from nine replicates after subtracting background hybridization to yeast genes. For the nirS graphs, bars 1 to 42 correspond to individual genes S1-S42 (see assigned designation in Table 1 on the web site). Similarly, bars 1 to 18 for nirK correspond to genes K1 to K18, and bars 1 to 22 for amoA and pmoA represent genes M1 to M22 (see our table on the website cited in Materials and Methods). The standard deviation of signal intensity is indicated on the top of each bar.

    Techniques Used: Microarray, Isolation, Environmental Sampling, Labeling, Random Hexamer Labeling, Hybridization, Clone Assay, Standard Deviation

    2) Product Images from "Oxidative stress-induced chromosome breaks within the ABL gene: a model for chromosome rearrangement in nasopharyngeal carcinoma"

    Article Title: Oxidative stress-induced chromosome breaks within the ABL gene: a model for chromosome rearrangement in nasopharyngeal carcinoma

    Journal: Human Genomics

    doi: 10.1186/s40246-018-0160-8

    A flowchart showing the manipulation steps in the preparation of genomic DNA for IPCR. The genomic DNA was subjected to RE digestions, Klenow fill-in and ligation prior to IPCR as reported before [ 80 ]
    Figure Legend Snippet: A flowchart showing the manipulation steps in the preparation of genomic DNA for IPCR. The genomic DNA was subjected to RE digestions, Klenow fill-in and ligation prior to IPCR as reported before [ 80 ]

    Techniques Used: Ligation

    3) Product Images from "Inhibitor of caspase-activated DNase expression enhances caspase-activated DNase expression and inhibits oxidative stress-induced chromosome breaks at the mixed lineage leukaemia gene in nasopharyngeal carcinoma cells"

    Article Title: Inhibitor of caspase-activated DNase expression enhances caspase-activated DNase expression and inhibits oxidative stress-induced chromosome breaks at the mixed lineage leukaemia gene in nasopharyngeal carcinoma cells

    Journal: Cancer Cell International

    doi: 10.1186/s12935-015-0205-1

    Flow chart showing DNA modification and IPCR. The arrow heads indicate the forward and reverse primers that were designed in opposite direction. Bam H I digestion yielded a mixture of intact chromosome and cleaved chromosome. Klenow fill-in produced blunt ended chromosome fragments which were then cyclilsed by T4 DNA ligase. The intact chromosome will become a large circle while the cleaved chromosome will become a smaller circle. Upon cyclisation, the primers are now in correct orientation for amplification. Msc I digestion cleaved both circles outside the amplification region, thus merely linearise the molecule. Amplification from intact MLL gene will produce longer PCR products while amplification from cleaved MLL gene will yield shorter PCR products
    Figure Legend Snippet: Flow chart showing DNA modification and IPCR. The arrow heads indicate the forward and reverse primers that were designed in opposite direction. Bam H I digestion yielded a mixture of intact chromosome and cleaved chromosome. Klenow fill-in produced blunt ended chromosome fragments which were then cyclilsed by T4 DNA ligase. The intact chromosome will become a large circle while the cleaved chromosome will become a smaller circle. Upon cyclisation, the primers are now in correct orientation for amplification. Msc I digestion cleaved both circles outside the amplification region, thus merely linearise the molecule. Amplification from intact MLL gene will produce longer PCR products while amplification from cleaved MLL gene will yield shorter PCR products

    Techniques Used: Flow Cytometry, Modification, Produced, Amplification, Polymerase Chain Reaction

    4) Product Images from "Divalent ions attenuate DNA synthesis by human DNA polymerase α by changing the structure of the template/primer or by perturbing the polymerase reaction"

    Article Title: Divalent ions attenuate DNA synthesis by human DNA polymerase α by changing the structure of the template/primer or by perturbing the polymerase reaction

    Journal: DNA repair

    doi: 10.1016/j.dnarep.2016.05.017

    Comparison effects of Mg 2+ concentration on the activity of polα-prim and the Klenow fragment on the template with random sequence Sequence of the 3’ portion of the template 73b (excludes the 5’ primer-binding region) that can potentially form two hairpins (marked by * and **) is shown. The extension of hetero-DNA primers annealed with the template contains a heterogeneous sequence (73b) by polα-prim (enzyme to primer/template ratio = 1:15) and the Klenow fragment (enzyme to primer/template ratio = 1: 5) in the absence or presence of 0.2–16.0 mM Mg 2+ . Reactions were carried out at 35 °C for three minutes (polα-prim) and one minute (Klenow fragment).
    Figure Legend Snippet: Comparison effects of Mg 2+ concentration on the activity of polα-prim and the Klenow fragment on the template with random sequence Sequence of the 3’ portion of the template 73b (excludes the 5’ primer-binding region) that can potentially form two hairpins (marked by * and **) is shown. The extension of hetero-DNA primers annealed with the template contains a heterogeneous sequence (73b) by polα-prim (enzyme to primer/template ratio = 1:15) and the Klenow fragment (enzyme to primer/template ratio = 1: 5) in the absence or presence of 0.2–16.0 mM Mg 2+ . Reactions were carried out at 35 °C for three minutes (polα-prim) and one minute (Klenow fragment).

