t4 ligase enzyme  (TaKaRa)

 
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    Name:
    T4 DNA Ligase
    Description:
    T4 DNA Ligase is a ligation enzyme that can be used to join DNA fragments by catalyzing the formation of phosphodiester bonds between juxtaposed 5 phosphate and 3 hydroxyl termini in double stranded DNA using ATP as a coenzyme Both blunt and cohesive end DNA ligation as well as single stranded nick repair of DNA RNA and DNA RNA are possible using the T4 DNA ligase
    Catalog Number:
    2011b
    Price:
    None
    Size:
    125 000 Units
    Category:
    T4 DNA Ligase Ligation enzymes Cloning
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    Structured Review

    TaKaRa t4 ligase enzyme
    T4 DNA Ligase is a ligation enzyme that can be used to join DNA fragments by catalyzing the formation of phosphodiester bonds between juxtaposed 5 phosphate and 3 hydroxyl termini in double stranded DNA using ATP as a coenzyme Both blunt and cohesive end DNA ligation as well as single stranded nick repair of DNA RNA and DNA RNA are possible using the T4 DNA ligase
    https://www.bioz.com/result/t4 ligase enzyme/product/TaKaRa
    Average 99 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    t4 ligase enzyme - by Bioz Stars, 2020-04
    99/100 stars

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    Related Articles

    Fluorescence:

    Article Title: Real-time monitoring of nucleic acid ligation in homogenous solutions using molecular beacons
    Article Snippet: .. The samples prepared by mixing MB solution with 300 nM N2 and N4, as well as the fluorescence measurements were carried out with the addition of variant concentrations of T4 DNA ligase. .. We have developed a simple MB based assay for real-time monitoring of nucleic acids ligation using T4 DNA ligase.

    Synthesized:

    Article Title: Simple fluorescence-based detection of protein kinase A activity using a molecular beacon probe
    Article Snippet: .. All sequences were synthesized by Takara Biological Engineering Co., Ltd. Other reagents used included dithiothreitol DTT (BBI), T4 DNA ligase (Takara), BSA (Bovogen Biologicals Pty Ltd), protein kinase A (protein kinase A from bovine heart, P5511, Sigma), cAMP (adenosine 3′, 5′-cyclic monophosphate sodium salt monohydrate, 6885, Sigma), ATP (Amresco), kemptide (kemptide acetate salt, K1127, Sigma), genistein (genistein, G6649, Sigma). .. Deionized water was obtained from a Nanopure InfinityTM ultrapure water system (Barnstead/thermolyne Corp, Dubuque, 1A).

    Article Title: Involvement of a site-specific trans-acting factor and a common RNA-binding protein in the editing of chloroplast mRNAs: development of a chloroplast in vitro RNA editing system
    Article Snippet: The downstream RNA including the C to be edited and the 3′ extension of a 15 nt sequence from the KS primer was chemically synthesized by TaKaRa. .. The labeled downstream RNA was mixed with the upstream RNA (100 pmol) and the bridge DNA oligonucleotide (200 pmol) (5′-CGGTATCGGATTGTGTCGTAGCTCTATAATTCGGATTAAG3′), and heated at 94°C for 3 min followed by cooling to room temperature for 3 h. Ligation was carried out by adding 1.4 U/µl T4 DNA ligase (TaKaRa) and incubating at 25°C overnight.

    Ligation:

    Article Title: Detection of Ligation Products of DNA Linkers with 5?-OH Ends by Denaturing PAGE Silver Stain
    Article Snippet: .. These results of CIAP treatments might perhaps give us at least 3 messages: (i) CIAP treatments of linkers A–B could block, but not completely, the ligation of linkers A–B, indicating that some of linkers A–B could still be joined by T4 DNA ligase even after CIAP treatment; (ii) the ligation of linkers A–B could be recovered after CIAP was inactivated at 85°C for 30–90 min, perhaps suggesting that some of linkers A–B could spontaneously delete one or more nucleotide(s) at their 5′-ends and generate some 5′-phosphate ends when the linkers were incubated at 85°C for 30–90 min; and (iii) these results of CIAP treatments again indicated that band 5 in was the ligation products of linkers A–B. .. Three Round Overlap PCR Products and DNA Sequencing To prepare the sequencing template, the ligation products of linkers A–B and C–D were amplified by using 3 round overlap PCR.

