nt alwi  (New England Biolabs)


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    Name:
    Nt AlwI
    Description:
    Nt AlwI 500 units
    Catalog Number:
    r0627l
    Price:
    70
    Size:
    500 units
    Category:
    Restriction Enzymes
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    Structured Review

    New England Biolabs nt alwi
    Nt AlwI
    Nt AlwI 500 units
    https://www.bioz.com/result/nt alwi/product/New England Biolabs
    Average 80 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    nt alwi - by Bioz Stars, 2020-01
    80/100 stars

    Images

    1) Product Images from "Meiotic association between Spo11 regulated by Rec102, Rec104 and Rec114"

    Article Title: Meiotic association between Spo11 regulated by Rec102, Rec104 and Rec114

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkl1162

    Detection of SSBs in the GAL2 UAS region. ( A ) Detection of SSBs by S1 nuclease. Plugs containing genomic DNA from wild-type cells were directly equilibrated in restriction digestion buffer and treated with NcoI and XbaI. Genomic DNA recovered from the melted plugs was then incubated in the presence (lanes designated +) or absence (lanes designated −) of S1 nuclease. Numbers above the panels are culture time (hours) in SPM. The diagram is labeled as for Figure 5 . ( B ) Schematic diagram of SSB detection in rad50S strains using denaturing polyacrylamide gel. Nt.AlwI introduces an SSB into specific sequences of DNA (5′-GGATCNNNN/N-3′). The GAL2 promoter has the sequence only on the + strand. Probes A and B were labeled by multiple round primer extension in the presence of radio-labeled dCTP. ( C ) and ( D ) Detection of SSBs on the −/+ strand by using strand-specific probes. All strains are homozygous for the rad50S allele. After genomic DNA was prepared from the meiotic cells at the indicated times (hours), it was treated with AccI and BspHI. The right two lanes in each panel contain 5% DNA fragments, which were further digested with HhaI or Nt.AlwI. Strains used were YHS363, YHS397, YHS427 and YHS514.
    Figure Legend Snippet: Detection of SSBs in the GAL2 UAS region. ( A ) Detection of SSBs by S1 nuclease. Plugs containing genomic DNA from wild-type cells were directly equilibrated in restriction digestion buffer and treated with NcoI and XbaI. Genomic DNA recovered from the melted plugs was then incubated in the presence (lanes designated +) or absence (lanes designated −) of S1 nuclease. Numbers above the panels are culture time (hours) in SPM. The diagram is labeled as for Figure 5 . ( B ) Schematic diagram of SSB detection in rad50S strains using denaturing polyacrylamide gel. Nt.AlwI introduces an SSB into specific sequences of DNA (5′-GGATCNNNN/N-3′). The GAL2 promoter has the sequence only on the + strand. Probes A and B were labeled by multiple round primer extension in the presence of radio-labeled dCTP. ( C ) and ( D ) Detection of SSBs on the −/+ strand by using strand-specific probes. All strains are homozygous for the rad50S allele. After genomic DNA was prepared from the meiotic cells at the indicated times (hours), it was treated with AccI and BspHI. The right two lanes in each panel contain 5% DNA fragments, which were further digested with HhaI or Nt.AlwI. Strains used were YHS363, YHS397, YHS427 and YHS514.

    Techniques Used: Incubation, Labeling, Sequencing

    2) Product Images from "Synthesizing topological structures containing RNA"