    Techniques Used: Concentration Assay, Activity Assay, Sequencing, Binding Assay

    Comparison of the effects of Zn 2+ alone and in combination with Mg 2+ on DNA synthesis by polα-prim and the Klenow fragment (A) Extension of hetero-DNA primers annealed with heterogeneous 73b template by polα-prim (enzyme to primer/template ratio = 1:10) and (B) the Klenow fragment. (enzyme to primer/template ratio = 1:5). Lanes 2–9, polα-prim for one minute; Lanes 10–17, polα-prim for eight minutes; Lanes 18–25, the Klenow fragment for one minute; all with 100 µM dNTP at 35 °C. Reactions contained no enzyme (lane 1), no additional Me 2+ (lanes 2, 10, 18), 8 mM Mg 2+ (lanes 3, 11, 19), 10 to 50 µM Zn 2+ (lanes 4–6, 12–14, 20–22), and 8 mM Mg 2+ with 10 to 50 µM Zn 2+ (lanes 7–9, 15–17, 23–25).
    Figure Legend Snippet: Comparison of the effects of Zn 2+ alone and in combination with Mg 2+ on DNA synthesis by polα-prim and the Klenow fragment (A) Extension of hetero-DNA primers annealed with heterogeneous 73b template by polα-prim (enzyme to primer/template ratio = 1:10) and (B) the Klenow fragment. (enzyme to primer/template ratio = 1:5). Lanes 2–9, polα-prim for one minute; Lanes 10–17, polα-prim for eight minutes; Lanes 18–25, the Klenow fragment for one minute; all with 100 µM dNTP at 35 °C. Reactions contained no enzyme (lane 1), no additional Me 2+ (lanes 2, 10, 18), 8 mM Mg 2+ (lanes 3, 11, 19), 10 to 50 µM Zn 2+ (lanes 4–6, 12–14, 20–22), and 8 mM Mg 2+ with 10 to 50 µM Zn 2+ (lanes 7–9, 15–17, 23–25).

    Techniques Used: DNA Synthesis

    Related Articles

    Binding Assay:

    Article Title: A CRISPR–Cas9-triggered strand displacement amplification method for ultrasensitive DNA detection
    Article Snippet: .. Proteins and other reagents such as single-strand binding protein (T4 gene 32 protein), Nb.BbvCI endonuclease, DNA polymerases (Klenow Fragment 3′– > 5′ exo− , KF), and dNTPs used in CRISDA amplification reactions were obtained from New England Biolabs (NEB). .. Bovine serum albumin (BSA, 20 mg mL−1 ), and nuclease free water were purchased from TAKARA.

    DNA Synthesis:

    Article Title: 5?CAG and 5?CTG Repeats Create Differential Impediment to the Progression of a Minimal Reconstituted T4 Replisome Depending on the Concentration of dNTPs
    Article Snippet: .. However, contrary to the gp43-gp41 replication couple, DNA synthesis performed by Klenow fragment was not stimulated by gp41 ( , compare lanes 2, 3, 5, and 6). .. Under both conditions (with or without gp41), DNA synthesis was highly distributive as indicated by the numerous pause sites that were clearly visible along the template strand.

    Fluorescence:

    Article Title: A CRISPR–Cas9-triggered strand displacement amplification method for ultrasensitive DNA detection
    Article Snippet: PNAs for strand invasion and fluorescence detection were synthesized by and Tahepna Biotechnologies. .. Proteins and other reagents such as single-strand binding protein (T4 gene 32 protein), Nb.BbvCI endonuclease, DNA polymerases (Klenow Fragment 3′– > 5′ exo− , KF), and dNTPs used in CRISDA amplification reactions were obtained from New England Biolabs (NEB).

    Magnetic Beads:

    Article Title: A CRISPR–Cas9-triggered strand displacement amplification method for ultrasensitive DNA detection
    Article Snippet: PlatinumTM Taq DNA polymerase, EZ-Link® Maleimide-PEG2-Biotin and magnetic beads coated with streptavidin (Dynabeads™ MyOne™ Streptavidin C1) were purchased from ThermoFisher. .. Proteins and other reagents such as single-strand binding protein (T4 gene 32 protein), Nb.BbvCI endonuclease, DNA polymerases (Klenow Fragment 3′– > 5′ exo− , KF), and dNTPs used in CRISDA amplification reactions were obtained from New England Biolabs (NEB).