    Article Title: Real-time monitoring of nucleic acid ligation in homogenous solutions using molecular beacons
    Article Snippet: .. Two samples containing 10 µl reaction solutions were moved from each sample before adding T4 DNA ligase, and after the ligation process had taken place for 360 s with the addition of ligase. ..

    Article Title: Real-time monitoring of nucleic acid ligation in homogenous solutions using molecular beacons
    Article Snippet: .. Therefore, 37°C was chosen for all ligation reactions to ensure a high sensitivity (the ratio reached 10.7) and a high activity of T4 DNA ligase. .. The ligation process can be affected by many molecular species including biomolecules and metal ions.

    Article Title: Real-time monitoring of nucleic acid ligation in homogenous solutions using molecular beacons
    Article Snippet: .. Figure shows five factors on ligation using T4 DNA ligase. .. Figure A and B shows that the ligation did not take place unless ATP or Mg2+ was added to the ligation mixtures.

    Article Title: Detection of Ligation Products of DNA Linkers with 5?-OH Ends by Denaturing PAGE Silver Stain
    Article Snippet: .. We supposed that the reasons might include: (i) CIAP mixture perhaps contained some inhibitors from CIAP or the other components of CIAP mixture; and (ii) an oligo might be hard to be phosphorylated by T4 DNA ligase if it were incubated in CIAP mixture at 85°C for more than 15 min. Our DNA sequencing results demonstrated one or more base deletion(s) at the ligation junction between linkers, but the base deletion background could be significantly reduced if the ligation products of linkers A–B and C–D were purified with a PCR product purification kit before PCR. .. These results might suggest that the ligation products of the linkers phosphorylated by T4 DNA ligase could be selectively collected by the PCR product purification kit.

    Article Title: Involvement of a site-specific trans-acting factor and a common RNA-binding protein in the editing of chloroplast mRNAs: development of a chloroplast in vitro RNA editing system
    Article Snippet: .. The labeled downstream RNA was mixed with the upstream RNA (100 pmol) and the bridge DNA oligonucleotide (200 pmol) (5′-CGGTATCGGATTGTGTCGTAGCTCTATAATTCGGATTAAG3′), and heated at 94°C for 3 min followed by cooling to room temperature for 3 h. Ligation was carried out by adding 1.4 U/µl T4 DNA ligase (TaKaRa) and incubating at 25°C overnight. .. The ligated RNA was purified by PAGE.

    Article Title: Efficient DNA ligation by selective heating of DNA ligase with a radio frequency alternating magnetic field
    Article Snippet: .. In summary, we carried out the ligation of DNA fragments with cohesive ends using T4 DNA ligase immobilized on ferromagnetic particles and found that the ligation efficiency was increased under a radio frequency alternating magnetic field caused by heat generation from the particles. .. In the present method, DNA ligase is immobilized on ferromagnetic particles and therefore, if DNA ligation is carried out under moderate temperature conditions, DNA ligase on particles after the reaction may be recovered using a magnet and reused.

    Blocking Assay:

    Article Title: Detection of Ligation Products of DNA Linkers with 5?-OH Ends by Denaturing PAGE Silver Stain
    Article Snippet: .. These results of CIAP treatments might perhaps give us at least 3 messages: (i) CIAP treatments of linkers A–B could block, but not completely, the ligation of linkers A–B, indicating that some of linkers A–B could still be joined by T4 DNA ligase even after CIAP treatment; (ii) the ligation of linkers A–B could be recovered after CIAP was inactivated at 85°C for 30–90 min, perhaps suggesting that some of linkers A–B could spontaneously delete one or more nucleotide(s) at their 5′-ends and generate some 5′-phosphate ends when the linkers were incubated at 85°C for 30–90 min; and (iii) these results of CIAP treatments again indicated that band 5 in was the ligation products of linkers A–B. .. Three Round Overlap PCR Products and DNA Sequencing To prepare the sequencing template, the ligation products of linkers A–B and C–D were amplified by using 3 round overlap PCR.

    Purification:

    Article Title: Detection of Ligation Products of DNA Linkers with 5?-OH Ends by Denaturing PAGE Silver Stain
    Article Snippet: .. We supposed that the reasons might include: (i) CIAP mixture perhaps contained some inhibitors from CIAP or the other components of CIAP mixture; and (ii) an oligo might be hard to be phosphorylated by T4 DNA ligase if it were incubated in CIAP mixture at 85°C for more than 15 min. Our DNA sequencing results demonstrated one or more base deletion(s) at the ligation junction between linkers, but the base deletion background could be significantly reduced if the ligation products of linkers A–B and C–D were purified with a PCR product purification kit before PCR. .. These results might suggest that the ligation products of the linkers phosphorylated by T4 DNA ligase could be selectively collected by the PCR product purification kit.