    Article Title: Synthesizing topological structures containing RNA

    Journal: Nature Communications

    doi: 10.1038/ncomms14936

    Constructing ssRNA topological structures with the junction-based method. ( a ) Preparation of the ssRNA strand with uniform ends and proper end groups for the DNA-splinted RNA ligation. ( b ) Both the positive ( TK j ( + )) and negative ( TK j ( − )) RNA trefoil knots of the same sequence are constructed by configuring tensegrity triangles with different handedness. The same scaffolds (blue) are threaded by different staple sets (grey or purple) to form a 17-bp-edged right-handed tensegrity triangle for the positive trefoil knot, or a 14-bp-edged left-handed tensegrity triangle for the negative one, respectively. Each topology is designated by the Alexander–Briggs notation n i or , where n is the minimal number of nodes, C is the number of components (for links), and i distinguishes different topologies with the same n and C . ( c ) dPAGE analysis of TK j ( + ) (lanes 1 and 2), TK j ( − ) (lanes 3 and 4), and their circular ( C j , lanes 5 and 6) and linear ( L j , lanes 7 and 8) counterparts. Lanes 2, 4, 6 and 8 contain samples digested by RNase R. ( d ) The assembly complex for the hybrid BR contains tensegrity triangles of both handedness to generate three positive nodes plus three negative nodes. ( e ) Topological analyses of the hybrid BR. Lane 1, gel-purified BR; lanes 2–6, BR treated by RNase H, Nt.AlwI (for cleaving the red ring), Nt.BspQI (for cleaving the green ring), DNase I, and E. coli DNA Topo I; lanes 7 and 8, DNA and RNA references of the three individual components. During the purification of BR, the breaking down of the 95-nt circular RNA component is unavoidable, and a portion of BR falls apart as a result. The treatment of BR by RNase H, Nt.AlwI and Nt.BspQI is conducted in the presence of an assisting DNA strand complementary to the corresponding ssRNA or ssDNA ring. LX and CX represent X-nt linear and circular species, respectively. In all the gels, lane M contains the DNA size markers.
    Figure Legend Snippet: Constructing ssRNA topological structures with the junction-based method. ( a ) Preparation of the ssRNA strand with uniform ends and proper end groups for the DNA-splinted RNA ligation. ( b ) Both the positive ( TK j ( + )) and negative ( TK j ( − )) RNA trefoil knots of the same sequence are constructed by configuring tensegrity triangles with different handedness. The same scaffolds (blue) are threaded by different staple sets (grey or purple) to form a 17-bp-edged right-handed tensegrity triangle for the positive trefoil knot, or a 14-bp-edged left-handed tensegrity triangle for the negative one, respectively. Each topology is designated by the Alexander–Briggs notation n i or , where n is the minimal number of nodes, C is the number of components (for links), and i distinguishes different topologies with the same n and C . ( c ) dPAGE analysis of TK j ( + ) (lanes 1 and 2), TK j ( − ) (lanes 3 and 4), and their circular ( C j , lanes 5 and 6) and linear ( L j , lanes 7 and 8) counterparts. Lanes 2, 4, 6 and 8 contain samples digested by RNase R. ( d ) The assembly complex for the hybrid BR contains tensegrity triangles of both handedness to generate three positive nodes plus three negative nodes. ( e ) Topological analyses of the hybrid BR. Lane 1, gel-purified BR; lanes 2–6, BR treated by RNase H, Nt.AlwI (for cleaving the red ring), Nt.BspQI (for cleaving the green ring), DNase I, and E. coli DNA Topo I; lanes 7 and 8, DNA and RNA references of the three individual components. During the purification of BR, the breaking down of the 95-nt circular RNA component is unavoidable, and a portion of BR falls apart as a result. The treatment of BR by RNase H, Nt.AlwI and Nt.BspQI is conducted in the presence of an assisting DNA strand complementary to the corresponding ssRNA or ssDNA ring. LX and CX represent X-nt linear and circular species, respectively. In all the gels, lane M contains the DNA size markers.

    Techniques Used: Ligation, Sequencing, Construct, Purification

    Related Articles

    Clone Assay:

    Article Title: Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Article Snippet: This vector was used for cloning Bam HI/Eco RI-digested PCR fragments of various lengths amplified from the lambda DNA template using a forward primer (5'-TTG CTG AGG ATC CTG TAC CGG CTG TCT GGT ATG TAT G-3') in combination with one of the following reverse primers (5'-TTG CTG AGA ATT CTC CTC CTG CGA TCC CTT C-3', 5'-TTG CTG AGA ATT CAT CGG CAG GGT GAT CGC-3', 5'-TTG CTG AGA ATT CTG GAA CTG GCG AGC CAT C-3', 5'-TTG CTG AGA ATT CGC GGC TTC AAG CGC AAG-3'). .. They were treated with a nicking endonuclease Nt.AlwI (New England BioLabs) to convert them into open circles, and purified by agarose-gel electrophoresis.

    Amplification:

    Article Title: Library-free Methylation Sequencing with Bisulfite Padlock Probes
    Article Snippet: The oligonucleotides were amplified by two-step PCR in a 200 μl reaction with 1nM template oligonucleotides, 400 nM each of eMIP_CA1_F primer and eMIP_CA1_R primer , and 100 μl of KAPA SYBR fast Universal qPCR Master Mix at 95 °C for 30 s, 5 cycles of 95 °C for 5 s; 52 °C for 1 min; and 72 °C for 30 s, 10-12 cycles of 95 °C for 5 s; 60 °C for 30 s; and 72 °C for 30sec, and 72 °C for 2 min. .. Approximately 4 μg of the purified amplicons were digested with 100 units of Nt.AlwI (100 U/μl, NEB) at 37 °C for 1 h in NEBuffer 2.

