nlaiii  (New England Biolabs)


Bioz Verified Symbol New England Biolabs is a verified supplier
Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Name:
    NlaIII
    Description:
    NlaIII 2 500 units
    Catalog Number:
    R0125L
    Price:
    282
    Category:
    Restriction Enzymes
    Size:
    2 500 units
    Buy from Supplier


    Structured Review

    New England Biolabs nlaiii
    NlaIII
    NlaIII 2 500 units
    https://www.bioz.com/result/nlaiii/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nlaiii - by Bioz Stars, 2021-05
    99/100 stars

    Images

    1) Product Images from "Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)"

    Article Title: Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

    Journal: Animals : an Open Access Journal from MDPI

    doi: 10.3390/ani11030899

    Density plots of genomic relatedness (GR) among full siblings and non-siblings for: ( A ) SbfI-SphI and ( B ) PstI-NlaIII.
    Figure Legend Snippet: Density plots of genomic relatedness (GR) among full siblings and non-siblings for: ( A ) SbfI-SphI and ( B ) PstI-NlaIII.

    Techniques Used:

    Manhattan and quantile–quantile plots of the association tests for length and log 2 K in the PstI-NlaIII scenario ( n = 179). The red horizontal line indicates the Bonferroni error rate-adjusted significance level. The blue line indicates the threshold of the significant markers after BH adjustment of p -values.
    Figure Legend Snippet: Manhattan and quantile–quantile plots of the association tests for length and log 2 K in the PstI-NlaIII scenario ( n = 179). The red horizontal line indicates the Bonferroni error rate-adjusted significance level. The blue line indicates the threshold of the significant markers after BH adjustment of p -values.

    Techniques Used:

    Distributions of post-filtering minor allele frequency (MAF) and single nucleotide polymorphism (SNP) call rate for SbfI-SphI ( n = 253) and the intersecting ( n = 175) animals that were also genotyped with PstI-NlaIII.
    Figure Legend Snippet: Distributions of post-filtering minor allele frequency (MAF) and single nucleotide polymorphism (SNP) call rate for SbfI-SphI ( n = 253) and the intersecting ( n = 175) animals that were also genotyped with PstI-NlaIII.

    Techniques Used:

    Heatmaps visualizing the relative frequencies (%) of family predictions according to the DAPC cross-validation scheme for ( A ) SbfI-SphI and ( B ) PstI-NlaIII.
    Figure Legend Snippet: Heatmaps visualizing the relative frequencies (%) of family predictions according to the DAPC cross-validation scheme for ( A ) SbfI-SphI and ( B ) PstI-NlaIII.

    Techniques Used:

    Discriminant analysis of principal components (DAPC) for ( A ) SbfI-SphI and ( B ) PstI-NlaIII genotyping scenarios. The represented population is the intersection ( n = 175) of the individuals that were genotyped in both scenarios.
    Figure Legend Snippet: Discriminant analysis of principal components (DAPC) for ( A ) SbfI-SphI and ( B ) PstI-NlaIII genotyping scenarios. The represented population is the intersection ( n = 175) of the individuals that were genotyped in both scenarios.

    Techniques Used:

    Principal component analysis for ( A ) SbfI-SphI and ( B ) PstI-NlaIII genotyping scenarios. The represented population is the intersection ( n = 175) of the individuals that were genotyped in both scenarios.
    Figure Legend Snippet: Principal component analysis for ( A ) SbfI-SphI and ( B ) PstI-NlaIII genotyping scenarios. The represented population is the intersection ( n = 175) of the individuals that were genotyped in both scenarios.

    Techniques Used:

    2) Product Images from "The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination"