    Article Title: Involvement of a site-specific trans-acting factor and a common RNA-binding protein in the editing of chloroplast mRNAs: development of a chloroplast in vitro RNA editing system
    Article Snippet: The downstream RNA (300 pmol) was labeled with 32 P at the 5′ end with T4 polynucleotide kinase and purified by passage through a Sephadex G25 spin column (Amersham Pharmacia Biotech). .. The labeled downstream RNA was mixed with the upstream RNA (100 pmol) and the bridge DNA oligonucleotide (200 pmol) (5′-CGGTATCGGATTGTGTCGTAGCTCTATAATTCGGATTAAG3′), and heated at 94°C for 3 min followed by cooling to room temperature for 3 h. Ligation was carried out by adding 1.4 U/µl T4 DNA ligase (TaKaRa) and incubating at 25°C overnight.

    Polymerase Chain Reaction:

    Article Title: Detection of Ligation Products of DNA Linkers with 5?-OH Ends by Denaturing PAGE Silver Stain
    Article Snippet: .. We supposed that the reasons might include: (i) CIAP mixture perhaps contained some inhibitors from CIAP or the other components of CIAP mixture; and (ii) an oligo might be hard to be phosphorylated by T4 DNA ligase if it were incubated in CIAP mixture at 85°C for more than 15 min. Our DNA sequencing results demonstrated one or more base deletion(s) at the ligation junction between linkers, but the base deletion background could be significantly reduced if the ligation products of linkers A–B and C–D were purified with a PCR product purification kit before PCR. .. These results might suggest that the ligation products of the linkers phosphorylated by T4 DNA ligase could be selectively collected by the PCR product purification kit.

    Incubation:

    Article Title: Detection of Ligation Products of DNA Linkers with 5?-OH Ends by Denaturing PAGE Silver Stain
    Article Snippet: .. These results of CIAP treatments might perhaps give us at least 3 messages: (i) CIAP treatments of linkers A–B could block, but not completely, the ligation of linkers A–B, indicating that some of linkers A–B could still be joined by T4 DNA ligase even after CIAP treatment; (ii) the ligation of linkers A–B could be recovered after CIAP was inactivated at 85°C for 30–90 min, perhaps suggesting that some of linkers A–B could spontaneously delete one or more nucleotide(s) at their 5′-ends and generate some 5′-phosphate ends when the linkers were incubated at 85°C for 30–90 min; and (iii) these results of CIAP treatments again indicated that band 5 in was the ligation products of linkers A–B. .. Three Round Overlap PCR Products and DNA Sequencing To prepare the sequencing template, the ligation products of linkers A–B and C–D were amplified by using 3 round overlap PCR.

    Article Title: Detection of Ligation Products of DNA Linkers with 5?-OH Ends by Denaturing PAGE Silver Stain
    Article Snippet: .. We supposed that the reasons might include: (i) CIAP mixture perhaps contained some inhibitors from CIAP or the other components of CIAP mixture; and (ii) an oligo might be hard to be phosphorylated by T4 DNA ligase if it were incubated in CIAP mixture at 85°C for more than 15 min. Our DNA sequencing results demonstrated one or more base deletion(s) at the ligation junction between linkers, but the base deletion background could be significantly reduced if the ligation products of linkers A–B and C–D were purified with a PCR product purification kit before PCR. .. These results might suggest that the ligation products of the linkers phosphorylated by T4 DNA ligase could be selectively collected by the PCR product purification kit.

    other:

    Article Title: Histone H1 Differentially Inhibits DNA Bending by Reduced and Oxidized HMGB1 Protein
    Article Snippet: In agreement with previous reports [ , ], histone H1 could stimulate formation of linear multimers by T4 DNA ligase at low H1-to-DNA ratios.

    Article Title: Detection of Ligation Products of DNA Linkers with 5?-OH Ends by Denaturing PAGE Silver Stain
    Article Snippet: The phosphorylation of oligo 11 by T4 DNA ligase could be inhibited by CIAP treatment of oligo 11.