    Article Title: Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Article Snippet: This vector was used for cloning Bam HI/Eco RI-digested PCR fragments of various lengths amplified from the lambda DNA template using a forward primer (5'-TTG CTG AGG ATC CTG TAC CGG CTG TCT GGT ATG TAT G-3') in combination with one of the following reverse primers (5'-TTG CTG AGA ATT CTC CTC CTG CGA TCC CTT C-3', 5'-TTG CTG AGA ATT CAT CGG CAG GGT GAT CGC-3', 5'-TTG CTG AGA ATT CTG GAA CTG GCG AGC CAT C-3', 5'-TTG CTG AGA ATT CGC GGC TTC AAG CGC AAG-3'). .. They were treated with a nicking endonuclease Nt.AlwI (New England BioLabs) to convert them into open circles, and purified by agarose-gel electrophoresis.

    Positive Control:

    Article Title: Meiotic association between Spo11 regulated by Rec102, Rec104 and Rec114
    Article Snippet: At the GAL2 locus, the purified genomic DNA was treated with AccI, BspHI, HhaI and Nt.AlwI (New England BioLabs) for several hours. .. Nt.AlwI was used as a positive control for SSB detection.

    Article Title: Meiotic association between Spo11 regulated by Rec102, Rec104 and Rec114
    Article Snippet: .. Nt.AlwI was used as a positive control for SSB detection. .. All samples were purified using a NucleoSpin Extract II kit (Macherey-Nagel) and suspended in TE and loading buffer (95% formamide, 10 mM EDTA, 0.1% xylene cyanol, 0.1% bromophenol blue).

    Synthesized:

    Article Title: Library-free Methylation Sequencing with Bisulfite Padlock Probes
    Article Snippet: Bisulfite padlock probe production (Oligonucleotides from LC Sciences) The oligonucleotides (100 nt) were synthesized using a programmable microfluidic microarray platform (LC Sciences) and released to form a mix of 3,918 oligoucleotides. .. Approximately 4 μg of the purified amplicons were digested with 100 units of Nt.AlwI (100 U/μl, NEB) at 37 °C for 1 h in NEBuffer 2.

    Lambda DNA Preparation:

    Article Title: Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Article Snippet: This vector was used for cloning Bam HI/Eco RI-digested PCR fragments of various lengths amplified from the lambda DNA template using a forward primer (5'-TTG CTG AGG ATC CTG TAC CGG CTG TCT GGT ATG TAT G-3') in combination with one of the following reverse primers (5'-TTG CTG AGA ATT CTC CTC CTG CGA TCC CTT C-3', 5'-TTG CTG AGA ATT CAT CGG CAG GGT GAT CGC-3', 5'-TTG CTG AGA ATT CTG GAA CTG GCG AGC CAT C-3', 5'-TTG CTG AGA ATT CGC GGC TTC AAG CGC AAG-3'). .. They were treated with a nicking endonuclease Nt.AlwI (New England BioLabs) to convert them into open circles, and purified by agarose-gel electrophoresis.

    Construct:

    Article Title: Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Article Snippet: The final constructs thus contained LoxP-PCR fragment-LoxP cassettes which were subsequently released by Cre-mediated recombination in the form of covalently closed circular molecules. .. They were treated with a nicking endonuclease Nt.AlwI (New England BioLabs) to convert them into open circles, and purified by agarose-gel electrophoresis.

    Real-time Polymerase Chain Reaction:

    Article Title: Library-free Methylation Sequencing with Bisulfite Padlock Probes
    Article Snippet: The resultant amplicons were purified with Qiaquick PCR purification columns and re-amplified by PCR in 32 reactions (100 μl each) with 0.02 nM first round amplicons, 400 nM each of eMIP_CA1_F primer and eMIP_CA1_R primer, and 50 μl of KAPA SYBR fast Universal qPCR Master Mix at 95 °C for 30 s, 13-15 cycles of 95 °C for 5 s; 60 °C for 30 sec; and 72 °C for 30 s, and 72 °C for 2 min. .. Approximately 4 μg of the purified amplicons were digested with 100 units of Nt.AlwI (100 U/μl, NEB) at 37 °C for 1 h in NEBuffer 2.

    Microarray:

    Article Title: Library-free Methylation Sequencing with Bisulfite Padlock Probes
    Article Snippet: Bisulfite padlock probe production (Oligonucleotides from LC Sciences) The oligonucleotides (100 nt) were synthesized using a programmable microfluidic microarray platform (LC Sciences) and released to form a mix of 3,918 oligoucleotides. .. Approximately 4 μg of the purified amplicons were digested with 100 units of Nt.AlwI (100 U/μl, NEB) at 37 °C for 1 h in NEBuffer 2.