    Article Title: The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination

    Journal: Nature

    doi: 10.1038/s41586-019-1547-y

    Working model for loop extrusion-mediated RAG downstream scanning. a-i, Model for cohesin-mediated loop extrusion of chromatin past nascent Igh RC in J H Δ v-Abl lines based on RAG2-deficient background analyses. For all examples, increased interactions of impediment sites with RC targets scanning activity in RAG-sufficient cells. a . Cohesin (red rings) are loaded at multiple sites in the RC-3'CBEs Igh sub-domain. Illustrations show cohesin loading at RC-downstream region. b. Cohesin-mediated extrusion promotes linear interaction of the nascent RC with downstream regions. c. Robust transcription (green arrow) across the Iγ2b/Sγ2b impedes loop extrusion. d. In a subset of cells, loop extrusion proceeds past Iγ2b/Sγ2b impediment to 3'CBEs loop anchor. e-i, Loop extrusion in J H Δ-dCas9-Sγ1-sgRNA lines is impeded, directly or indirectly, by the dCas9-bound Sγ1. As dCas9 impediment is not a complete block, loop extrusion in a subset of cells proceeds downstream, allowing dynamic sub-loop formation of RC with Iγ2b/Sγ2b or 3’CBEs. j-l, In RAG-sufficient cells, RC-bound RAG might enhance the dCas9-bound Sγ1 extrusion impediment. m-p, Elimination of Iγ2b-promoter-driven transcription permits unimpeded RAG-bound RC extrusion to 3’CBEs anchor, increasing RAG scanning activity there. q-r, 3C-HTGTS analysis of RC interactions with D H and flanking regions in J H Δ-dCas9 line ( q ) and D H -J H +/− line ( r ). DpnII ( n = 4, biological replicates) and NlaIII ( n = 3, biological replicates) digestions are shown for the J H Δ-dCas9 line. NlaIII digestion more clearly reveals interaction peak near D H 3-2 due to paucity of DpnII sites in that region. NlaIII digestion of D H -J H +/− line shows a similar RC interaction pattern to that of J H Δ-dCas9 line ( r, n = 2, technical repeats). Bar graphs show relative RC interaction of the 25kb intervening D H region (from D H 2-3 to D H 2-8) versus that of the same-size neighboring regions ( n as indicated above). Data represents mean ± s.d ( q ) or mean ( r ). P values calculated via two-tailed paired t -test.
    Figure Legend Snippet: Working model for loop extrusion-mediated RAG downstream scanning. a-i, Model for cohesin-mediated loop extrusion of chromatin past nascent Igh RC in J H Δ v-Abl lines based on RAG2-deficient background analyses. For all examples, increased interactions of impediment sites with RC targets scanning activity in RAG-sufficient cells. a . Cohesin (red rings) are loaded at multiple sites in the RC-3'CBEs Igh sub-domain. Illustrations show cohesin loading at RC-downstream region. b. Cohesin-mediated extrusion promotes linear interaction of the nascent RC with downstream regions. c. Robust transcription (green arrow) across the Iγ2b/Sγ2b impedes loop extrusion. d. In a subset of cells, loop extrusion proceeds past Iγ2b/Sγ2b impediment to 3'CBEs loop anchor. e-i, Loop extrusion in J H Δ-dCas9-Sγ1-sgRNA lines is impeded, directly or indirectly, by the dCas9-bound Sγ1. As dCas9 impediment is not a complete block, loop extrusion in a subset of cells proceeds downstream, allowing dynamic sub-loop formation of RC with Iγ2b/Sγ2b or 3’CBEs. j-l, In RAG-sufficient cells, RC-bound RAG might enhance the dCas9-bound Sγ1 extrusion impediment. m-p, Elimination of Iγ2b-promoter-driven transcription permits unimpeded RAG-bound RC extrusion to 3’CBEs anchor, increasing RAG scanning activity there. q-r, 3C-HTGTS analysis of RC interactions with D H and flanking regions in J H Δ-dCas9 line ( q ) and D H -J H +/− line ( r ). DpnII ( n = 4, biological replicates) and NlaIII ( n = 3, biological replicates) digestions are shown for the J H Δ-dCas9 line. NlaIII digestion more clearly reveals interaction peak near D H 3-2 due to paucity of DpnII sites in that region. NlaIII digestion of D H -J H +/− line shows a similar RC interaction pattern to that of J H Δ-dCas9 line ( r, n = 2, technical repeats). Bar graphs show relative RC interaction of the 25kb intervening D H region (from D H 2-3 to D H 2-8) versus that of the same-size neighboring regions ( n as indicated above). Data represents mean ± s.d ( q ) or mean ( r ). P values calculated via two-tailed paired t -test.

    Techniques Used: Activity Assay, Blocking Assay, Two Tailed Test

    3) Product Images from "The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination"

    Article Title: The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination

    Journal: Nature

    doi: 10.1038/s41586-019-1547-y

    Working model for loop extrusion-mediated RAG downstream scanning. a-i, Model for cohesin-mediated loop extrusion of chromatin past nascent Igh RC in J H Δ v-Abl lines based on RAG2-deficient background analyses. For all examples, increased interactions of impediment sites with RC targets scanning activity in RAG-sufficient cells. a . Cohesin (red rings) are loaded at multiple sites in the RC-3'CBEs Igh sub-domain. Illustrations show cohesin loading at RC-downstream region. b. Cohesin-mediated extrusion promotes linear interaction of the nascent RC with downstream regions. c. Robust transcription (green arrow) across the Iγ2b/Sγ2b impedes loop extrusion. d. In a subset of cells, loop extrusion proceeds past Iγ2b/Sγ2b impediment to 3'CBEs loop anchor. e-i, Loop extrusion in J H Δ-dCas9-Sγ1-sgRNA lines is impeded, directly or indirectly, by the dCas9-bound Sγ1. As dCas9 impediment is not a complete block, loop extrusion in a subset of cells proceeds downstream, allowing dynamic sub-loop formation of RC with Iγ2b/Sγ2b or 3’CBEs. j-l, In RAG-sufficient cells, RC-bound RAG might enhance the dCas9-bound Sγ1 extrusion impediment. m-p, Elimination of Iγ2b-promoter-driven transcription permits unimpeded RAG-bound RC extrusion to 3’CBEs anchor, increasing RAG scanning activity there. q-r, 3C-HTGTS analysis of RC interactions with D H and flanking regions in J H Δ-dCas9 line ( q ) and D H -J H +/− line ( r ). DpnII ( n = 4, biological replicates) and NlaIII ( n = 3, biological replicates) digestions are shown for the J H Δ-dCas9 line. NlaIII digestion more clearly reveals interaction peak near D H 3-2 due to paucity of DpnII sites in that region. NlaIII digestion of D H -J H +/− line shows a similar RC interaction pattern to that of J H Δ-dCas9 line ( r, n = 2, technical repeats). Bar graphs show relative RC interaction of the 25kb intervening D H region (from D H 2-3 to D H 2-8) versus that of the same-size neighboring regions ( n as indicated above). Data represents mean ± s.d ( q ) or mean ( r ). P values calculated via two-tailed paired t -test.
    Figure Legend Snippet: Working model for loop extrusion-mediated RAG downstream scanning. a-i, Model for cohesin-mediated loop extrusion of chromatin past nascent Igh RC in J H Δ v-Abl lines based on RAG2-deficient background analyses. For all examples, increased interactions of impediment sites with RC targets scanning activity in RAG-sufficient cells. a . Cohesin (red rings) are loaded at multiple sites in the RC-3'CBEs Igh sub-domain. Illustrations show cohesin loading at RC-downstream region. b. Cohesin-mediated extrusion promotes linear interaction of the nascent RC with downstream regions. c. Robust transcription (green arrow) across the Iγ2b/Sγ2b impedes loop extrusion. d. In a subset of cells, loop extrusion proceeds past Iγ2b/Sγ2b impediment to 3'CBEs loop anchor. e-i, Loop extrusion in J H Δ-dCas9-Sγ1-sgRNA lines is impeded, directly or indirectly, by the dCas9-bound Sγ1. As dCas9 impediment is not a complete block, loop extrusion in a subset of cells proceeds downstream, allowing dynamic sub-loop formation of RC with Iγ2b/Sγ2b or 3’CBEs. j-l, In RAG-sufficient cells, RC-bound RAG might enhance the dCas9-bound Sγ1 extrusion impediment. m-p, Elimination of Iγ2b-promoter-driven transcription permits unimpeded RAG-bound RC extrusion to 3’CBEs anchor, increasing RAG scanning activity there. q-r, 3C-HTGTS analysis of RC interactions with D H and flanking regions in J H Δ-dCas9 line ( q ) and D H -J H +/− line ( r ). DpnII ( n = 4, biological replicates) and NlaIII ( n = 3, biological replicates) digestions are shown for the J H Δ-dCas9 line. NlaIII digestion more clearly reveals interaction peak near D H 3-2 due to paucity of DpnII sites in that region. NlaIII digestion of D H -J H +/− line shows a similar RC interaction pattern to that of J H Δ-dCas9 line ( r, n = 2, technical repeats). Bar graphs show relative RC interaction of the 25kb intervening D H region (from D H 2-3 to D H 2-8) versus that of the same-size neighboring regions ( n as indicated above). Data represents mean ± s.d ( q ) or mean ( r ). P values calculated via two-tailed paired t -test.