    Activity Assay:

    Article Title: Real-time monitoring of nucleic acid ligation in homogenous solutions using molecular beacons
    Article Snippet: .. Therefore, 37°C was chosen for all ligation reactions to ensure a high sensitivity (the ratio reached 10.7) and a high activity of T4 DNA ligase. .. The ligation process can be affected by many molecular species including biomolecules and metal ions.

    Labeling:

    Article Title: Simple fluorescence-based detection of protein kinase A activity using a molecular beacon probe
    Article Snippet: Its 5′-terminal was labeled with a fluorescent group, tetramethyl rhodamine (TAMRA). .. All sequences were synthesized by Takara Biological Engineering Co., Ltd. Other reagents used included dithiothreitol DTT (BBI), T4 DNA ligase (Takara), BSA (Bovogen Biologicals Pty Ltd), protein kinase A (protein kinase A from bovine heart, P5511, Sigma), cAMP (adenosine 3′, 5′-cyclic monophosphate sodium salt monohydrate, 6885, Sigma), ATP (Amresco), kemptide (kemptide acetate salt, K1127, Sigma), genistein (genistein, G6649, Sigma).

    Article Title: Involvement of a site-specific trans-acting factor and a common RNA-binding protein in the editing of chloroplast mRNAs: development of a chloroplast in vitro RNA editing system
    Article Snippet: .. The labeled downstream RNA was mixed with the upstream RNA (100 pmol) and the bridge DNA oligonucleotide (200 pmol) (5′-CGGTATCGGATTGTGTCGTAGCTCTATAATTCGGATTAAG3′), and heated at 94°C for 3 min followed by cooling to room temperature for 3 h. Ligation was carried out by adding 1.4 U/µl T4 DNA ligase (TaKaRa) and incubating at 25°C overnight. .. The ligated RNA was purified by PAGE.

    Polyacrylamide Gel Electrophoresis:

    Article Title: Involvement of a site-specific trans-acting factor and a common RNA-binding protein in the editing of chloroplast mRNAs: development of a chloroplast in vitro RNA editing system
    Article Snippet: The labeled downstream RNA was mixed with the upstream RNA (100 pmol) and the bridge DNA oligonucleotide (200 pmol) (5′-CGGTATCGGATTGTGTCGTAGCTCTATAATTCGGATTAAG3′), and heated at 94°C for 3 min followed by cooling to room temperature for 3 h. Ligation was carried out by adding 1.4 U/µl T4 DNA ligase (TaKaRa) and incubating at 25°C overnight. .. The ligated RNA was purified by PAGE.

    Sequencing:

    Article Title: Involvement of a site-specific trans-acting factor and a common RNA-binding protein in the editing of chloroplast mRNAs: development of a chloroplast in vitro RNA editing system
    Article Snippet: The downstream RNA including the C to be edited and the 3′ extension of a 15 nt sequence from the KS primer was chemically synthesized by TaKaRa. .. The labeled downstream RNA was mixed with the upstream RNA (100 pmol) and the bridge DNA oligonucleotide (200 pmol) (5′-CGGTATCGGATTGTGTCGTAGCTCTATAATTCGGATTAAG3′), and heated at 94°C for 3 min followed by cooling to room temperature for 3 h. Ligation was carried out by adding 1.4 U/µl T4 DNA ligase (TaKaRa) and incubating at 25°C overnight.

    Variant Assay:

    Article Title: Real-time monitoring of nucleic acid ligation in homogenous solutions using molecular beacons
    Article Snippet: .. The samples prepared by mixing MB solution with 300 nM N2 and N4, as well as the fluorescence measurements were carried out with the addition of variant concentrations of T4 DNA ligase. .. We have developed a simple MB based assay for real-time monitoring of nucleic acids ligation using T4 DNA ligase.

    Concentration Assay:

    Article Title: Efficient DNA ligation by selective heating of DNA ligase with a radio frequency alternating magnetic field
    Article Snippet: .. Note that the inactivation temperature of T4 DNA ligase has been experimentally estimated to be 38 °C, where the inactivation temperature is defined as the temperature at which the concentration of active enzyme becomes half of the total enzyme concentration . .. In the present case, although T4 DNA ligase immobilized on the ferromagnetic particles was heated under the ac magnetic field, the particle's surface temperature, ranging from 20 to 27 °C, was much lower than the above inactivation temperature since the ambient temperature was as low as 16 °C.