    Incubation:

    Article Title: Library-free Methylation Sequencing with Bisulfite Padlock Probes
    Article Snippet: Approximately 4 μg of the purified amplicons were digested with 100 units of Nt.AlwI (100 U/μl, NEB) at 37 °C for 1 h in NEBuffer 2. .. The digested amplicons were then incubated with 100 units of Nb.BrsDI (10 U/μl, NEB) at 65 °C for 1 h. The nicked DNA was purified by Qiaquick PCR purification column.

    Article Title: Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Article Snippet: The fragment was cloned into Bam HI/Eco RI-digested plasmid vector and this construct was further modified by incubation with Cre recombinase (New England BioLabs, USA) and the linear LoxP fragment (in a 20 μl reaction mixture containing 2 μg LoxP vector, 0.5 μM annealed LoxP oligonucleotides, 1 × ligase buffer (Fermentas International Inc.), 10 U Cre recombinase, at 37°C for 30 min and heat-inactivated at 70°C for 10 min), producing linearized plasmid carrying one LoxP sequence terminated with a Bam HI and Eco RI overhang at each end, respectively. .. They were treated with a nicking endonuclease Nt.AlwI (New England BioLabs) to convert them into open circles, and purified by agarose-gel electrophoresis.

    Article Title: Meiotic association between Spo11 regulated by Rec102, Rec104 and Rec114
    Article Snippet: After the agarose plugs were melted at 65°C for 10 min, S1 nuclease was added and the mixture was incubated for 30 min at 37°C ( , ). .. At the GAL2 locus, the purified genomic DNA was treated with AccI, BspHI, HhaI and Nt.AlwI (New England BioLabs) for several hours.

    Article Title: Novel Method For Quantifying Radiation-Induced Single-Strand-Break Yields In Plasmid DNA Highlights Tenfold Discrepancy
    Article Snippet: Nicking endonucleases Nb.BsrDI, Nb.BtsI, Nt.BstNBI and Nt.AlwI (New England Biolabs, Beverly, MA) were used to create 3 HT-pUC19 (20 μg) plasmid DNA molecules with known number of SSBs (2, 3, 4 and 10, respectively). .. For Nb.BtsI digestion, DNA was incubated (37°C for 18 hrs) in 1X NEBuffer 4 (New England Biolabs, Inc.); for Nt.

    Modification:

    Article Title: Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Article Snippet: The fragment was cloned into Bam HI/Eco RI-digested plasmid vector and this construct was further modified by incubation with Cre recombinase (New England BioLabs, USA) and the linear LoxP fragment (in a 20 μl reaction mixture containing 2 μg LoxP vector, 0.5 μM annealed LoxP oligonucleotides, 1 × ligase buffer (Fermentas International Inc.), 10 U Cre recombinase, at 37°C for 30 min and heat-inactivated at 70°C for 10 min), producing linearized plasmid carrying one LoxP sequence terminated with a Bam HI and Eco RI overhang at each end, respectively. .. They were treated with a nicking endonuclease Nt.AlwI (New England BioLabs) to convert them into open circles, and purified by agarose-gel electrophoresis.

    Hybridization:

    Article Title: Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Article Snippet: They were treated with a nicking endonuclease Nt.AlwI (New England BioLabs) to convert them into open circles, and purified by agarose-gel electrophoresis. .. 50 pg of each of these markers were added into genomic DNA samples prior to 2-D electrophoresis and their positions on the gel were determined using Southern hybridization with the lambda DNA probe.

    other:

    Article Title: Remote control of DNA-acting enzymes by varying the Brownian dynamics of a distant DNA end
    Article Snippet: Reactions with vaccinia topo IB (Epicentre Biotechnologies), Nt.AlwI (New England Biolabs), and PvuII (Promega) were performed in a buffer containing 50 mM potassium glutamate, 10 mM Hepes (pH 7.5), 1 mM MgCl2 , and 1 mM DTT.

    Article Title: Synthesizing topological structures containing RNA
    Article Snippet: Digestion with various nucleases Various nucleases were used in this work, including Nt.AlwI (NEB), Nt.BspQI (NEB), RNase H (NEB), DNase I (NEB) and RNase R (Epicentre).

    Sequencing:

    Article Title: Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Article Snippet: The fragment was cloned into Bam HI/Eco RI-digested plasmid vector and this construct was further modified by incubation with Cre recombinase (New England BioLabs, USA) and the linear LoxP fragment (in a 20 μl reaction mixture containing 2 μg LoxP vector, 0.5 μM annealed LoxP oligonucleotides, 1 × ligase buffer (Fermentas International Inc.), 10 U Cre recombinase, at 37°C for 30 min and heat-inactivated at 70°C for 10 min), producing linearized plasmid carrying one LoxP sequence terminated with a Bam HI and Eco RI overhang at each end, respectively. .. They were treated with a nicking endonuclease Nt.AlwI (New England BioLabs) to convert them into open circles, and purified by agarose-gel electrophoresis.