    Techniques Used: Activity Assay, Blocking Assay, Two Tailed Test

    4) Product Images from "Short interspersed elements (SINEs) are a major source of canine genomic diversity"

    Article Title: Short interspersed elements (SINEs) are a major source of canine genomic diversity

    Journal: Genome Research

    doi: 10.1101/gr.3765505

    Construction of libraries that are enriched for SINEC_Cf elements and flanking sequence. ( A ) Genomic DNA is cleaved with the frequently cutting restriction enzyme, NlaIII. ( B ) The cleaved fragments are self-ligated. ( C ) The circularized products are subjected to PCR using SINEC_Cf-specific primers. ( D ) The linear products are size-selected and cloned in a plasmid vector. ( E ) Inserts are sequenced with a vector-specific primer.
    Figure Legend Snippet: Construction of libraries that are enriched for SINEC_Cf elements and flanking sequence. ( A ) Genomic DNA is cleaved with the frequently cutting restriction enzyme, NlaIII. ( B ) The cleaved fragments are self-ligated. ( C ) The circularized products are subjected to PCR using SINEC_Cf-specific primers. ( D ) The linear products are size-selected and cloned in a plasmid vector. ( E ) Inserts are sequenced with a vector-specific primer.

    Techniques Used: Sequencing, Polymerase Chain Reaction, Clone Assay, Plasmid Preparation

    5) Product Images from "CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples"