    DNA Sequencing:

    Article Title: Detection of Ligation Products of DNA Linkers with 5?-OH Ends by Denaturing PAGE Silver Stain
    Article Snippet: .. We supposed that the reasons might include: (i) CIAP mixture perhaps contained some inhibitors from CIAP or the other components of CIAP mixture; and (ii) an oligo might be hard to be phosphorylated by T4 DNA ligase if it were incubated in CIAP mixture at 85°C for more than 15 min. Our DNA sequencing results demonstrated one or more base deletion(s) at the ligation junction between linkers, but the base deletion background could be significantly reduced if the ligation products of linkers A–B and C–D were purified with a PCR product purification kit before PCR. .. These results might suggest that the ligation products of the linkers phosphorylated by T4 DNA ligase could be selectively collected by the PCR product purification kit.

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  • 99
    TaKaRa t4 dna ligase
    Stimulation of DNA ligation by histone H1 and deletion mutants. The 5´-end 32 P-labeled 123-bp DNA fragment (~1 nM) was pre-incubated with 1–15 nM ( left to right ) histone H1 (fl) or deletion mutants within the highly basic C-terminus, followed by ligation by <t>T4</t> DNA ligase. Deproteinised DNA samples were separated by electrophoresis on 5% non-denaturing polyacrylamide gels in 0.5x TBE buffer.
    T4 Dna Ligase, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 297 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t4 dna ligase/product/TaKaRa
    Average 99 stars, based on 297 article reviews
    Price from $9.99 to $1999.99
    t4 dna ligase - by Bioz Stars, 2020-04
    99/100 stars
      Buy from Supplier

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    Stimulation of DNA ligation by histone H1 and deletion mutants. The 5´-end 32 P-labeled 123-bp DNA fragment (~1 nM) was pre-incubated with 1–15 nM ( left to right ) histone H1 (fl) or deletion mutants within the highly basic C-terminus, followed by ligation by T4 DNA ligase. Deproteinised DNA samples were separated by electrophoresis on 5% non-denaturing polyacrylamide gels in 0.5x TBE buffer.

    Journal: PLoS ONE

    Article Title: Histone H1 Differentially Inhibits DNA Bending by Reduced and Oxidized HMGB1 Protein

    doi: 10.1371/journal.pone.0138774

    Figure Lengend Snippet: Stimulation of DNA ligation by histone H1 and deletion mutants. The 5´-end 32 P-labeled 123-bp DNA fragment (~1 nM) was pre-incubated with 1–15 nM ( left to right ) histone H1 (fl) or deletion mutants within the highly basic C-terminus, followed by ligation by T4 DNA ligase. Deproteinised DNA samples were separated by electrophoresis on 5% non-denaturing polyacrylamide gels in 0.5x TBE buffer.

    Article Snippet: In agreement with previous reports [ , ], histone H1 could stimulate formation of linear multimers by T4 DNA ligase at low H1-to-DNA ratios.

    Techniques: DNA Ligation, Labeling, Incubation, Ligation, Electrophoresis

    Histone H1 inhibits the ability of HMGB1 to bend DNA. A , formation of DNA circles by HMGB1 is inhibited by the full-length histone H1 (DNA circularization assay). The 5´-end 32 P-labeled 123-bp DNA fragment (~1 nM) was pre-incubated with 5 nM HMGB1, followed by titration with increasing concentrations of H1 (0.2–15 nM, left to right ) and ligation by T4 DNA ligase. Deproteinised DNA samples were separated by electrophoresis on 5% non-denaturing polyacrylamide gels in 0.5x TBE buffer. Panels B - E , DNA circularization assays in the presence of the full-length histone H1(fl) or peptides H1Δ24, H1Δ48 and H1Δ72. The percentage of DNA circles by reduced or oxidized HMGB1 or HMGB1ΔC (50 nM) in the presence of increasing concentrations of H1 or H1 peptides (1–15 nM, left to right ) is indicated. The percentage of the minicircles formed by HMGB1 or HMGB1ΔC in the absence of H1 or peptides was arbitrary set to 100%. Oxidized HMGB1 or HMGB1ΔC proteins are indicated in red.