    Size-exclusion Chromatography:

    Article Title: Library-free Methylation Sequencing with Bisulfite Padlock Probes
    Article Snippet: The resultant amplicons were purified with Qiaquick PCR purification columns and re-amplified by PCR in 32 reactions (100 μl each) with 0.02 nM first round amplicons, 400 nM each of eMIP_CA1_F primer and eMIP_CA1_R primer, and 50 μl of KAPA SYBR fast Universal qPCR Master Mix at 95 °C for 30 s, 13-15 cycles of 95 °C for 5 s; 60 °C for 30 sec; and 72 °C for 30 s, and 72 °C for 2 min. .. Approximately 4 μg of the purified amplicons were digested with 100 units of Nt.AlwI (100 U/μl, NEB) at 37 °C for 1 h in NEBuffer 2.

    Purification:

    Article Title: Library-free Methylation Sequencing with Bisulfite Padlock Probes
    Article Snippet: .. Approximately 4 μg of the purified amplicons were digested with 100 units of Nt.AlwI (100 U/μl, NEB) at 37 °C for 1 h in NEBuffer 2. .. The digested amplicons were then incubated with 100 units of Nb.BrsDI (10 U/μl, NEB) at 65 °C for 1 h. The nicked DNA was purified by Qiaquick PCR purification column.

    Article Title: Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Article Snippet: .. They were treated with a nicking endonuclease Nt.AlwI (New England BioLabs) to convert them into open circles, and purified by agarose-gel electrophoresis. .. 50 pg of each of these markers were added into genomic DNA samples prior to 2-D electrophoresis and their positions on the gel were determined using Southern hybridization with the lambda DNA probe.

    Article Title: Meiotic association between Spo11 regulated by Rec102, Rec104 and Rec114
    Article Snippet: .. At the GAL2 locus, the purified genomic DNA was treated with AccI, BspHI, HhaI and Nt.AlwI (New England BioLabs) for several hours. .. Nt.AlwI was used as a positive control for SSB detection.

    Polymerase Chain Reaction:

    Article Title: Library-free Methylation Sequencing with Bisulfite Padlock Probes
    Article Snippet: The resultant amplicons were purified by ethanol precipitation and re-purified with Qiaquick PCR purification columns as described above. .. Approximately 4 μg of the purified amplicons were digested with 100 units of Nt.AlwI (100 U/μl, NEB) at 37 °C for 1 h in NEBuffer 2.

    Article Title: Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Article Snippet: This vector was used for cloning Bam HI/Eco RI-digested PCR fragments of various lengths amplified from the lambda DNA template using a forward primer (5'-TTG CTG AGG ATC CTG TAC CGG CTG TCT GGT ATG TAT G-3') in combination with one of the following reverse primers (5'-TTG CTG AGA ATT CTC CTC CTG CGA TCC CTT C-3', 5'-TTG CTG AGA ATT CAT CGG CAG GGT GAT CGC-3', 5'-TTG CTG AGA ATT CTG GAA CTG GCG AGC CAT C-3', 5'-TTG CTG AGA ATT CGC GGC TTC AAG CGC AAG-3'). .. They were treated with a nicking endonuclease Nt.AlwI (New England BioLabs) to convert them into open circles, and purified by agarose-gel electrophoresis.

    Polyacrylamide Gel Electrophoresis:

    Article Title: Library-free Methylation Sequencing with Bisulfite Padlock Probes
    Article Snippet: Approximately 4 μg of the purified amplicons were digested with 100 units of Nt.AlwI (100 U/μl, NEB) at 37 °C for 1 h in NEBuffer 2. .. The probe molecules (with size of approximately 70 bases) were purified by 6% denaturing PAGE (6% TB-urea 2D gel).

    Chloramphenicol Acetyltransferase Assay:

    Article Title: Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Article Snippet: This vector was used for cloning Bam HI/Eco RI-digested PCR fragments of various lengths amplified from the lambda DNA template using a forward primer (5'-TTG CTG AGG ATC CTG TAC CGG CTG TCT GGT ATG TAT G-3') in combination with one of the following reverse primers (5'-TTG CTG AGA ATT CTC CTC CTG CGA TCC CTT C-3', 5'-TTG CTG AGA ATT CAT CGG CAG GGT GAT CGC-3', 5'-TTG CTG AGA ATT CTG GAA CTG GCG AGC CAT C-3', 5'-TTG CTG AGA ATT CGC GGC TTC AAG CGC AAG-3'). .. They were treated with a nicking endonuclease Nt.AlwI (New England BioLabs) to convert them into open circles, and purified by agarose-gel electrophoresis.

