dra i  (New England Biolabs)


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    Name:
    DraI
    Description:
    DraI 10 000 units
    Catalog Number:
    r0129l
    Price:
    269
    Size:
    10 000 units
    Category:
    Restriction Enzymes
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    Structured Review

    New England Biolabs dra i
    DraI
    DraI 10 000 units
    https://www.bioz.com/result/dra i/product/New England Biolabs
    Average 95 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    dra i - by Bioz Stars, 2020-02
    95/100 stars

    Images

    1) Product Images from "Atypical 16S rRNA Gene Copies in Ochrobactrum intermedium Strains Reveal a Large Genomic Rearrangement by Recombination between rrn Copies"

    Article Title: Atypical 16S rRNA Gene Copies in Ochrobactrum intermedium Strains Reveal a Large Genomic Rearrangement by Recombination between rrn Copies

    Journal: Journal of Bacteriology

    doi: 10.1128/JB.185.9.2901-2909.2003

    Expression of the 46-bp insertion and detection of the two types of 16S rRNA by RT-PCR. The strains analyzed are indicated at the top. (A) Lanes +, use of consensual primer pair 27f and 590r; lanes ins, use of an insertion-specific pair of primers, ins1 and 590r. (B) Lanes +, RT-PCR products obtained with the primers 27f and 590r; lanes Dra I, RT-PCR products obtained in + lanes digested by Dra I. Lanes − (A and B), negative controls performed on the RNA of strain PR17/sat without reverse transcription and with the primers 27f and 590r (negative controls were also obtained for other strains and for the primers ins1 and 590r but are not shown); lane M, 100-bp DNA ladder (Promega) as a molecular weight marker.
    Figure Legend Snippet: Expression of the 46-bp insertion and detection of the two types of 16S rRNA by RT-PCR. The strains analyzed are indicated at the top. (A) Lanes +, use of consensual primer pair 27f and 590r; lanes ins, use of an insertion-specific pair of primers, ins1 and 590r. (B) Lanes +, RT-PCR products obtained with the primers 27f and 590r; lanes Dra I, RT-PCR products obtained in + lanes digested by Dra I. Lanes − (A and B), negative controls performed on the RNA of strain PR17/sat without reverse transcription and with the primers 27f and 590r (negative controls were also obtained for other strains and for the primers ins1 and 590r but are not shown); lane M, 100-bp DNA ladder (Promega) as a molecular weight marker.

    Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, Molecular Weight, Marker

    2) Product Images from "Characterization of DNA synthesis catalyzed by bacteriophage T4 replication complexes reconstituted on synthetic circular substrates"

    Article Title: Characterization of DNA synthesis catalyzed by bacteriophage T4 replication complexes reconstituted on synthetic circular substrates

    Journal: Nucleic Acids Research

    doi:

    Effect of an abasic site on DNA synthesis by reconstituted phage T4 replication complexes. ( A ) An abasic site blocks DNA synthesis by T4 DNA polymerase holoenzyme. 32 P-end-labeled 21mer #7 annealed with 120mer #3 (lanes 1, 3, 5, 7, 9, 11, 13 and 15) or with the same oligomer containing an abasic site at position 99 (120mer #4) (lanes 2, 4, 6, 8, 10, 12, 14 and 16) was incubated with either T4 gp43 (lanes 5, 6, 13 and 14) or the exonuclease-deficient gp43D219A (lanes 7, 8, 15 and 16) in the presence of gp44/62, gp45 and gp32 for the indicated times, and the products were separated in a 10% polyacrylamide gel + 6 M urea. Note that in the substrate with an abasic site, the first nucleotide to be incorporated into the 32 P-end-labeled 21mer is opposite the abasic site. ( B ) Block to lagging-strand synthesis imposed by the abasic site. Products of DNA synthesized by reconstituted T4 replication complexes in the presence of [α- 32 P]dCTP and 240mer circular ssDNA annealed with the 120mer ssDNA without (lanes 1 and 2) or with (lanes 3 and 4) abasic site were digested (lanes 2 and 4) or not (lanes 1 and 3) by Dra I and separated in a 6% polyacrylamide gel + 6 M urea along with marker DNA. Note that the 240mer circular ssDNA has a unique Dra I site. Upon Dra I cleavage of the replication products, the major 240mer fragment is formed along with other fragments that are located between the Dra I site and either the 3′ or 5′ ends of Okazaki fragments. Arrows show positions of the major 240-nt Dra I fragment and the 126-nt fragment located between the Dra I site and the 3′ end of the nascent fragment terminated by the abasic site. ( C ) DNA products were synthesized by reconstituted T4 replication complexes in the presence of [α- 32 P]dTTP and of 240mer circular ssDNA annealed with 120mer ssDNA without (lanes 1–3) or with (lanes 4–6) an abasic site, and separated in a 0.6% alkali gel.
    Figure Legend Snippet: Effect of an abasic site on DNA synthesis by reconstituted phage T4 replication complexes. ( A ) An abasic site blocks DNA synthesis by T4 DNA polymerase holoenzyme. 32 P-end-labeled 21mer #7 annealed with 120mer #3 (lanes 1, 3, 5, 7, 9, 11, 13 and 15) or with the same oligomer containing an abasic site at position 99 (120mer #4) (lanes 2, 4, 6, 8, 10, 12, 14 and 16) was incubated with either T4 gp43 (lanes 5, 6, 13 and 14) or the exonuclease-deficient gp43D219A (lanes 7, 8, 15 and 16) in the presence of gp44/62, gp45 and gp32 for the indicated times, and the products were separated in a 10% polyacrylamide gel + 6 M urea. Note that in the substrate with an abasic site, the first nucleotide to be incorporated into the 32 P-end-labeled 21mer is opposite the abasic site. ( B ) Block to lagging-strand synthesis imposed by the abasic site. Products of DNA synthesized by reconstituted T4 replication complexes in the presence of [α- 32 P]dCTP and 240mer circular ssDNA annealed with the 120mer ssDNA without (lanes 1 and 2) or with (lanes 3 and 4) abasic site were digested (lanes 2 and 4) or not (lanes 1 and 3) by Dra I and separated in a 6% polyacrylamide gel + 6 M urea along with marker DNA. Note that the 240mer circular ssDNA has a unique Dra I site. Upon Dra I cleavage of the replication products, the major 240mer fragment is formed along with other fragments that are located between the Dra I site and either the 3′ or 5′ ends of Okazaki fragments. Arrows show positions of the major 240-nt Dra I fragment and the 126-nt fragment located between the Dra I site and the 3′ end of the nascent fragment terminated by the abasic site. ( C ) DNA products were synthesized by reconstituted T4 replication complexes in the presence of [α- 32 P]dTTP and of 240mer circular ssDNA annealed with 120mer ssDNA without (lanes 1–3) or with (lanes 4–6) an abasic site, and separated in a 0.6% alkali gel.

    Techniques Used: DNA Synthesis, Labeling, Incubation, Blocking Assay, Synthesized, Marker

    3) Product Images from "Chromosomal Integration of a Cephalosporinase Gene from Acinetobacter baumannii into Oligella urethralis as a Source of Acquired Resistance to ?-Lactams"

    Article Title: Chromosomal Integration of a Cephalosporinase Gene from Acinetobacter baumannii into Oligella urethralis as a Source of Acquired Resistance to ?-Lactams

    Journal: Antimicrobial Agents and Chemotherapy

    doi: 10.1128/AAC.47.5.1536-1542.2003

    PFGE profiles of Sfi I-, Apa I-, Dra I-, Spe I-, and Xba I-digested whole-cell DNA of O. urethralis COH-1 (A; lanes 1 to 5) and their Southern transfer, followed by hybridization with internal probes specific for bla ABA-1 (B) and bla CARB-8 (C). Lanes M, molecular size markers
    Figure Legend Snippet: PFGE profiles of Sfi I-, Apa I-, Dra I-, Spe I-, and Xba I-digested whole-cell DNA of O. urethralis COH-1 (A; lanes 1 to 5) and their Southern transfer, followed by hybridization with internal probes specific for bla ABA-1 (B) and bla CARB-8 (C). Lanes M, molecular size markers