    Mutagenesis:

    Article Title: DNA Polymerase I Is Essential for Growth of Methylobacterium dichloromethanicum DM4 with Dichloromethane
    Article Snippet: .. In contrast, extracts of wild-type DM4 and of the mutant strain complemented with plasmid pME8112 containing an intact polA gene showed bands of very similar sizes to DNA polymerase I and Klenow fragment of E. coli run as controls (Fig. ). .. These results suggest that the lack of a functional polA gene product is responsible for the observed growth defect of mutant DM4-1445 with DCM as the carbon source.

    Article Title: THE WERNER AND BLOOM SYNDROME PROTEINS HELP RESOLVE REPLICATION BLOCKAGE BY CONVERTING (REGRESSED) HOLLIDAY JUNCTIONS TO FUNCTIONAL REPLICATION FORKS
    Article Snippet: Human wild type BLM and BLM-D795A protein containing an aspartate to alanine mutation that abolishes its ATPase and helicase activities were gifts from Joanna Groden (Ohio State University), while human RPA and human (four-subunit) DNA polymerase δ were gifts from Guo-Min Li (University of Kentucky). .. Klenow Fragment (3’ to 5’ exo− ), from New England Biolabs, is an N-terminal truncation of E. coli DNA Polymerase I that lacks both 5’ to 3’ and 3’ to 5’ exonuclease activities but retains polymerase activity.

    Article Title: An evolved xylose transporter from Zymomonas mobilis enhances sugar transport in Escherichia coli
    Article Snippet: Paragraph title: Construction of random mutant library by random deletion ... To facilitate the re-ligation (see below), the purified DNA was blunt-ended with 3.2 U Klenow fragment in 10× NEBuffer 2 (New England Biolabs) and dNTPs (final concentration 33 μM each nucleotide) for 15 min at 25°C.

    Synthesized:

    Article Title: A CRISPR–Cas9-triggered strand displacement amplification method for ultrasensitive DNA detection
    Article Snippet: PNAs for strand invasion and fluorescence detection were synthesized by and Tahepna Biotechnologies. .. Proteins and other reagents such as single-strand binding protein (T4 gene 32 protein), Nb.BbvCI endonuclease, DNA polymerases (Klenow Fragment 3′– > 5′ exo− , KF), and dNTPs used in CRISDA amplification reactions were obtained from New England Biolabs (NEB).

    Polymerase Chain Reaction:

    Article Title: Establishment of conditional vectors for hairpin siRNA knockdowns
    Article Snippet: The human U6 promoter was amplified by PCR from the genomic DNA of T24 cells with the primers U6proTop (5′-AGGCAAAACGCACCACGTGACGGAG-3′) and U6proBottomSphI (5′-GCATGCGGTGTTTCGTCCTTTCCACAAGAT-3′), then ligated into a TA cloning vector, pGEM-T Easy (Promega, Madison, WI) (Fig. B). .. The plasmid was then digested with SphI (New England Biolabs, Beverly, MA) and blunted with Klenow fragment (New England Biolabs) (Fig. C).

    TA Cloning:

    Article Title: Establishment of conditional vectors for hairpin siRNA knockdowns
    Article Snippet: The human U6 promoter was amplified by PCR from the genomic DNA of T24 cells with the primers U6proTop (5′-AGGCAAAACGCACCACGTGACGGAG-3′) and U6proBottomSphI (5′-GCATGCGGTGTTTCGTCCTTTCCACAAGAT-3′), then ligated into a TA cloning vector, pGEM-T Easy (Promega, Madison, WI) (Fig. B). .. The plasmid was then digested with SphI (New England Biolabs, Beverly, MA) and blunted with Klenow fragment (New England Biolabs) (Fig. C).

    Infection:

    Article Title: THE WERNER AND BLOOM SYNDROME PROTEINS HELP RESOLVE REPLICATION BLOCKAGE BY CONVERTING (REGRESSED) HOLLIDAY JUNCTIONS TO FUNCTIONAL REPLICATION FORKS
    Article Snippet: To generate mock preparations, insect cells infected with baculovirus without WRN sequences were lysed and subject to identical purification procedures as WRN proteins. .. Klenow Fragment (3’ to 5’ exo− ), from New England Biolabs, is an N-terminal truncation of E. coli DNA Polymerase I that lacks both 5’ to 3’ and 3’ to 5’ exonuclease activities but retains polymerase activity.