    Journal: PLoS ONE

    Article Title: Histone H1 Differentially Inhibits DNA Bending by Reduced and Oxidized HMGB1 Protein

    doi: 10.1371/journal.pone.0138774

    Figure Lengend Snippet: Histone H1 inhibits the ability of HMGB1 to bend DNA. A , formation of DNA circles by HMGB1 is inhibited by the full-length histone H1 (DNA circularization assay). The 5´-end 32 P-labeled 123-bp DNA fragment (~1 nM) was pre-incubated with 5 nM HMGB1, followed by titration with increasing concentrations of H1 (0.2–15 nM, left to right ) and ligation by T4 DNA ligase. Deproteinised DNA samples were separated by electrophoresis on 5% non-denaturing polyacrylamide gels in 0.5x TBE buffer. Panels B - E , DNA circularization assays in the presence of the full-length histone H1(fl) or peptides H1Δ24, H1Δ48 and H1Δ72. The percentage of DNA circles by reduced or oxidized HMGB1 or HMGB1ΔC (50 nM) in the presence of increasing concentrations of H1 or H1 peptides (1–15 nM, left to right ) is indicated. The percentage of the minicircles formed by HMGB1 or HMGB1ΔC in the absence of H1 or peptides was arbitrary set to 100%. Oxidized HMGB1 or HMGB1ΔC proteins are indicated in red.

    Article Snippet: In agreement with previous reports [ , ], histone H1 could stimulate formation of linear multimers by T4 DNA ligase at low H1-to-DNA ratios.

    Techniques: Labeling, Incubation, Titration, Ligation, Electrophoresis

    The effect of oxidization and mutation of Cys22/Cys44 or Phe37 of HMGB1ΔC on DNA bending. A , the 5´-end 32 P-labeled 123-bp DNA fragment (~1 nM) was pre-incubated with 2, 5, 10, 15, 25, 50 and 100 nM of HMGB1 lacking the acidic C-tail (HMGB1ΔC, left to right ), followed by ligation by T4 DNA ligase (DNA circularization assay). Deproteinised DNA samples were separated by electrophoresis on 5% non-denaturing polyacrylamide gels in 0.5x TBE buffer. B , percentage of DNA circles formed by reduced (black triangle) or oxidized (empty triangle) HMGB1ΔC, as compared to DNA circles formed under the same conditions by reduced (black circles) or oxidized (empty circles) full-length HMGB1. The percentage of the minicircles formed at 100 nM HMGB1 was arbitrary set to 100% (each of the curves represent an average of three independent experiments). C , representative circularization assay using reduced HMGB1ΔC, oxidized HMGB1ΔC, and HMGB1ΔC(F37A). Concentrations of proteins were 5, 10, 25, 50 and 100 nM ( left to right ).

    Journal: PLoS ONE

    Article Title: Histone H1 Differentially Inhibits DNA Bending by Reduced and Oxidized HMGB1 Protein

    doi: 10.1371/journal.pone.0138774

    Figure Lengend Snippet: The effect of oxidization and mutation of Cys22/Cys44 or Phe37 of HMGB1ΔC on DNA bending. A , the 5´-end 32 P-labeled 123-bp DNA fragment (~1 nM) was pre-incubated with 2, 5, 10, 15, 25, 50 and 100 nM of HMGB1 lacking the acidic C-tail (HMGB1ΔC, left to right ), followed by ligation by T4 DNA ligase (DNA circularization assay). Deproteinised DNA samples were separated by electrophoresis on 5% non-denaturing polyacrylamide gels in 0.5x TBE buffer. B , percentage of DNA circles formed by reduced (black triangle) or oxidized (empty triangle) HMGB1ΔC, as compared to DNA circles formed under the same conditions by reduced (black circles) or oxidized (empty circles) full-length HMGB1. The percentage of the minicircles formed at 100 nM HMGB1 was arbitrary set to 100% (each of the curves represent an average of three independent experiments). C , representative circularization assay using reduced HMGB1ΔC, oxidized HMGB1ΔC, and HMGB1ΔC(F37A). Concentrations of proteins were 5, 10, 25, 50 and 100 nM ( left to right ).

    Article Snippet: In agreement with previous reports [ , ], histone H1 could stimulate formation of linear multimers by T4 DNA ligase at low H1-to-DNA ratios.