    Article Title: CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples

    Journal: Nature Communications

    doi: 10.1038/s41467-019-12570-2

    CUTseq implementation and reproducibility. a CUTseq workflow. (1) RE, restriction enzyme. T7, T7 phage promoter. IVT, in vitro transcription. RA5, RA3, SP7, and SP9: Illumina’s sequencing adapters. b BT474 cells copy number profiles (100 kb resolution). ρ , Pearson’s correlation. c Pearson’s correlation ( ρ ) between the copy number profiles (100 kb resolution) of five cancer cell lines digested with HindIII (rows) or NlaIII (columns). d Chr17 copy number profiles (NlaIII, 100 kb resolution) in two HER2-positive (SKBR3 and BT474) and one HER2-negative cell line (MCF7). ERBB2/HER2 is highlighted in red. e Copy number profiles (NlaIII, 100 kb resolution) in five replicates (Rep) from FFPE tumor samples. COAD, colon adenocarcinoma. MELA, melanoma. ρ , Pearson’s correlation. f Pearson’s correlation ( ρ ) between the replicates shown in e at different resolutions. Each dot represents one pair of replicates. Error bars indicate the median and interquartile range. g Pearson’s correlation ( ρ ) between the fraction of the genome (100 kb resolution) either amplified or deleted in the replicates (Rep) shown in e . Each dot represents one pair of replicates. Dashed line: linear regression. h , i Length of amplified (AMP) or deleted (DEL) genomic segments in Rep1 ( h ) and Rep2 ( i ) samples shown in e , at various resolutions. j Zoom-in view on chr9 q-arm in sample TRN4 shown in e . Arrows indicate focal amplifications detected only at 10 kb resolution in both replicates. Red: centromeric region. The p-arm is not shown. k Copy number profiles (NlaIII, 100 kb resolution) determined using 120 pg of gDNA extracted from one FFPE breast cancer (BRCA) sample and three different numbers of PCR cycles. l Pearson’s correlation ( ρ ) between copy number profiles (100 kb resolution) determined using different amounts of gDNA extracted from the sample shown in k . In all the profiles, gray dots represent individual genomic windows, whereas black lines indicate segmented genomic intervals after circular binary segmentation 37 . The numbers below each box indicate chromosomes from chr1 (leftmost) to chr22 (rightmost). In all the cases, TRN refers to the ID of Turin samples, as shown in Supplementary Table 2 . All the source data for this figure are provided as a Source Data file
    Figure Legend Snippet: CUTseq implementation and reproducibility. a CUTseq workflow. (1) RE, restriction enzyme. T7, T7 phage promoter. IVT, in vitro transcription. RA5, RA3, SP7, and SP9: Illumina’s sequencing adapters. b BT474 cells copy number profiles (100 kb resolution). ρ , Pearson’s correlation. c Pearson’s correlation ( ρ ) between the copy number profiles (100 kb resolution) of five cancer cell lines digested with HindIII (rows) or NlaIII (columns). d Chr17 copy number profiles (NlaIII, 100 kb resolution) in two HER2-positive (SKBR3 and BT474) and one HER2-negative cell line (MCF7). ERBB2/HER2 is highlighted in red. e Copy number profiles (NlaIII, 100 kb resolution) in five replicates (Rep) from FFPE tumor samples. COAD, colon adenocarcinoma. MELA, melanoma. ρ , Pearson’s correlation. f Pearson’s correlation ( ρ ) between the replicates shown in e at different resolutions. Each dot represents one pair of replicates. Error bars indicate the median and interquartile range. g Pearson’s correlation ( ρ ) between the fraction of the genome (100 kb resolution) either amplified or deleted in the replicates (Rep) shown in e . Each dot represents one pair of replicates. Dashed line: linear regression. h , i Length of amplified (AMP) or deleted (DEL) genomic segments in Rep1 ( h ) and Rep2 ( i ) samples shown in e , at various resolutions. j Zoom-in view on chr9 q-arm in sample TRN4 shown in e . Arrows indicate focal amplifications detected only at 10 kb resolution in both replicates. Red: centromeric region. The p-arm is not shown. k Copy number profiles (NlaIII, 100 kb resolution) determined using 120 pg of gDNA extracted from one FFPE breast cancer (BRCA) sample and three different numbers of PCR cycles. l Pearson’s correlation ( ρ ) between copy number profiles (100 kb resolution) determined using different amounts of gDNA extracted from the sample shown in k . In all the profiles, gray dots represent individual genomic windows, whereas black lines indicate segmented genomic intervals after circular binary segmentation 37 . The numbers below each box indicate chromosomes from chr1 (leftmost) to chr22 (rightmost). In all the cases, TRN refers to the ID of Turin samples, as shown in Supplementary Table 2 . All the source data for this figure are provided as a Source Data file

    Techniques Used: In Vitro, Sequencing, Formalin-fixed Paraffin-Embedded, Amplification, Polymerase Chain Reaction

    6) Product Images from "The Glu727 Allele of Thyroid Stimulating Hormone Receptor Gene is Associated with Osteoporosis"

    Article Title: The Glu727 Allele of Thyroid Stimulating Hormone Receptor Gene is Associated with Osteoporosis

    Journal: North American Journal of Medical Sciences

    doi: 10.4103/1947-2714.98588

    Polymerase chain reaction (PCR) products at D727E site. PCR products were cut by NlaIII endonuclease and separated by agarose gel electrophoresis
    Figure Legend Snippet: Polymerase chain reaction (PCR) products at D727E site. PCR products were cut by NlaIII endonuclease and separated by agarose gel electrophoresis

    Techniques Used: Polymerase Chain Reaction, Agarose Gel Electrophoresis

    7) Product Images from "DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells"

    Article Title: DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkz717

    Workflow of DNA Analysis by Restriction Enzyme (DARE) assay. ( A ) Workflow of DARE assay—cell lysis and protease treatment are followed by digestion of unmethylated CCGG sites with methylation sensitive HpaII enzyme. U-tag adapters are ligated and the remaining CCGG sites are digested by methylation insensitive MspI enzyme. NlaIII digestion is included to reduce the fragment length. This is followed by ligation with the respective adapters (M-tag and N-tag adapters). Thermolabile USER ® II enzyme is used to remove excess uracil-containing adapters after each ligation. ( B ) Adapter system: U-tag adapter consists of Read 1 primer sequence of Illumina adapter, unique molecular identifier (UMI), unmethylated site specific tag (U-tag), and CG overhang. M-tag adapter similarly consists of Read 1 primer sequence of Illumina adapter, UMI, methylated site specific tag (M-tag), and CG overhang. N-tag adapter consists of Read 2 primer sequence of Illumina adapter and CATG overhang.
    Figure Legend Snippet: Workflow of DNA Analysis by Restriction Enzyme (DARE) assay. ( A ) Workflow of DARE assay—cell lysis and protease treatment are followed by digestion of unmethylated CCGG sites with methylation sensitive HpaII enzyme. U-tag adapters are ligated and the remaining CCGG sites are digested by methylation insensitive MspI enzyme. NlaIII digestion is included to reduce the fragment length. This is followed by ligation with the respective adapters (M-tag and N-tag adapters). Thermolabile USER ® II enzyme is used to remove excess uracil-containing adapters after each ligation. ( B ) Adapter system: U-tag adapter consists of Read 1 primer sequence of Illumina adapter, unique molecular identifier (UMI), unmethylated site specific tag (U-tag), and CG overhang. M-tag adapter similarly consists of Read 1 primer sequence of Illumina adapter, UMI, methylated site specific tag (M-tag), and CG overhang. N-tag adapter consists of Read 2 primer sequence of Illumina adapter and CATG overhang.