    Ligation:

    Article Title: A library-based method to rapidly analyse chromatin accessibility at multiple genomic regions
    Article Snippet: .. To allow for ligation with the blunt-end of the double-stranded adaptors, 15 µl of purified MNase digested DNA fragments were blunt-ended in a final volume of 20 µl by Klenow fragment of Escherichia coli DNA polymerase (New England Biolabs, CA, USA) and phosphorylated by T4 polynucleotide kinase (New England Biolabs) in a final volume of 30 µl. .. Adaptor ligation The blunt-ended and phosphorylated DNA fragments were ligated to the double-stranded adaptors A and B as described in ( ) with the following modifications.

    other:

    Article Title: Protein Displacement by Herpes Helicase-Primase and the Key Role of UL42 During Helicase-Coupled DNA Synthesis by the Herpes Polymerase
    Article Snippet: Both polymerases could replace UL30-UL42, with Klenow Fragment generating products ~1 kB long.

    Article Title: Protein Displacement by Herpes Helicase-Primase and the Key Role of UL42 During Helicase-Coupled DNA Synthesis by the Herpes Polymerase
    Article Snippet: The absence of any products longer than ~100 nucleotides in assays containing UL30 is not due to either the lower processivity of UL30 relative to UL30-UL42 since UL30 and Klenow Fragment have similar processivity ( ) and Klenow Fragment generates long products.

    Article Title: Cleavage of deoxyoxanosine-containing oligodeoxyribonucleotides by bacterial endonuclease V
    Article Snippet: Klenow Fragment (3′–5′ exo-) was purchased from New England Biolabs (Beverly, MA).

    Article Title: Protein Displacement by Herpes Helicase-Primase and the Key Role of UL42 During Helicase-Coupled DNA Synthesis by the Herpes Polymerase
    Article Snippet: Even without ICP8, we found that non-cognate polymerases such as Klenow Fragment and T4 DNA polymerase allow the herpes helicase to more efficiently unwind DNA and allow the synthesis of long products.

    Concentration Assay:

    Article Title: An evolved xylose transporter from Zymomonas mobilis enhances sugar transport in Escherichia coli
    Article Snippet: .. To facilitate the re-ligation (see below), the purified DNA was blunt-ended with 3.2 U Klenow fragment in 10× NEBuffer 2 (New England Biolabs) and dNTPs (final concentration 33 μM each nucleotide) for 15 min at 25°C. .. Then EDTA was added to a final concentration of 10 mM, and the tube was incubated at 75°C for 20 min (Figure ).

    Purification:

    Article Title: THE WERNER AND BLOOM SYNDROME PROTEINS HELP RESOLVE REPLICATION BLOCKAGE BY CONVERTING (REGRESSED) HOLLIDAY JUNCTIONS TO FUNCTIONAL REPLICATION FORKS
    Article Snippet: Purified E. coli RuvA was purchased from B-Bridge International. .. Klenow Fragment (3’ to 5’ exo− ), from New England Biolabs, is an N-terminal truncation of E. coli DNA Polymerase I that lacks both 5’ to 3’ and 3’ to 5’ exonuclease activities but retains polymerase activity.

    Article Title: A CRISPR–Cas9-triggered strand displacement amplification method for ultrasensitive DNA detection
    Article Snippet: Proteins and other reagents such as single-strand binding protein (T4 gene 32 protein), Nb.BbvCI endonuclease, DNA polymerases (Klenow Fragment 3′– > 5′ exo− , KF), and dNTPs used in CRISDA amplification reactions were obtained from New England Biolabs (NEB). .. The other chemicals used in this study were purchased from Sigma-Aldrich in analytical reagent grade and used without further purification.

    Article Title: Aptamer Conformation Switching-Induced Two-Stage Amplification for Fluorescent Detection of Proteins
    Article Snippet: The deoxynucleotide solution mixture (dNTPs), polymerase Klenow Fragment exo- (10 U/μL) accompanied by 10× Klenow Fragment exo- buffer, and the nicking endonuclease Nt.BbvCI accompanied by 10× New England Biolabs (NEB) buffer were purchased from New England Biolabs Ltd (Beijing, China). .. All other reagents of analytical reagent grade were used as received without further purification.

    Article Title: An evolved xylose transporter from Zymomonas mobilis enhances sugar transport in Escherichia coli
    Article Snippet: .. To facilitate the re-ligation (see below), the purified DNA was blunt-ended with 3.2 U Klenow fragment in 10× NEBuffer 2 (New England Biolabs) and dNTPs (final concentration 33 μM each nucleotide) for 15 min at 25°C. .. Then EDTA was added to a final concentration of 10 mM, and the tube was incubated at 75°C for 20 min (Figure ).