    Plasmid Preparation:

    Article Title: Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Article Snippet: This vector was used for cloning Bam HI/Eco RI-digested PCR fragments of various lengths amplified from the lambda DNA template using a forward primer (5'-TTG CTG AGG ATC CTG TAC CGG CTG TCT GGT ATG TAT G-3') in combination with one of the following reverse primers (5'-TTG CTG AGA ATT CTC CTC CTG CGA TCC CTT C-3', 5'-TTG CTG AGA ATT CAT CGG CAG GGT GAT CGC-3', 5'-TTG CTG AGA ATT CTG GAA CTG GCG AGC CAT C-3', 5'-TTG CTG AGA ATT CGC GGC TTC AAG CGC AAG-3'). .. They were treated with a nicking endonuclease Nt.AlwI (New England BioLabs) to convert them into open circles, and purified by agarose-gel electrophoresis.

    Article Title: Novel Method For Quantifying Radiation-Induced Single-Strand-Break Yields In Plasmid DNA Highlights Tenfold Discrepancy
    Article Snippet: .. Nicking endonucleases Nb.BsrDI, Nb.BtsI, Nt.BstNBI and Nt.AlwI (New England Biolabs, Beverly, MA) were used to create 3 HT-pUC19 (20 μg) plasmid DNA molecules with known number of SSBs (2, 3, 4 and 10, respectively). .. In essence, 3 HT-pUC19 (20 μg) plasmid SC DNA samples were each digested with 100 units (10 units/μl) of one of the above mentioned nicking endonucleases in 100 μl volume under appropriate conditions.

    Electrophoresis:

    Article Title: Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Article Snippet: .. They were treated with a nicking endonuclease Nt.AlwI (New England BioLabs) to convert them into open circles, and purified by agarose-gel electrophoresis. .. 50 pg of each of these markers were added into genomic DNA samples prior to 2-D electrophoresis and their positions on the gel were determined using Southern hybridization with the lambda DNA probe.

    Agarose Gel Electrophoresis:

    Article Title: Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Article Snippet: .. They were treated with a nicking endonuclease Nt.AlwI (New England BioLabs) to convert them into open circles, and purified by agarose-gel electrophoresis. .. 50 pg of each of these markers were added into genomic DNA samples prior to 2-D electrophoresis and their positions on the gel were determined using Southern hybridization with the lambda DNA probe.

    Ethanol Precipitation:

    Article Title: Library-free Methylation Sequencing with Bisulfite Padlock Probes
    Article Snippet: The resultant amplicons were purified by ethanol precipitation and re-purified with Qiaquick PCR purification columns as described above. .. Approximately 4 μg of the purified amplicons were digested with 100 units of Nt.AlwI (100 U/μl, NEB) at 37 °C for 1 h in NEBuffer 2.

    Two-Dimensional Gel Electrophoresis:

    Article Title: Library-free Methylation Sequencing with Bisulfite Padlock Probes
    Article Snippet: Approximately 4 μg of the purified amplicons were digested with 100 units of Nt.AlwI (100 U/μl, NEB) at 37 °C for 1 h in NEBuffer 2. .. The probe molecules (with size of approximately 70 bases) were purified by 6% denaturing PAGE (6% TB-urea 2D gel).

    Article Title: Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Article Snippet: They were treated with a nicking endonuclease Nt.AlwI (New England BioLabs) to convert them into open circles, and purified by agarose-gel electrophoresis. .. 50 pg of each of these markers were added into genomic DNA samples prior to 2-D electrophoresis and their positions on the gel were determined using Southern hybridization with the lambda DNA probe.

    CTG Assay:

    Article Title: Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Article Snippet: This vector was used for cloning Bam HI/Eco RI-digested PCR fragments of various lengths amplified from the lambda DNA template using a forward primer (5'-TTG CTG AGG ATC CTG TAC CGG CTG TCT GGT ATG TAT G-3') in combination with one of the following reverse primers (5'-TTG CTG AGA ATT CTC CTC CTG CGA TCC CTT C-3', 5'-TTG CTG AGA ATT CAT CGG CAG GGT GAT CGC-3', 5'-TTG CTG AGA ATT CTG GAA CTG GCG AGC CAT C-3', 5'-TTG CTG AGA ATT CGC GGC TTC AAG CGC AAG-3'). .. They were treated with a nicking endonuclease Nt.AlwI (New England BioLabs) to convert them into open circles, and purified by agarose-gel electrophoresis.