    Techniques Used: Lysis, Methylation, Ligation, Sequencing

    Related Articles

    Ligation:

    Article Title: CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning
    Article Snippet: Cells were lysed in 50 mM Tris-HCl, pH 7.5, containing 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100 and protease inhibitors (Roche, #11836153001). .. Nuclei were digested with 700 units of Nla III (NEB, #R0125) or Mse I (NEB, #R0525) restriction enzyme at 37°C overnight, followed by ligation under dilute conditions at 16°C overnight. .. Crosslinks were reversed and samples were treated with Proteinase K (Roche, #03115852001) and RNase A (Invitrogen, #8003089) prior to DNA precipitation.

    Amplification:

    Article Title: Detection of Ethambutol-Resistant Mycobacterium tuberculosis Strains by Multiplex Allele-Specific PCR Assay Targeting embB306 Mutations
    Article Snippet: A primer pair EmbF (5′-ATTCGGCTTCCTGCTCTGG) and EmbR (5′-GAACCAGCGGAAATAGTTGG) was used to amplify a shorter embB fragment-spanning codon 306 ( embB positions 852 to 969 in strain H37Rv [accession number , positions 33387 to 33504 ]) under the following PCR conditions: initial denaturation at 95 °C for 4 min; followed by 30 cycles of 94 °C for 1 min, 60 °C for 40 s, and 72 °C for 20 s; with a final elongation step at 72 °C for 2 min. .. The amplified 118-bp fragment was subjected to cleavage by Nla III (New England Biolabs) and Hae III (Amersham Pharmacia Biotech) restriction endonucleases, and the digests obtained were separated in 3% MetaPhor agarose gels (FMC BioProducts). .. The 34 M. tuberculosis strains studied included 10 EMBs strains and all available EMBr strains (i.e., 24 strains) isolated in the St. Petersburg area of the Russian Federation from 1999 to 2001.

    Article Title: Genomic Signature Tags (GSTs): A System for Profiling Genomic DNA
    Article Snippet: Typically, 1 mL of sample is amplified, and any unincorporated primers are hydrolyzed by incubation with Exo I as above. .. After P/C extraction and ethanol precipitation, the amplified DNA is digested with 20 U of Nla III in 400 μL for 4 h at 37°C (after 2 h, the completion of digestion is checked by electrophoresis of a small aliquot on a 10% polyacrylamide gel). ..

    Molecular Weight:

    Article Title: Telomeric circles are abundant in the stn1-M1 mutant that maintains its telomeres through recombination
    Article Snippet: .. For examination of high molecular weight telomeric DNA, isolated genomic DNA was digested with Alu I, Hpa II and Nla III (NEB Beverly, MA), at enzyme concentration of 1 U/mg for 2 h, and then supplemented with an equal amount of each enzyme for an additional 2 h. The telomere restriction fragments were then separated by size exclusion chromatography and the eluted fractions monitored for DNA concentration and telomeric DNA abundance. ..

    Isolation:

    Article Title: Telomeric circles are abundant in the stn1-M1 mutant that maintains its telomeres through recombination
    Article Snippet: .. For examination of high molecular weight telomeric DNA, isolated genomic DNA was digested with Alu I, Hpa II and Nla III (NEB Beverly, MA), at enzyme concentration of 1 U/mg for 2 h, and then supplemented with an equal amount of each enzyme for an additional 2 h. The telomere restriction fragments were then separated by size exclusion chromatography and the eluted fractions monitored for DNA concentration and telomeric DNA abundance. ..

    Concentration Assay:

    Article Title: Telomeric circles are abundant in the stn1-M1 mutant that maintains its telomeres through recombination
    Article Snippet: .. For examination of high molecular weight telomeric DNA, isolated genomic DNA was digested with Alu I, Hpa II and Nla III (NEB Beverly, MA), at enzyme concentration of 1 U/mg for 2 h, and then supplemented with an equal amount of each enzyme for an additional 2 h. The telomere restriction fragments were then separated by size exclusion chromatography and the eluted fractions monitored for DNA concentration and telomeric DNA abundance. ..

    Size-exclusion Chromatography:

    Article Title: Telomeric circles are abundant in the stn1-M1 mutant that maintains its telomeres through recombination
    Article Snippet: .. For examination of high molecular weight telomeric DNA, isolated genomic DNA was digested with Alu I, Hpa II and Nla III (NEB Beverly, MA), at enzyme concentration of 1 U/mg for 2 h, and then supplemented with an equal amount of each enzyme for an additional 2 h. The telomere restriction fragments were then separated by size exclusion chromatography and the eluted fractions monitored for DNA concentration and telomeric DNA abundance. ..

    Ethanol Precipitation:

    Article Title: Genomic Signature Tags (GSTs): A System for Profiling Genomic DNA
    Article Snippet: Typically, 1 mL of sample is amplified, and any unincorporated primers are hydrolyzed by incubation with Exo I as above. .. After P/C extraction and ethanol precipitation, the amplified DNA is digested with 20 U of Nla III in 400 μL for 4 h at 37°C (after 2 h, the completion of digestion is checked by electrophoresis of a small aliquot on a 10% polyacrylamide gel). ..