    Article Title: A library-based method to rapidly analyse chromatin accessibility at multiple genomic regions
    Article Snippet: .. To allow for ligation with the blunt-end of the double-stranded adaptors, 15 µl of purified MNase digested DNA fragments were blunt-ended in a final volume of 20 µl by Klenow fragment of Escherichia coli DNA polymerase (New England Biolabs, CA, USA) and phosphorylated by T4 polynucleotide kinase (New England Biolabs) in a final volume of 30 µl. .. Adaptor ligation The blunt-ended and phosphorylated DNA fragments were ligated to the double-stranded adaptors A and B as described in ( ) with the following modifications.

    Amplification:

    Article Title: A CRISPR–Cas9-triggered strand displacement amplification method for ultrasensitive DNA detection
    Article Snippet: .. Proteins and other reagents such as single-strand binding protein (T4 gene 32 protein), Nb.BbvCI endonuclease, DNA polymerases (Klenow Fragment 3′– > 5′ exo− , KF), and dNTPs used in CRISDA amplification reactions were obtained from New England Biolabs (NEB). .. Bovine serum albumin (BSA, 20 mg mL−1 ), and nuclease free water were purchased from TAKARA.

    Article Title: Establishment of conditional vectors for hairpin siRNA knockdowns
    Article Snippet: The human U6 promoter was amplified by PCR from the genomic DNA of T24 cells with the primers U6proTop (5′-AGGCAAAACGCACCACGTGACGGAG-3′) and U6proBottomSphI (5′-GCATGCGGTGTTTCGTCCTTTCCACAAGAT-3′), then ligated into a TA cloning vector, pGEM-T Easy (Promega, Madison, WI) (Fig. B). .. The plasmid was then digested with SphI (New England Biolabs, Beverly, MA) and blunted with Klenow fragment (New England Biolabs) (Fig. C).

    Activity Assay:

    Article Title: THE WERNER AND BLOOM SYNDROME PROTEINS HELP RESOLVE REPLICATION BLOCKAGE BY CONVERTING (REGRESSED) HOLLIDAY JUNCTIONS TO FUNCTIONAL REPLICATION FORKS
    Article Snippet: .. Klenow Fragment (3’ to 5’ exo− ), from New England Biolabs, is an N-terminal truncation of E. coli DNA Polymerase I that lacks both 5’ to 3’ and 3’ to 5’ exonuclease activities but retains polymerase activity. .. T4 DNA Polymerase and T4 polynucleotide kinase were purchased from New England Biolabs.

    Sequencing:

    Article Title: Establishment of conditional vectors for hairpin siRNA knockdowns
    Article Snippet: The plasmid was then digested with SphI (New England Biolabs, Beverly, MA) and blunted with Klenow fragment (New England Biolabs) (Fig. C). .. Oligo1 consists of a targeted DNA methyltransferase 1 (DNMT1) sequence ( ) (nucleotides 1627–1647 of GenBank accession no. XM_ 086566) with an AatII recognition sequence.

    Recombinant:

    Article Title: THE WERNER AND BLOOM SYNDROME PROTEINS HELP RESOLVE REPLICATION BLOCKAGE BY CONVERTING (REGRESSED) HOLLIDAY JUNCTIONS TO FUNCTIONAL REPLICATION FORKS
    Article Snippet: Recombinant human RECQ4 was purified as described ( ). .. Klenow Fragment (3’ to 5’ exo− ), from New England Biolabs, is an N-terminal truncation of E. coli DNA Polymerase I that lacks both 5’ to 3’ and 3’ to 5’ exonuclease activities but retains polymerase activity.

    Recombinase Polymerase Amplification:

    Article Title: THE WERNER AND BLOOM SYNDROME PROTEINS HELP RESOLVE REPLICATION BLOCKAGE BY CONVERTING (REGRESSED) HOLLIDAY JUNCTIONS TO FUNCTIONAL REPLICATION FORKS
    Article Snippet: Human wild type BLM and BLM-D795A protein containing an aspartate to alanine mutation that abolishes its ATPase and helicase activities were gifts from Joanna Groden (Ohio State University), while human RPA and human (four-subunit) DNA polymerase δ were gifts from Guo-Min Li (University of Kentucky). .. Klenow Fragment (3’ to 5’ exo− ), from New England Biolabs, is an N-terminal truncation of E. coli DNA Polymerase I that lacks both 5’ to 3’ and 3’ to 5’ exonuclease activities but retains polymerase activity.

    Incubation:

    Article Title: An evolved xylose transporter from Zymomonas mobilis enhances sugar transport in Escherichia coli
    Article Snippet: To facilitate the re-ligation (see below), the purified DNA was blunt-ended with 3.2 U Klenow fragment in 10× NEBuffer 2 (New England Biolabs) and dNTPs (final concentration 33 μM each nucleotide) for 15 min at 25°C. .. Then EDTA was added to a final concentration of 10 mM, and the tube was incubated at 75°C for 20 min (Figure ).

