alwi  (New England Biolabs)


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    Name:
    AlwI
    Description:
    AlwI 2 500 units
    Catalog Number:
    R0513L
    Price:
    282
    Category:
    Restriction Enzymes
    Size:
    2 500 units
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    New England Biolabs alwi
    AlwI
    AlwI 2 500 units
    https://www.bioz.com/result/alwi/product/New England Biolabs
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    alwi - by Bioz Stars, 2021-07
    94/100 stars

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    other:

    Article Title: Visualizing Sequence-Governed Nucleotide Selectivities and Mutagenic Consequences through a Replicative Cycle: Processing of a Bulky Carcinogen N2-dG Lesion in a Y-family DNA olymerase †
    Article Snippet: The incubations of the duplexes with the restriction enzymes TspI and AlwI (4 units each) were carried out at 37 and 65°C, respectively, as described by the supplier (New England BioLabs Inc.).

    Article Title: Addressing the link between paraoxonase-1 gene variants and the incidence of early onset myocardial infarction
    Article Snippet: The nucleotide substitution corresponding to position 192 (Q/R) creates an AlwI (New England Biolabs) restriction site.

    Polymerase Chain Reaction:

    Article Title: Paraoxonase 1 R/Q alleles are associated with differential accumulation of saturated versus 20:5n3 fatty acid in human adipose tissue
    Article Snippet: The reaction mix consisted of PCR buffer, 1.5 mM MgCl2 , 0.2 mM of each dNTP, 0.5 mM of each primer, and 1.2 units/reaction Taq DNA polymerase (Invitrogen). .. Approximately 2 μg of PCR product was digested with the appropriate restriction endonucleases at 37°C for 4 h. CYP1A1 was detected with MspI, PON1 L/M with NlaIII, and PON1 Q/R with AlwI (New England Biolabs). .. All PCR samples with an undigested or partial-digested result were submitted to redigestion with 20 units/reaction of enzyme and overnight incubation.

    Article Title: Cell type-specific profiling of protein-DNA interactions without cell isolation using Targeted DamID with next-generation sequencing
    Article Snippet: DpnII and DpnII buffer (NEB, cat. no. R0543S) Advantage 2 cDNA polymerase (Clontech, cat. no. 639201) (An alternative polymerase is MyTaq HS DNA Polymerase (Bioline, cat. no. BIO-21112); S. S. de Vries and B. van Steensel, personal communication.) .. ▲ CRITICAL STEP A polymerase with hotstart is required to prevent primer dimer formation during PCR AlwI (NEB, cat. no. R0513S) RNase A (DNase-free) (Roche, cat. no. 11119915001) diluted to 12.5μg/ml Qubit assay tubes (Invitrogen, cat. no. ) Qubit dsDNA HS assay kit, (Invitrogen, cat. no. ) Agilent reagents for TapeStation: Genomic DNA ScreenTape(5067-5365) and reagents (5067-5366) Agilent reagents for Bioanalyzer:Agilent DNA 1000 Kit (5067-1504) Agencourt AMPure XP Beads (Beckman Coulter, cat. no. A63880) (Seramag SpeedBeads, 3 EDAC/PA5 (Fisher Scientific, cat. no. 12326433) prepared using the method of Rohland and Reich, 2012 with 20%(w/v) PEG-8000 are a cost-effective alternative to AMPure XP beads) Quick ligase (NEB, cat. no. M2200S) T4 DNA ligase (400,000U/ml) and 10x buffer (NEB, cat. no. M0202S) T4 DNA polymerase (NEB, cat. no. M0203S) Klenow Fragment (NEB, cat. no. M0210S) Klenow 3' to 5' exo- (NEB, cat. no. M0541S) T4 polynucleotide kinase (NEB, cat. no. M0201S) NEBNext High-Fidelity 2X PCR Master Mix (NEB, cat. no. M0541S) dNTPs (NEB, cat. no. N0446S) .. Temperature controlled heat block capable of heating to 95°C.

    Sonication:

    Article Title: Novel CHD8 genomic targets identified in fetal mouse brain by in vivo Targeted DamID
    Article Snippet: PCR amplification of DpnII-digested fragments using MyTaq (Bioline, BIO-21112) enriched for methylated fragments before samples were sonicated and prepped for sequencing. .. Sonicated samples were subjected to AlwI digestion (NEB, R0513S) to remove previously ligated adaptors and initial GATC sequences from fragments. .. A modified TruSeq protocol was used to generate sequencing libraries involving end repair, 3’ end adenylation, sequencing adaptor ligation, and DNA fragment enrichment using a reduced number of PCR cycles.

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  • 93
    New England Biolabs nt alwi
    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, <t>Nt.AlwI</t> (for cleaving the red ring), <t>Nt.BspQI</t> (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.
    Nt Alwi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nt alwi/product/New England Biolabs
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nt alwi - by Bioz Stars, 2021-07
    93/100 stars
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    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