    Electrophoresis:

    Article Title: Genomic Signature Tags (GSTs): A System for Profiling Genomic DNA
    Article Snippet: Typically, 1 mL of sample is amplified, and any unincorporated primers are hydrolyzed by incubation with Exo I as above. .. After P/C extraction and ethanol precipitation, the amplified DNA is digested with 20 U of Nla III in 400 μL for 4 h at 37°C (after 2 h, the completion of digestion is checked by electrophoresis of a small aliquot on a 10% polyacrylamide gel). ..

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    New England Biolabs nlaiii
    Density plots of genomic relatedness (GR) among full siblings and non-siblings for: ( A ) <t>SbfI-SphI</t> and ( B ) <t>PstI-NlaIII.</t>
    Nlaiii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nlaiii/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nlaiii - by Bioz Stars, 2021-05
    99/100 stars
      Buy from Supplier

    Image Search Results


    Density plots of genomic relatedness (GR) among full siblings and non-siblings for: ( A ) SbfI-SphI and ( B ) PstI-NlaIII.

    Journal: Animals : an Open Access Journal from MDPI

    Article Title: Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

    doi: 10.3390/ani11030899

    Figure Lengend Snippet: Density plots of genomic relatedness (GR) among full siblings and non-siblings for: ( A ) SbfI-SphI and ( B ) PstI-NlaIII.

    Article Snippet: Briefly, each sample (15 ng/μL DNA) was digested at 37 °C for 60 min in the same reaction with either SbfI (recognizing the CCTGCA|GG motif) and SphI (recognizing the GCATG|C motif) or PstI (recognizing the CTGCA|G motif) and NlaIII (recognizing the CATG|N motif) high fidelity restriction enzymes (New England Biolabs, UK; NEB), by using 6 U of each enzyme per microgram of genomic DNA in 1× Reaction Buffer 4 (NEB).

    Techniques:

    Manhattan and quantile–quantile plots of the association tests for length and log 2 K in the PstI-NlaIII scenario ( n = 179). The red horizontal line indicates the Bonferroni error rate-adjusted significance level. The blue line indicates the threshold of the significant markers after BH adjustment of p -values.

    Journal: Animals : an Open Access Journal from MDPI

    Article Title: Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

    doi: 10.3390/ani11030899

    Figure Lengend Snippet: Manhattan and quantile–quantile plots of the association tests for length and log 2 K in the PstI-NlaIII scenario ( n = 179). The red horizontal line indicates the Bonferroni error rate-adjusted significance level. The blue line indicates the threshold of the significant markers after BH adjustment of p -values.

    Article Snippet: Briefly, each sample (15 ng/μL DNA) was digested at 37 °C for 60 min in the same reaction with either SbfI (recognizing the CCTGCA|GG motif) and SphI (recognizing the GCATG|C motif) or PstI (recognizing the CTGCA|G motif) and NlaIII (recognizing the CATG|N motif) high fidelity restriction enzymes (New England Biolabs, UK; NEB), by using 6 U of each enzyme per microgram of genomic DNA in 1× Reaction Buffer 4 (NEB).

    Techniques:

    Distributions of post-filtering minor allele frequency (MAF) and single nucleotide polymorphism (SNP) call rate for SbfI-SphI ( n = 253) and the intersecting ( n = 175) animals that were also genotyped with PstI-NlaIII.

    Journal: Animals : an Open Access Journal from MDPI

    Article Title: Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

    doi: 10.3390/ani11030899

    Figure Lengend Snippet: Distributions of post-filtering minor allele frequency (MAF) and single nucleotide polymorphism (SNP) call rate for SbfI-SphI ( n = 253) and the intersecting ( n = 175) animals that were also genotyped with PstI-NlaIII.

    Article Snippet: Briefly, each sample (15 ng/μL DNA) was digested at 37 °C for 60 min in the same reaction with either SbfI (recognizing the CCTGCA|GG motif) and SphI (recognizing the GCATG|C motif) or PstI (recognizing the CTGCA|G motif) and NlaIII (recognizing the CATG|N motif) high fidelity restriction enzymes (New England Biolabs, UK; NEB), by using 6 U of each enzyme per microgram of genomic DNA in 1× Reaction Buffer 4 (NEB).

    Techniques:

    Heatmaps visualizing the relative frequencies (%) of family predictions according to the DAPC cross-validation scheme for ( A ) SbfI-SphI and ( B ) PstI-NlaIII.

    Journal: Animals : an Open Access Journal from MDPI

    Article Title: Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

    doi: 10.3390/ani11030899

    Figure Lengend Snippet: Heatmaps visualizing the relative frequencies (%) of family predictions according to the DAPC cross-validation scheme for ( A ) SbfI-SphI and ( B ) PstI-NlaIII.

    Article Snippet: Briefly, each sample (15 ng/μL DNA) was digested at 37 °C for 60 min in the same reaction with either SbfI (recognizing the CCTGCA|GG motif) and SphI (recognizing the GCATG|C motif) or PstI (recognizing the CTGCA|G motif) and NlaIII (recognizing the CATG|N motif) high fidelity restriction enzymes (New England Biolabs, UK; NEB), by using 6 U of each enzyme per microgram of genomic DNA in 1× Reaction Buffer 4 (NEB).

    Techniques:

    Discriminant analysis of principal components (DAPC) for ( A ) SbfI-SphI and ( B ) PstI-NlaIII genotyping scenarios. The represented population is the intersection ( n = 175) of the individuals that were genotyped in both scenarios.

    Journal: Animals : an Open Access Journal from MDPI

    Article Title: Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

    doi: 10.3390/ani11030899

    Figure Lengend Snippet: Discriminant analysis of principal components (DAPC) for ( A ) SbfI-SphI and ( B ) PstI-NlaIII genotyping scenarios. The represented population is the intersection ( n = 175) of the individuals that were genotyped in both scenarios.