    Plasmid Preparation:

    Article Title: DNA Polymerase I Is Essential for Growth of Methylobacterium dichloromethanicum DM4 with Dichloromethane
    Article Snippet: .. In contrast, extracts of wild-type DM4 and of the mutant strain complemented with plasmid pME8112 containing an intact polA gene showed bands of very similar sizes to DNA polymerase I and Klenow fragment of E. coli run as controls (Fig. ). .. These results suggest that the lack of a functional polA gene product is responsible for the observed growth defect of mutant DM4-1445 with DCM as the carbon source.

    Article Title: A CRISPR–Cas9-triggered strand displacement amplification method for ultrasensitive DNA detection
    Article Snippet: The sequences of the Cas9 coding regions in plasmid pET28a/Cas9(H840A)-Cys and pET28a/S3C-dCas9 are listed in Supplementary Tables and , respectively. .. Proteins and other reagents such as single-strand binding protein (T4 gene 32 protein), Nb.BbvCI endonuclease, DNA polymerases (Klenow Fragment 3′– > 5′ exo− , KF), and dNTPs used in CRISDA amplification reactions were obtained from New England Biolabs (NEB).

    Article Title: Efficient enzymatic synthesis and dual-colour fluorescent labelling of DNA probes using long chain azido-dUTP and BCN dyes
    Article Snippet: Klenow large fragment, Therminator™ II, M-MuLV (RNase H− ) reverse transcriptase, AMV reverse transcriptase, RNase inhibitor and λ-exonuclease were purchased from New England Biolabs. .. Plasmid HydGdCTD5 (5.176 kb,PCR template) was provided by Professor Peter Roach at Southampton University School of Chemistry.

    Article Title: Establishment of conditional vectors for hairpin siRNA knockdowns
    Article Snippet: .. The plasmid was then digested with SphI (New England Biolabs, Beverly, MA) and blunted with Klenow fragment (New England Biolabs) (Fig. C). .. Oligo1 [a mixture of two DNA oligomers, DNMTO1F (5′-GGAATGGCAGATGCCAACAGGACGT-3′) and DNMTO1R (5′-CCTGTTGGCATCTGCCATTCC-3′)] was ligated following restriction digestion with AatII (New England Biolabs) (Fig. D).

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    New England Biolabs klenow large fragment
    Primer extension using AHP dUTP (1.5 h). ( A ) Template T2 and primer P3. ( B ) Twenty percent denaturing PAGE analysis of reactions using Gotaq (Go, 72°C), <t>Klenow</t> (Kl, 37°C), KOD (KO, 72°C) and <t>Therminator™</t> II (Th, 72°C) polymerases. Lane P: primer P3. ( C ) Reactions using Gotaq polymerase at 60°C. ( D ) Mass spectrum of AHP-modified fully extended product using Klenow (calculated mass: 10621).
    Klenow Large Fragment, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 105 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Primer extension using AHP dUTP (1.5 h). ( A ) Template T2 and primer P3. ( B ) Twenty percent denaturing PAGE analysis of reactions using Gotaq (Go, 72°C), Klenow (Kl, 37°C), KOD (KO, 72°C) and Therminator™ II (Th, 72°C) polymerases. Lane P: primer P3. ( C ) Reactions using Gotaq polymerase at 60°C. ( D ) Mass spectrum of AHP-modified fully extended product using Klenow (calculated mass: 10621).

    Journal: Nucleic Acids Research

    Article Title: Efficient enzymatic synthesis and dual-colour fluorescent labelling of DNA probes using long chain azido-dUTP and BCN dyes

    doi: 10.1093/nar/gkw028

    Figure Lengend Snippet: Primer extension using AHP dUTP (1.5 h). ( A ) Template T2 and primer P3. ( B ) Twenty percent denaturing PAGE analysis of reactions using Gotaq (Go, 72°C), Klenow (Kl, 37°C), KOD (KO, 72°C) and Therminator™ II (Th, 72°C) polymerases. Lane P: primer P3. ( C ) Reactions using Gotaq polymerase at 60°C. ( D ) Mass spectrum of AHP-modified fully extended product using Klenow (calculated mass: 10621).

    Article Snippet: Klenow large fragment, Therminator™ II, M-MuLV (RNase H− ) reverse transcriptase, AMV reverse transcriptase, RNase inhibitor and λ-exonuclease were purchased from New England Biolabs.