    Techniques Used: Hybridization

    4) Product Images from "Rapid single nucleotide polymorphism mapping in C. elegans"

    Article Title: Rapid single nucleotide polymorphism mapping in C. elegans

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-6-118

    Interval mapping . Individual recombinants are singled from heterozygotes and the animal, or a representative sample of their progeny, are placed in wells of a 96-well PCR plate and lysed. The plate may also contain three control wells, with Bristol, Hawaiian, and a 50-50 mix of animals. DNAs from the lysed animals are pin-replicated into a PCR master mix containing primers for the desired SNP. The plates are processed for PCR amplification, digested with Dra I and samples run on an agarose gel.
    Figure Legend Snippet: Interval mapping . Individual recombinants are singled from heterozygotes and the animal, or a representative sample of their progeny, are placed in wells of a 96-well PCR plate and lysed. The plate may also contain three control wells, with Bristol, Hawaiian, and a 50-50 mix of animals. DNAs from the lysed animals are pin-replicated into a PCR master mix containing primers for the desired SNP. The plates are processed for PCR amplification, digested with Dra I and samples run on an agarose gel.

    Techniques Used: Polymerase Chain Reaction, Amplification, Agarose Gel Electrophoresis

    5) Product Images from "Culture time of vitrified/warmed zygotes before microinjection affects the production efficiency of CRISPR-Cas9-mediated knock-in mice"

    Article Title: Culture time of vitrified/warmed zygotes before microinjection affects the production efficiency of CRISPR-Cas9-mediated knock-in mice

    Journal: Biology Open

    doi: 10.1242/bio.025122

    Generation of knock-in mice at the Spp1 locus. (A) Schematic illustration to generate a PITChed allele at the Spp1 locus, mediated by the CRIS-PITCh (v2) system. Four glutamine residues in exons 3 and 4 (three in exon 3 and one in exon 4) were replaced with alanine residues (red stars). Two gene-specific gRNAs were designed within exon 3 and downstream of exon 4. A PITCh donor plasmid was designed to carry the substituted sequences encoding four alanine residues, silent mutations for RFLP analysis (from T to G in exon 3 and from G to A in exon 4) and a point mutation (from T to C) in intron region. Bold black arrows indicate primers for PCR. Yellow and blue arrows indicate the recognition sites of restriction enzymes for the RFLP analyses. (B) Sequence analysis of subcloned PCR products from pups harboring the knock-in allele. The sequences around exon 3 and exon 4 are displayed in the upper and lower panels, respectively. The modified codons encoding four alanines are enclosed in red boxes. The silent mutations for RFLP analyses are enclosed in green boxes. The gRNA-blocking mutation is enclosed in a purple box. The wild-type allele is shown at the top ( Spp1 Wild) with the gRNA target sequences (underlined in yellow and blue). The PAM sequences are enclosed in yellow and blue boxes. Uppercase letters indicate exon sequences. Dots indicate the same bases as the wild-type sequence. Dashes indicate deletions. Unintended mutations are enclosed in black boxes. Black underlined sequences indicate Nar I and Dra I sites in exons 3 and exon 4, respectively.
    Figure Legend Snippet: Generation of knock-in mice at the Spp1 locus. (A) Schematic illustration to generate a PITChed allele at the Spp1 locus, mediated by the CRIS-PITCh (v2) system. Four glutamine residues in exons 3 and 4 (three in exon 3 and one in exon 4) were replaced with alanine residues (red stars). Two gene-specific gRNAs were designed within exon 3 and downstream of exon 4. A PITCh donor plasmid was designed to carry the substituted sequences encoding four alanine residues, silent mutations for RFLP analysis (from T to G in exon 3 and from G to A in exon 4) and a point mutation (from T to C) in intron region. Bold black arrows indicate primers for PCR. Yellow and blue arrows indicate the recognition sites of restriction enzymes for the RFLP analyses. (B) Sequence analysis of subcloned PCR products from pups harboring the knock-in allele. The sequences around exon 3 and exon 4 are displayed in the upper and lower panels, respectively. The modified codons encoding four alanines are enclosed in red boxes. The silent mutations for RFLP analyses are enclosed in green boxes. The gRNA-blocking mutation is enclosed in a purple box. The wild-type allele is shown at the top ( Spp1 Wild) with the gRNA target sequences (underlined in yellow and blue). The PAM sequences are enclosed in yellow and blue boxes. Uppercase letters indicate exon sequences. Dots indicate the same bases as the wild-type sequence. Dashes indicate deletions. Unintended mutations are enclosed in black boxes. Black underlined sequences indicate Nar I and Dra I sites in exons 3 and exon 4, respectively.