    Article Snippet: Briefly, each sample (15 ng/μL DNA) was digested at 37 °C for 60 min in the same reaction with either SbfI (recognizing the CCTGCA|GG motif) and SphI (recognizing the GCATG|C motif) or PstI (recognizing the CTGCA|G motif) and NlaIII (recognizing the CATG|N motif) high fidelity restriction enzymes (New England Biolabs, UK; NEB), by using 6 U of each enzyme per microgram of genomic DNA in 1× Reaction Buffer 4 (NEB).

    Techniques:

    Principal component analysis for ( A ) SbfI-SphI and ( B ) PstI-NlaIII genotyping scenarios. The represented population is the intersection ( n = 175) of the individuals that were genotyped in both scenarios.

    Journal: Animals : an Open Access Journal from MDPI

    Article Title: Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

    doi: 10.3390/ani11030899

    Figure Lengend Snippet: Principal component analysis for ( A ) SbfI-SphI and ( B ) PstI-NlaIII genotyping scenarios. The represented population is the intersection ( n = 175) of the individuals that were genotyped in both scenarios.

    Article Snippet: Briefly, each sample (15 ng/μL DNA) was digested at 37 °C for 60 min in the same reaction with either SbfI (recognizing the CCTGCA|GG motif) and SphI (recognizing the GCATG|C motif) or PstI (recognizing the CTGCA|G motif) and NlaIII (recognizing the CATG|N motif) high fidelity restriction enzymes (New England Biolabs, UK; NEB), by using 6 U of each enzyme per microgram of genomic DNA in 1× Reaction Buffer 4 (NEB).

    Techniques:

    V H 81X-CBE Promotes Interactions of Its Flanking V H with the DJ H RC (A) Schematic representation of the 3C-HTGTS method for studying chromosomal looping interactions of a bait region of interest with the rest of Igh locus (see text and STAR Methods for details). (B) Schematic of the Nla III restriction fragment (indicated by a blue asterisk) and the relative positions of the biotinylated (cayenne arrow) and nested (blue arrow) PCR primers used for 3C-HTGTS from V H 81X bait in (C). (C) Top panel: schematic representation of chromosome interactions of V H 81X-CBE containing Nla III fragment with other Igh locales. Bottom two panels: 3C-HTGTS profiles of Rag2 −/− derivatives of control, V H 81X-CBE del , and V H 81X-CBE inv D H FL16.1J H 4 v-Abl lines using V H 81X-CBE locale as bait (blue asterisk). Owing to a D H FL16.1 to J H 4 rearrangement in the lines, the region spanning IGCR1, DJ H substrate and iEm appears as a broad interaction peak. As v-Abl lines lack locus contraction, we detected few substantial interactions with the upstream Igh locus beyond the most proximal V H ). Two independent datasets are shown from libraries normalized to 105,638 total junctions. .

    Journal: Cell

    Article Title: CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning

    doi: 10.1016/j.cell.2018.04.035

    Figure Lengend Snippet: V H 81X-CBE Promotes Interactions of Its Flanking V H with the DJ H RC (A) Schematic representation of the 3C-HTGTS method for studying chromosomal looping interactions of a bait region of interest with the rest of Igh locus (see text and STAR Methods for details). (B) Schematic of the Nla III restriction fragment (indicated by a blue asterisk) and the relative positions of the biotinylated (cayenne arrow) and nested (blue arrow) PCR primers used for 3C-HTGTS from V H 81X bait in (C). (C) Top panel: schematic representation of chromosome interactions of V H 81X-CBE containing Nla III fragment with other Igh locales. Bottom two panels: 3C-HTGTS profiles of Rag2 −/− derivatives of control, V H 81X-CBE del , and V H 81X-CBE inv D H FL16.1J H 4 v-Abl lines using V H 81X-CBE locale as bait (blue asterisk). Owing to a D H FL16.1 to J H 4 rearrangement in the lines, the region spanning IGCR1, DJ H substrate and iEm appears as a broad interaction peak. As v-Abl lines lack locus contraction, we detected few substantial interactions with the upstream Igh locus beyond the most proximal V H ). Two independent datasets are shown from libraries normalized to 105,638 total junctions. .

    Article Snippet: Nuclei were digested with 700 units of Nla III (NEB, #R0125) or Mse I (NEB, #R0525) restriction enzyme at 37°C overnight, followed by ligation under dilute conditions at 16°C overnight.

    Techniques: Polymerase Chain Reaction

    Visualization of DNA circles from high molecular weight telomere-enriched DNA from stn1-M1 . ( A–E ) Electron micrographs of DNA circles observed in the telomere-enriched fractions from stn1-M1 . Circle lengths for the molecules in A–E, respectively, are estimated at 15.7, 12.1, 3.1, 1.2 and 1.2, and 0.9 kb for fractions A–E, respectively. Note that there is also a ∼0.8 kb linear fragment in the lower right portion of panel A. Samples were prepared by coating the DNA in denatured cytochrome c and are shown in negative contrast. Bar is equivalent to 1.5 kb. ( F ) Relative DNA abundance and telomeric DNA content of eluted fractions from gel chromatography separation of Alu I, Hpa II and Nla III dirgest of stn1-M1 genomic DNA. Molecules shown in A–E are from fractions 26 to 28 (F). Size distribution of the measured circles from fractions 26 to 27 ( n = 29) and 28 ( n = 32).