    Lysis:

    Article Title: Meiotic association between Spo11 regulated by Rec102, Rec104 and Rec114
    Article Snippet: After cells were spheroplasted with Zymolyase-20T (MP Biomedicals, Inc.) in spheroplast buffer (1% 2-mercaptoethanol, 1 M sorbitol, 0.1 M EDTA [pH 8.0]), they were lysed and digested in lysis buffer (50 mM EDTA [pH 8.0], 50 mM Tris [pH 8.0], 0.5% SDS, 200 µg of proteinase K). .. At the GAL2 locus, the purified genomic DNA was treated with AccI, BspHI, HhaI and Nt.AlwI (New England BioLabs) for several hours.

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    New England Biolabs nt alwi
    Detection of SSBs in the GAL2 UAS region. ( A ) Detection of SSBs by S1 nuclease. Plugs containing genomic <t>DNA</t> from wild-type cells were directly equilibrated in restriction digestion buffer and treated with NcoI and XbaI. Genomic DNA recovered from the melted plugs was then incubated in the presence (lanes designated +) or absence (lanes designated −) of S1 nuclease. Numbers above the panels are culture time (hours) in SPM. The diagram is labeled as for Figure 5 . ( B ) Schematic diagram of SSB detection in rad50S strains using denaturing polyacrylamide gel. <t>Nt.AlwI</t> introduces an SSB into specific sequences of DNA (5′-GGATCNNNN/N-3′). The GAL2 promoter has the sequence only on the + strand. Probes A and B were labeled by multiple round primer extension in the presence of radio-labeled dCTP. ( C ) and ( D ) Detection of SSBs on the −/+ strand by using strand-specific probes. All strains are homozygous for the rad50S allele. After genomic DNA was prepared from the meiotic cells at the indicated times (hours), it was treated with AccI and BspHI. The right two lanes in each panel contain 5% DNA fragments, which were further digested with HhaI or Nt.AlwI. Strains used were YHS363, YHS397, YHS427 and YHS514.
    Nt Alwi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 80/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nt alwi/product/New England Biolabs
    Average 80 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    nt alwi - by Bioz Stars, 2020-01
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    Detection of SSBs in the GAL2 UAS region. ( A ) Detection of SSBs by S1 nuclease. Plugs containing genomic DNA from wild-type cells were directly equilibrated in restriction digestion buffer and treated with NcoI and XbaI. Genomic DNA recovered from the melted plugs was then incubated in the presence (lanes designated +) or absence (lanes designated −) of S1 nuclease. Numbers above the panels are culture time (hours) in SPM. The diagram is labeled as for Figure 5 . ( B ) Schematic diagram of SSB detection in rad50S strains using denaturing polyacrylamide gel. Nt.AlwI introduces an SSB into specific sequences of DNA (5′-GGATCNNNN/N-3′). The GAL2 promoter has the sequence only on the + strand. Probes A and B were labeled by multiple round primer extension in the presence of radio-labeled dCTP. ( C ) and ( D ) Detection of SSBs on the −/+ strand by using strand-specific probes. All strains are homozygous for the rad50S allele. After genomic DNA was prepared from the meiotic cells at the indicated times (hours), it was treated with AccI and BspHI. The right two lanes in each panel contain 5% DNA fragments, which were further digested with HhaI or Nt.AlwI. Strains used were YHS363, YHS397, YHS427 and YHS514.

    Journal: Nucleic Acids Research

    Article Title: Meiotic association between Spo11 regulated by Rec102, Rec104 and Rec114

    doi: 10.1093/nar/gkl1162

    Figure Lengend Snippet: Detection of SSBs in the GAL2 UAS region. ( A ) Detection of SSBs by S1 nuclease. Plugs containing genomic DNA from wild-type cells were directly equilibrated in restriction digestion buffer and treated with NcoI and XbaI. Genomic DNA recovered from the melted plugs was then incubated in the presence (lanes designated +) or absence (lanes designated −) of S1 nuclease. Numbers above the panels are culture time (hours) in SPM. The diagram is labeled as for Figure 5 . ( B ) Schematic diagram of SSB detection in rad50S strains using denaturing polyacrylamide gel. Nt.AlwI introduces an SSB into specific sequences of DNA (5′-GGATCNNNN/N-3′). The GAL2 promoter has the sequence only on the + strand. Probes A and B were labeled by multiple round primer extension in the presence of radio-labeled dCTP. ( C ) and ( D ) Detection of SSBs on the −/+ strand by using strand-specific probes. All strains are homozygous for the rad50S allele. After genomic DNA was prepared from the meiotic cells at the indicated times (hours), it was treated with AccI and BspHI. The right two lanes in each panel contain 5% DNA fragments, which were further digested with HhaI or Nt.AlwI. Strains used were YHS363, YHS397, YHS427 and YHS514.