    Techniques: Polyacrylamide Gel Electrophoresis, Modification

    A flowchart showing the manipulation steps in the preparation of genomic DNA for IPCR. The genomic DNA was subjected to RE digestions, Klenow fill-in and ligation prior to IPCR as reported before [ 80 ]

    Journal: Human Genomics

    Article Title: Oxidative stress-induced chromosome breaks within the ABL gene: a model for chromosome rearrangement in nasopharyngeal carcinoma

    doi: 10.1186/s40246-018-0160-8

    Figure Lengend Snippet: A flowchart showing the manipulation steps in the preparation of genomic DNA for IPCR. The genomic DNA was subjected to RE digestions, Klenow fill-in and ligation prior to IPCR as reported before [ 80 ]

    Article Snippet: DNA Polymerase I Large (Klenow) Fragment, restriction enzymes and T4 DNA Ligase were obtained from New England Biolabs (NEB), USA. dNTP mix was purchased from Promega, USA.

    Techniques: Ligation

    Quantitative analysis of functional gene arrays. (A) Relationship of hybridization signal intensity to DNA target concentration from a single pure culture. Genomic DNA from nirS -containing P. stutzeri E4-2 was labeled with Cy5 and hybridized to the microarrays at the following target concentrations: 0.5, 1, 2.5, 5, 10, 25, 50, and 100 ng. The plot shows the log-transformed average hybridization intensity versus the log-transformed target DNA concentration. (B) Relationship of hybridization signal intensity to DNA target concentration using a mixture of target DNAs. The PCR products from the following nine strains were mixed together in different quantities (in picograms): E4-2 ( nirS ), 1,000; G179 ( nirK ), 500; wc301–37 ( amoA ), 250; ps-47 ( amoA ), 125; pB49 ( nirS ), 62.5; Y32K ( nirK ), 31.3; wA15 ( nirS ), 15.6; ps-80 ( amoA ), 7.8; wB54 ( nirK ), 3.9. All of these genes are less than 80% identical. The mixed templates were labeled with Cy5. The plot shows the log-transformed average hybridization intensity versus the log-transformed target DNA concentration for each strain. (C) Effects of probe DNA size and composition on hybridization signal intensity. Microarrays contained DNA fragments (200 ng μl −1 ) of different sizes amplified from different regions in the S. oneidensis MR-1 genome. The target DNA was prepared by labeling MR-1 genomic DNA with Cy5 using the Klenow fragment with random hexamer primers. For panels A and B, the data points are mean values derived from three independent microarray slides, with three replicates on each slide (a total of nine data points). Error bars showing the standard deviations are presented.

    Journal: Applied and Environmental Microbiology

    Article Title: Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment

    doi: 10.1128/AEM.67.12.5780-5790.2001

    Figure Lengend Snippet: Quantitative analysis of functional gene arrays. (A) Relationship of hybridization signal intensity to DNA target concentration from a single pure culture. Genomic DNA from nirS -containing P. stutzeri E4-2 was labeled with Cy5 and hybridized to the microarrays at the following target concentrations: 0.5, 1, 2.5, 5, 10, 25, 50, and 100 ng. The plot shows the log-transformed average hybridization intensity versus the log-transformed target DNA concentration. (B) Relationship of hybridization signal intensity to DNA target concentration using a mixture of target DNAs. The PCR products from the following nine strains were mixed together in different quantities (in picograms): E4-2 ( nirS ), 1,000; G179 ( nirK ), 500; wc301–37 ( amoA ), 250; ps-47 ( amoA ), 125; pB49 ( nirS ), 62.5; Y32K ( nirK ), 31.3; wA15 ( nirS ), 15.6; ps-80 ( amoA ), 7.8; wB54 ( nirK ), 3.9. All of these genes are less than 80% identical. The mixed templates were labeled with Cy5. The plot shows the log-transformed average hybridization intensity versus the log-transformed target DNA concentration for each strain. (C) Effects of probe DNA size and composition on hybridization signal intensity. Microarrays contained DNA fragments (200 ng μl −1 ) of different sizes amplified from different regions in the S. oneidensis MR-1 genome. The target DNA was prepared by labeling MR-1 genomic DNA with Cy5 using the Klenow fragment with random hexamer primers. For panels A and B, the data points are mean values derived from three independent microarray slides, with three replicates on each slide (a total of nine data points). Error bars showing the standard deviations are presented.

    Article Snippet: Each 40-μl labeling reaction mixture contained denatured genomic DNA; 1.5 μg of random hexamers (Gibco BRL, Gaithersburg, Md.); 1× EcoPol buffer (New England Biolabs, Beverly, Mass.); 50 μM dATP, dTTP, and dGTP; 20 μM dCTP; 10 μM Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, Piscataway, N.J.); 2.5 mM dithiothreitol; and 10 U of the large Klenow fragment of DNA polymerase I (New England Biolabs).