    Confirmation of RPA, GQ-catalysed TMB oxidation and LSDA reactions. a) RPA with SC1 forward and reverse primers containing Nt.AlwI or Nt.BstNBI recognition site . Each reaction was performed using genomic S. cerevisiae BY4741 DNA as a target sequence. The target sequence is absent in the negative control. The positive control was performed with the primers and target templates provided by the TwistAmp Basic kit (TwistDx). b) Average TMB oxidation rate of different GQ DNAzyme sequences. Here, the catalytic activities of EAD2+3’A, BBa_K1614007, and BBa_K1614007+3’A GQ DNAzymes (Table S2) in pH 6.0 phosphate buffer were compared. The concentration of DNAzyme was kept at 1 μM in all measurements. EAD2+3’A was identified as the most potent DNAzyme in catalysing TMB oxidation. The error bars represented the standard deviation of three replicates. c) TMB oxidation by EAD2+3’A DNAzyme. Kinetic parameters of the DNAzyme were measured based on its ability to catalyse TMB oxidation reaction at different TMB concentrations. In the figure, data points represent initial oxidation rate measured from each experimental replicate while the curve represents model-predicted kinetics at each given TMB concentration. Rate kinetics of EAD2+3’A were assumed to follow Michaelis-Menten kinetics. The initial rate of each individual replicates was calculated based on differences in oxidized TMB absorbance value at 650 nm for the first minute of the observation. The resulting model could sufficiently describe each individual replicate measurement (Fig. S1). d) GQ DNAzyme production using LSDA reaction. LSDA was performed using different nickases. Here we identified Nt.BstNBI as the most potent GQ-producer. Synthetic (pure) oligonucleotides (Table S3) containing the targeted S. cerevisiae genome, nickase site and EAD2+3’A DNAzyme sequences were used as template for the LSDA reaction. The figure shows the average of two replicates.

    Journal: bioRxiv

    Article Title: Rapidemic, a versatile and label-free DNAzyme-based platform for visual nucleic acid detection

    doi: 10.1101/2020.10.14.337808

    Figure Lengend Snippet: Confirmation of RPA, GQ-catalysed TMB oxidation and LSDA reactions. a) RPA with SC1 forward and reverse primers containing Nt.AlwI or Nt.BstNBI recognition site . Each reaction was performed using genomic S. cerevisiae BY4741 DNA as a target sequence. The target sequence is absent in the negative control. The positive control was performed with the primers and target templates provided by the TwistAmp Basic kit (TwistDx). b) Average TMB oxidation rate of different GQ DNAzyme sequences. Here, the catalytic activities of EAD2+3’A, BBa_K1614007, and BBa_K1614007+3’A GQ DNAzymes (Table S2) in pH 6.0 phosphate buffer were compared. The concentration of DNAzyme was kept at 1 μM in all measurements. EAD2+3’A was identified as the most potent DNAzyme in catalysing TMB oxidation. The error bars represented the standard deviation of three replicates. c) TMB oxidation by EAD2+3’A DNAzyme. Kinetic parameters of the DNAzyme were measured based on its ability to catalyse TMB oxidation reaction at different TMB concentrations. In the figure, data points represent initial oxidation rate measured from each experimental replicate while the curve represents model-predicted kinetics at each given TMB concentration. Rate kinetics of EAD2+3’A were assumed to follow Michaelis-Menten kinetics. The initial rate of each individual replicates was calculated based on differences in oxidized TMB absorbance value at 650 nm for the first minute of the observation. The resulting model could sufficiently describe each individual replicate measurement (Fig. S1). d) GQ DNAzyme production using LSDA reaction. LSDA was performed using different nickases. Here we identified Nt.BstNBI as the most potent GQ-producer. Synthetic (pure) oligonucleotides (Table S3) containing the targeted S. cerevisiae genome, nickase site and EAD2+3’A DNAzyme sequences were used as template for the LSDA reaction. The figure shows the average of two replicates.

    Article Snippet: Nicking endonucleases, including Nt.BstNBI, Nt.AlwI and Nt.BsmAI, and Bst 2.0 DNA Polymerase were acquired from New England Biolabs (NEB).

    Techniques: Recombinase Polymerase Amplification, Sequencing, Negative Control, Positive Control, Concentration Assay, Standard Deviation

    RecN binding to nicked DNA. Nt.AlwI-treated EcoRV-linear DNA (150 nM in nt) and RecN (10 nM) were incubated for 10 min at 37°C. Reaction was fixed with 0.1 glutaraldehyde and deposited on freshly cut mica. ( A ) AFM images of Nt.AlwI-treated DNA–RecN complexes analysed. ( B ) Geometrical analyses of Nt.AlwI-treated DNA–RecN complexes. The length from the end of the substrate to DNA-bound RecN was measured and shown as a histogram in 250 bp bin. A schematic map of plasmid DNA with the target localization for Nt.AlwI endonuclease and relevant high dA + dT regions ( P lac , pUC ori and f1 ori ) are shown at the same scale of the histogram.

    Journal: Nucleic Acids Research

    Article Title: Dynamic structures of Bacillus subtilis RecN-DNA complexes

    doi: 10.1093/nar/gkm759

    Figure Lengend Snippet: RecN binding to nicked DNA. Nt.AlwI-treated EcoRV-linear DNA (150 nM in nt) and RecN (10 nM) were incubated for 10 min at 37°C. Reaction was fixed with 0.1 glutaraldehyde and deposited on freshly cut mica. ( A ) AFM images of Nt.AlwI-treated DNA–RecN complexes analysed. ( B ) Geometrical analyses of Nt.AlwI-treated DNA–RecN complexes. The length from the end of the substrate to DNA-bound RecN was measured and shown as a histogram in 250 bp bin. A schematic map of plasmid DNA with the target localization for Nt.AlwI endonuclease and relevant high dA + dT regions ( P lac , pUC ori and f1 ori ) are shown at the same scale of the histogram.

    Article Snippet: EcoRV-cleaved pBluescript was exposed to Nt.AlwI endonuclease (NEB) to obtain blunt-ended DNA molecules with internal single-strand nicks.

    Techniques: Binding Assay, Incubation, Plasmid Preparation

    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