    Techniques Used: Knock-In, Mouse Assay, Plasmid Preparation, Mutagenesis, Polymerase Chain Reaction, Sequencing, Modification, Blocking Assay

    6) Product Images from "Circular RNA biogenesis can proceed through an exon-containing lariat precursor"

    Article Title: Circular RNA biogenesis can proceed through an exon-containing lariat precursor

    Journal: eLife

    doi: 10.7554/eLife.07540

    Additional Dra I restriction digest PCR for Y-shaped intermediate product. Panel 2D with additional lanes indicating attempted amplification of the Y-shaped intermediate. As in 2D, primers used are indicated above the gel and observed products are illustrated below. The off-target product is the higher molecular weight species (lane 13) and represents mispriming of the reverse primer to a downstream site in exon 3. DOI: http://dx.doi.org/10.7554/eLife.07540.010
    Figure Legend Snippet: Additional Dra I restriction digest PCR for Y-shaped intermediate product. Panel 2D with additional lanes indicating attempted amplification of the Y-shaped intermediate. As in 2D, primers used are indicated above the gel and observed products are illustrated below. The off-target product is the higher molecular weight species (lane 13) and represents mispriming of the reverse primer to a downstream site in exon 3. DOI: http://dx.doi.org/10.7554/eLife.07540.010

    Techniques Used: Polymerase Chain Reaction, Amplification, Molecular Weight

    7) Product Images from "SMN1 dosage analysis in spinal muscular atrophy from India"

    Article Title: SMN1 dosage analysis in spinal muscular atrophy from India

    Journal: BMC Medical Genetics

    doi: 10.1186/1471-2350-6-22

    SMN1 copy number analysis for the family of Case 3. 1A The pedigree of the family of Case 3. 1B: Exon 7 PCR-RFLP Polyacrylamide gels showing the undigested and digested products of SMN exon 7 after Dra I digestion. Lane 1, undigested product of patient; Lane 2, digested product of patient with SMN1 deletion; Lane 3, undigested product of sibling; Lane 4, digested product of sibling with no SMN1 deletion. 1C: Exon 8 PCR-RFLP after Dde I digestion. Lanes 1 and 3, undigested PCR product; Lane 2, digested product of patient with homozygous deletion of exon 8 of the SMN1 gene; Lane 4, digested product of sibling with no homozygous deletion of SMN1 . 1D Quantitative PCR gel scans of Father (I: 1), Mother (I: 2) and sibling (II: 4). Band sizes in base pairs are shown in the upper boxes and peak areas in the lower boxes. IS, internal standards.
    Figure Legend Snippet: SMN1 copy number analysis for the family of Case 3. 1A The pedigree of the family of Case 3. 1B: Exon 7 PCR-RFLP Polyacrylamide gels showing the undigested and digested products of SMN exon 7 after Dra I digestion. Lane 1, undigested product of patient; Lane 2, digested product of patient with SMN1 deletion; Lane 3, undigested product of sibling; Lane 4, digested product of sibling with no SMN1 deletion. 1C: Exon 8 PCR-RFLP after Dde I digestion. Lanes 1 and 3, undigested PCR product; Lane 2, digested product of patient with homozygous deletion of exon 8 of the SMN1 gene; Lane 4, digested product of sibling with no homozygous deletion of SMN1 . 1D Quantitative PCR gel scans of Father (I: 1), Mother (I: 2) and sibling (II: 4). Band sizes in base pairs are shown in the upper boxes and peak areas in the lower boxes. IS, internal standards.