    Techniques: Functional Assay, Hybridization, Concentration Assay, Labeling, Transformation Assay, Polymerase Chain Reaction, Amplification, Random Hexamer Labeling, Derivative Assay, Microarray

    The normalized distribution of signal intensity levels for nirS, nirK , and amoA genes as determined by microarray-based analysis of community DNA from marine sediment (W303) and surface soil (O22) environments. Bulk community DNA isolated from two different environmental samples was directly labeled with Cy5 using Klenow fragment with random hexamer primers and hybridized with the microarrays at 65°C in separate experiments. The hybridization signal intensity for each gene is presented. Shaded bars represent probes from environmental clones, and striped boxes represent pmo A probes from environmental clones. Open bars designate probes from pure cultures. The data represent mean values obtained from nine replicates after subtracting background hybridization to yeast genes. For the nirS graphs, bars 1 to 42 correspond to individual genes S1-S42 (see assigned designation in Table 1 on the web site). Similarly, bars 1 to 18 for nirK correspond to genes K1 to K18, and bars 1 to 22 for amoA and pmoA represent genes M1 to M22 (see our table on the website cited in Materials and Methods). The standard deviation of signal intensity is indicated on the top of each bar.

    Journal: Applied and Environmental Microbiology

    Article Title: Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment

    doi: 10.1128/AEM.67.12.5780-5790.2001

    Figure Lengend Snippet: The normalized distribution of signal intensity levels for nirS, nirK , and amoA genes as determined by microarray-based analysis of community DNA from marine sediment (W303) and surface soil (O22) environments. Bulk community DNA isolated from two different environmental samples was directly labeled with Cy5 using Klenow fragment with random hexamer primers and hybridized with the microarrays at 65°C in separate experiments. The hybridization signal intensity for each gene is presented. Shaded bars represent probes from environmental clones, and striped boxes represent pmo A probes from environmental clones. Open bars designate probes from pure cultures. The data represent mean values obtained from nine replicates after subtracting background hybridization to yeast genes. For the nirS graphs, bars 1 to 42 correspond to individual genes S1-S42 (see assigned designation in Table 1 on the web site). Similarly, bars 1 to 18 for nirK correspond to genes K1 to K18, and bars 1 to 22 for amoA and pmoA represent genes M1 to M22 (see our table on the website cited in Materials and Methods). The standard deviation of signal intensity is indicated on the top of each bar.

    Article Snippet: Each 40-μl labeling reaction mixture contained denatured genomic DNA; 1.5 μg of random hexamers (Gibco BRL, Gaithersburg, Md.); 1× EcoPol buffer (New England Biolabs, Beverly, Mass.); 50 μM dATP, dTTP, and dGTP; 20 μM dCTP; 10 μM Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, Piscataway, N.J.); 2.5 mM dithiothreitol; and 10 U of the large Klenow fragment of DNA polymerase I (New England Biolabs).

    Techniques: Microarray, Isolation, Environmental Sampling, Labeling, Random Hexamer Labeling, Hybridization, Clone Assay, Standard Deviation

    PAGE analysis of primer extension experiments with single OXP-modified and PDE primers. Primer extension with Klenow fragment of DNA polymerase I of nonheated ( A ) and preheated ( B ) single OXP-modified reverse primer, respectively along template 2. The extension reactions were incubated at 25°C for the indicated times after which the reaction mixtures were quenched and analyzed. ( C ) Primer extension with Taq DNA polymerase of PDE and OXP forward primers (nonheated control and preheated sample) along template oligonucleotide 1. Extension reactions were incubated at 25°C for 15 min, after which the aliquots from reaction mixtures were quenched and analyzed.

    Journal: Nucleic Acids Research

    Article Title: Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance

    doi: 10.1093/nar/gkn575

    Figure Lengend Snippet: PAGE analysis of primer extension experiments with single OXP-modified and PDE primers. Primer extension with Klenow fragment of DNA polymerase I of nonheated ( A ) and preheated ( B ) single OXP-modified reverse primer, respectively along template 2. The extension reactions were incubated at 25°C for the indicated times after which the reaction mixtures were quenched and analyzed. ( C ) Primer extension with Taq DNA polymerase of PDE and OXP forward primers (nonheated control and preheated sample) along template oligonucleotide 1. Extension reactions were incubated at 25°C for 15 min, after which the aliquots from reaction mixtures were quenched and analyzed.

    Article Snippet: Primer extension with Klenow fragment of DNA polymerase Primer extension experiments using large fragment (Klenow) of DNA polymerase I (New England Biolabs) were performed at 25°C using the HIV-1 tat reverse primer (5′-AATACTATGGTCCACACAACTATTGCT-3′) that was unmodified or contained a single OXP modification.

    Techniques: Polyacrylamide Gel Electrophoresis, Modification, Incubation