    Journal: Nucleic Acids Research

    Article Title: Telomeric circles are abundant in the stn1-M1 mutant that maintains its telomeres through recombination

    doi: 10.1093/nar/gkp814

    Figure Lengend Snippet: Visualization of DNA circles from high molecular weight telomere-enriched DNA from stn1-M1 . ( A–E ) Electron micrographs of DNA circles observed in the telomere-enriched fractions from stn1-M1 . Circle lengths for the molecules in A–E, respectively, are estimated at 15.7, 12.1, 3.1, 1.2 and 1.2, and 0.9 kb for fractions A–E, respectively. Note that there is also a ∼0.8 kb linear fragment in the lower right portion of panel A. Samples were prepared by coating the DNA in denatured cytochrome c and are shown in negative contrast. Bar is equivalent to 1.5 kb. ( F ) Relative DNA abundance and telomeric DNA content of eluted fractions from gel chromatography separation of Alu I, Hpa II and Nla III dirgest of stn1-M1 genomic DNA. Molecules shown in A–E are from fractions 26 to 28 (F). Size distribution of the measured circles from fractions 26 to 27 ( n = 29) and 28 ( n = 32).

    Article Snippet: For examination of high molecular weight telomeric DNA, isolated genomic DNA was digested with Alu I, Hpa II and Nla III (NEB Beverly, MA), at enzyme concentration of 1 U/mg for 2 h, and then supplemented with an equal amount of each enzyme for an additional 2 h. The telomere restriction fragments were then separated by size exclusion chromatography and the eluted fractions monitored for DNA concentration and telomeric DNA abundance.

    Techniques: Molecular Weight, Chromatography

    Schematic view of the embB gene fragment targeted by the MAS-PCR assay. Short arrows indicate the primers, long double-sided arrows indicate the allele-specific PCR fragments amplified in the absence of respective mutation. An X represents any base (A, T, C, or G). The embB codon 306 ATG is in boldface and in a shaded box. Nla III and Hae III restriction enzymes' sites related to embB 306 ATG are shown in the enlarged image.

    Journal: Journal of Clinical Microbiology

    Article Title: Detection of Ethambutol-Resistant Mycobacterium tuberculosis Strains by Multiplex Allele-Specific PCR Assay Targeting embB306 Mutations

    doi: 10.1128/JCM.40.5.1617-1620.2002

    Figure Lengend Snippet: Schematic view of the embB gene fragment targeted by the MAS-PCR assay. Short arrows indicate the primers, long double-sided arrows indicate the allele-specific PCR fragments amplified in the absence of respective mutation. An X represents any base (A, T, C, or G). The embB codon 306 ATG is in boldface and in a shaded box. Nla III and Hae III restriction enzymes' sites related to embB 306 ATG are shown in the enlarged image.

    Article Snippet: The amplified 118-bp fragment was subjected to cleavage by Nla III (New England Biolabs) and Hae III (Amersham Pharmacia Biotech) restriction endonucleases, and the digests obtained were separated in 3% MetaPhor agarose gels (FMC BioProducts).

    Techniques: Polymerase Chain Reaction, Amplification, Mutagenesis

    PCR-RFLP analysis of the amplified 118-bp embB306 fragment of M. tuberculosis strains with Nla III and Hae III. Lanes: 2 to 4, Nla III-RFLP profiles; 5 to 7, Hae III-RFLP profiles; 1, undigested PCR product (118 bp), 2 and 5, strains with embB 306 wild-type allele (ATG); 3 and 6, strains with embB codon 306 mutated in the first base (ATG→BTG); 4 and 7, strains with embB codon 306 mutated in the third base (ATG→ATH). Lane M, 50-bp DNA ladder (Amersham Pharmacia Biotech). Short triangular arrows indicate specific digests produced by Nla III (21/23, 30, and 44 bp in lane 2; 21/23 and 74 bp in lanes 3 and 4) and Hae III (50 and 68 bp in lanes 5 and 6). The 21- and 23-bp fragments present one weak band.

    Journal: Journal of Clinical Microbiology

    Article Title: Detection of Ethambutol-Resistant Mycobacterium tuberculosis Strains by Multiplex Allele-Specific PCR Assay Targeting embB306 Mutations

    doi: 10.1128/JCM.40.5.1617-1620.2002

    Figure Lengend Snippet: PCR-RFLP analysis of the amplified 118-bp embB306 fragment of M. tuberculosis strains with Nla III and Hae III. Lanes: 2 to 4, Nla III-RFLP profiles; 5 to 7, Hae III-RFLP profiles; 1, undigested PCR product (118 bp), 2 and 5, strains with embB 306 wild-type allele (ATG); 3 and 6, strains with embB codon 306 mutated in the first base (ATG→BTG); 4 and 7, strains with embB codon 306 mutated in the third base (ATG→ATH). Lane M, 50-bp DNA ladder (Amersham Pharmacia Biotech). Short triangular arrows indicate specific digests produced by Nla III (21/23, 30, and 44 bp in lane 2; 21/23 and 74 bp in lanes 3 and 4) and Hae III (50 and 68 bp in lanes 5 and 6). The 21- and 23-bp fragments present one weak band.

    Article Snippet: The amplified 118-bp fragment was subjected to cleavage by Nla III (New England Biolabs) and Hae III (Amersham Pharmacia Biotech) restriction endonucleases, and the digests obtained were separated in 3% MetaPhor agarose gels (FMC BioProducts).

    Techniques: Polymerase Chain Reaction, Amplification, Produced