    Techniques: Mutagenesis, Labeling, Incubation, Ligation, Electrophoresis

    The effect of oxidization and mutation of Cys22/Cys44 or Phe37 of HMGB1 on DNA bending. A , the 5´-end 32 P-labeled 123-bp DNA fragment (~1 nM) was preincubated with 2, 5, 10, 15, 25, 50 and 100 nM HMGB1 proteins ( left to right ), followed by ligation by T4 DNA ligase (DNA circularization assay). Deproteinised DNA samples were separated by electrophoresis on 5% non-denaturing polyacrylamide gels in 0.5x TBE buffer. B , percentage of DNA circles formed by reduced HMGB1, oxidized HMGB1 or HMGB1(Cys22A/Cys44A) mutant. The percentage of the minicircles formed at 100 nM HMGB1 was arbitrary set to 100% (each of the curves represent an average of three independent experiments). C , representative circularization assay using reduced HMGB1 and HMGB1(F37A) mutant (5, 20, 50 and 100 nM HMGB1, left to right ). C22/C44, HMGB1(Cys22A/Cys44A) mutant.

    Journal: PLoS ONE

    Article Title: Histone H1 Differentially Inhibits DNA Bending by Reduced and Oxidized HMGB1 Protein

    doi: 10.1371/journal.pone.0138774

    Figure Lengend Snippet: The effect of oxidization and mutation of Cys22/Cys44 or Phe37 of HMGB1 on DNA bending. A , the 5´-end 32 P-labeled 123-bp DNA fragment (~1 nM) was preincubated with 2, 5, 10, 15, 25, 50 and 100 nM HMGB1 proteins ( left to right ), followed by ligation by T4 DNA ligase (DNA circularization assay). Deproteinised DNA samples were separated by electrophoresis on 5% non-denaturing polyacrylamide gels in 0.5x TBE buffer. B , percentage of DNA circles formed by reduced HMGB1, oxidized HMGB1 or HMGB1(Cys22A/Cys44A) mutant. The percentage of the minicircles formed at 100 nM HMGB1 was arbitrary set to 100% (each of the curves represent an average of three independent experiments). C , representative circularization assay using reduced HMGB1 and HMGB1(F37A) mutant (5, 20, 50 and 100 nM HMGB1, left to right ). C22/C44, HMGB1(Cys22A/Cys44A) mutant.

    Article Snippet: In agreement with previous reports [ , ], histone H1 could stimulate formation of linear multimers by T4 DNA ligase at low H1-to-DNA ratios.

    Techniques: Mutagenesis, Labeling, Ligation, Electrophoresis

    Dependence of the efficiency of DNA ligation using T4 DNA ligase immobilized on ferromagnetic particles in the absence of a magnetic field on the ambient temperature. The ordinate axis represents the ligation efficiency, which is normalized by that at 16 °C. The standard deviations are obtained from 6 independent experiments.

    Journal: Biochemistry and Biophysics Reports

    Article Title: Efficient DNA ligation by selective heating of DNA ligase with a radio frequency alternating magnetic field

    doi: 10.1016/j.bbrep.2016.10.006

    Figure Lengend Snippet: Dependence of the efficiency of DNA ligation using T4 DNA ligase immobilized on ferromagnetic particles in the absence of a magnetic field on the ambient temperature. The ordinate axis represents the ligation efficiency, which is normalized by that at 16 °C. The standard deviations are obtained from 6 independent experiments.

    Article Snippet: In summary, we carried out the ligation of DNA fragments with cohesive ends using T4 DNA ligase immobilized on ferromagnetic particles and found that the ligation efficiency was increased under a radio frequency alternating magnetic field caused by heat generation from the particles.

    Techniques: DNA Ligation, Ligation

    Dependence of the efficiency of DNA ligation using T4 DNA ligase immobilized on ferromagnetic particles under an ac magnetic field of 0.34 MHz on the amplitude of the magnetic field. The ambient temperature is 16 °C. The ordinate axis represents the ligation efficiency under an ac magnetic field, which is normalized by that in the absence of a magnetic field. The inset shows the ligation efficiency under the ac magnetic field as a function of the average surface temperature of ferromagnetic particles, noting that the surface temperature increases with an increase in the field amplitude. The standard deviations are obtained from 6 independent experiments.