    Article Snippet: At the GAL2 locus, the purified genomic DNA was treated with AccI, BspHI, HhaI and Nt.AlwI (New England BioLabs) for several hours.

    Techniques: Incubation, Labeling, Sequencing

    Constructing ssRNA topological structures with the junction-based method. ( a ) Preparation of the ssRNA strand with uniform ends and proper end groups for the DNA-splinted RNA ligation. ( b ) Both the positive ( TK j ( + )) and negative ( TK j ( − )) RNA trefoil knots of the same sequence are constructed by configuring tensegrity triangles with different handedness. The same scaffolds (blue) are threaded by different staple sets (grey or purple) to form a 17-bp-edged right-handed tensegrity triangle for the positive trefoil knot, or a 14-bp-edged left-handed tensegrity triangle for the negative one, respectively. Each topology is designated by the Alexander–Briggs notation n i or , where n is the minimal number of nodes, C is the number of components (for links), and i distinguishes different topologies with the same n and C . ( c ) dPAGE analysis of TK j ( + ) (lanes 1 and 2), TK j ( − ) (lanes 3 and 4), and their circular ( C j , lanes 5 and 6) and linear ( L j , lanes 7 and 8) counterparts. Lanes 2, 4, 6 and 8 contain samples digested by RNase R. ( d ) The assembly complex for the hybrid BR contains tensegrity triangles of both handedness to generate three positive nodes plus three negative nodes. ( e ) Topological analyses of the hybrid BR. Lane 1, gel-purified BR; lanes 2–6, BR treated by RNase H, Nt.AlwI (for cleaving the red ring), Nt.BspQI (for cleaving the green ring), DNase I, and E. coli DNA Topo I; lanes 7 and 8, DNA and RNA references of the three individual components. During the purification of BR, the breaking down of the 95-nt circular RNA component is unavoidable, and a portion of BR falls apart as a result. The treatment of BR by RNase H, Nt.AlwI and Nt.BspQI is conducted in the presence of an assisting DNA strand complementary to the corresponding ssRNA or ssDNA ring. LX and CX represent X-nt linear and circular species, respectively. In all the gels, lane M contains the DNA size markers.

    Journal: Nature Communications

    Article Title: Synthesizing topological structures containing RNA

    doi: 10.1038/ncomms14936

    Figure Lengend Snippet: Constructing ssRNA topological structures with the junction-based method. ( a ) Preparation of the ssRNA strand with uniform ends and proper end groups for the DNA-splinted RNA ligation. ( b ) Both the positive ( TK j ( + )) and negative ( TK j ( − )) RNA trefoil knots of the same sequence are constructed by configuring tensegrity triangles with different handedness. The same scaffolds (blue) are threaded by different staple sets (grey or purple) to form a 17-bp-edged right-handed tensegrity triangle for the positive trefoil knot, or a 14-bp-edged left-handed tensegrity triangle for the negative one, respectively. Each topology is designated by the Alexander–Briggs notation n i or , where n is the minimal number of nodes, C is the number of components (for links), and i distinguishes different topologies with the same n and C . ( c ) dPAGE analysis of TK j ( + ) (lanes 1 and 2), TK j ( − ) (lanes 3 and 4), and their circular ( C j , lanes 5 and 6) and linear ( L j , lanes 7 and 8) counterparts. Lanes 2, 4, 6 and 8 contain samples digested by RNase R. ( d ) The assembly complex for the hybrid BR contains tensegrity triangles of both handedness to generate three positive nodes plus three negative nodes. ( e ) Topological analyses of the hybrid BR. Lane 1, gel-purified BR; lanes 2–6, BR treated by RNase H, Nt.AlwI (for cleaving the red ring), Nt.BspQI (for cleaving the green ring), DNase I, and E. coli DNA Topo I; lanes 7 and 8, DNA and RNA references of the three individual components. During the purification of BR, the breaking down of the 95-nt circular RNA component is unavoidable, and a portion of BR falls apart as a result. The treatment of BR by RNase H, Nt.AlwI and Nt.BspQI is conducted in the presence of an assisting DNA strand complementary to the corresponding ssRNA or ssDNA ring. LX and CX represent X-nt linear and circular species, respectively. In all the gels, lane M contains the DNA size markers.

    Article Snippet: Digestion with various nucleases Various nucleases were used in this work, including Nt.AlwI (NEB), Nt.BspQI (NEB), RNase H (NEB), DNase I (NEB) and RNase R (Epicentre).

    Techniques: Ligation, Sequencing, Construct, Purification