    Journal: Biochemistry and Biophysics Reports

    Article Title: Efficient DNA ligation by selective heating of DNA ligase with a radio frequency alternating magnetic field

    doi: 10.1016/j.bbrep.2016.10.006

    Figure Lengend Snippet: Dependence of the efficiency of DNA ligation using T4 DNA ligase immobilized on ferromagnetic particles under an ac magnetic field of 0.34 MHz on the amplitude of the magnetic field. The ambient temperature is 16 °C. The ordinate axis represents the ligation efficiency under an ac magnetic field, which is normalized by that in the absence of a magnetic field. The inset shows the ligation efficiency under the ac magnetic field as a function of the average surface temperature of ferromagnetic particles, noting that the surface temperature increases with an increase in the field amplitude. The standard deviations are obtained from 6 independent experiments.

    Article Snippet: In summary, we carried out the ligation of DNA fragments with cohesive ends using T4 DNA ligase immobilized on ferromagnetic particles and found that the ligation efficiency was increased under a radio frequency alternating magnetic field caused by heat generation from the particles.

    Techniques: DNA Ligation, Ligation

    Ligation assay by T4 DNA ligase. Time scan curves of liga tion catalyzed by various concentrations of T4 DNA ligase. The curves from top to bottom are those obtained with different T4 DNA ligase concentrations: 2.3, 0.23, 0.115, 6.9 × 10 –2 , 2.3 × 10 –2 , 1.2 × 10 –2 , 6.9 × 10 –3 , 2.3 × 10 –3 , 1.2 × 10 –3 and 2.3 × 10 –4 U/ml. (Insert) The initial ligation velocity is plotted as a function of the concentration of T4 DNA ligase.

    Journal: Nucleic Acids Research

    Article Title: Real-time monitoring of nucleic acid ligation in homogenous solutions using molecular beacons

    doi: 10.1093/nar/gng146

    Figure Lengend Snippet: Ligation assay by T4 DNA ligase. Time scan curves of liga tion catalyzed by various concentrations of T4 DNA ligase. The curves from top to bottom are those obtained with different T4 DNA ligase concentrations: 2.3, 0.23, 0.115, 6.9 × 10 –2 , 2.3 × 10 –2 , 1.2 × 10 –2 , 6.9 × 10 –3 , 2.3 × 10 –3 , 1.2 × 10 –3 and 2.3 × 10 –4 U/ml. (Insert) The initial ligation velocity is plotted as a function of the concentration of T4 DNA ligase.

    Article Snippet: Two samples containing 10 µl reaction solutions were moved from each sample before adding T4 DNA ligase, and after the ligation process had taken place for 360 s with the addition of ligase.

    Techniques: Ligation, Concentration Assay

    Real-time fluorescence scans and corresponding gel electrophoresis. (Left) Curve A is a time scan of fluorescence intensity of MB with N1; B is of MB with N2 and N4; C is of MB with N2 and N3; curve D is of MB itself. t 0 is the time when T4 DNA ligase is added into the MB/oligo solution. (Right) Gel electrophoresis images. Lanes 1 and 2 are for sample D; 3 and 4 for sample C; 5 and 6 for sample B; and 7 and 8 for sample A. Lanes 1, 3, 5 and 7 represent samples D, C, B and A before the addition of T4 DNA ligase, while lanes 2, 4, 6 and 8 represent corresponding samples obtained at 360 s after the addition of ligase. There is a major difference between lanes 5 and 6, while there is basically no difference for all the other pairs.

    Journal: Nucleic Acids Research

    Article Title: Real-time monitoring of nucleic acid ligation in homogenous solutions using molecular beacons

    doi: 10.1093/nar/gng146

    Figure Lengend Snippet: Real-time fluorescence scans and corresponding gel electrophoresis. (Left) Curve A is a time scan of fluorescence intensity of MB with N1; B is of MB with N2 and N4; C is of MB with N2 and N3; curve D is of MB itself. t 0 is the time when T4 DNA ligase is added into the MB/oligo solution. (Right) Gel electrophoresis images. Lanes 1 and 2 are for sample D; 3 and 4 for sample C; 5 and 6 for sample B; and 7 and 8 for sample A. Lanes 1, 3, 5 and 7 represent samples D, C, B and A before the addition of T4 DNA ligase, while lanes 2, 4, 6 and 8 represent corresponding samples obtained at 360 s after the addition of ligase. There is a major difference between lanes 5 and 6, while there is basically no difference for all the other pairs.

    Article Snippet: Two samples containing 10 µl reaction solutions were moved from each sample before adding T4 DNA ligase, and after the ligation process had taken place for 360 s with the addition of ligase.

    Techniques: Fluorescence, Nucleic Acid Electrophoresis