    Techniques Used: Polymerase Chain Reaction, Real-time Polymerase Chain Reaction

    Related Articles

    Clone Assay:

    Article Title: Tight clustering and hemizygosity of apomixis-linked molecular markers in Pennisetum squamulatum implies genetic control of apospory by a divergent locus that may have no allelic form in sexual genotypes
    Article Snippet: DNA (15 μg) was digested overnight with 50 units of Dra I (New England Biolabs) and separated by electrophoresis for 16 hours in 1% GTG agarose (FMC) in 1× TBE buffer. .. DNA was transferred to Genescreen Plus nylon membrane (NEN) and hybridized with labeled insert DNA generated by PCR amplification from RAPD clones using SCAR-specific primers.

    Centrifugation:

    Article Title: Polymorphisms in thymidylate synthase gene and susceptibility to breast cancer in a Chinese population: a case-control analysis
    Article Snippet: Genotype analyses By centrifugation of 5-ml whole blood, genomic DNA was extracted from the leukocyte pellet obtained from the buffy coat of each blood sample. .. For the TS 3'-UTR del6 polymorphism, 152 bp (i.e. del6) or 158 bp fragments (i.e. ins6) were amplified and then digested by Dra I (New England BioLabs, Inc., Beverly, MA).

    Amplification:

    Article Title: Chromatin Landscapes of Retroviral and Transposon Integration Profiles
    Article Snippet: The ligated DNA was cut with Dra-I (New England Biolabs). .. The ligation reactions were amplified in two rounds of PCR to generate high throughput sequencing libraries (for details see ).

    Article Title: Atypical 16S rRNA Gene Copies in Ochrobactrum intermedium Strains Reveal a Large Genomic Rearrangement by Recombination between rrn Copies
    Article Snippet: Paragraph title: rDNA amplification, sequencing, and analysis. ... Restriction analysis of PCR products was done with 10 U of Dra I (New England Biolabs, Hertfordshire, United Kingdom) by following the supplier's recommendations. ) and with sequences deposited in the Ribosomal Database Project, version 7.0, by using SIMILARITY RANK and SUGGEST TREE ( ).

    Article Title: Association between folate metabolism-related polymorphisms and colorectal cancer risk
    Article Snippet: The TSER polymorphism was genotyped according to amplified fragment size; 2R corresponded to a 220 bp amplicon and 3R corresponded to a 248 bp amplicon. .. The TS 1494del6 polymorphism was characterized using Dra I (New England BioLabs, Ipswich, MA, USA) digestion.

    Article Title: Tight clustering and hemizygosity of apomixis-linked molecular markers in Pennisetum squamulatum implies genetic control of apospory by a divergent locus that may have no allelic form in sexual genotypes
    Article Snippet: DNA (15 μg) was digested overnight with 50 units of Dra I (New England Biolabs) and separated by electrophoresis for 16 hours in 1% GTG agarose (FMC) in 1× TBE buffer. .. DNA was transferred to Genescreen Plus nylon membrane (NEN) and hybridized with labeled insert DNA generated by PCR amplification from RAPD clones using SCAR-specific primers.

    Article Title: Nicotiana attenuata LECTIN RECEPTOR KINASE1 Suppresses the Insect-Mediated Inhibition of Induced Defense Responses during Manduca sexta Herbivory [C] Herbivory [C] [W]
    Article Snippet: For the generation of N. attenuata plants ectopically expressing the bacterial salicylate hydroxylase gene ( nahG ) from Pseudomonas putida , a 690-bp fragment corresponding to this gene was amplified with primers NahG1-33 and NahG1-34 (see online) using P. putida genomic DNA as template and subcloned using Xho I and Bst EII (New England Biolabs) restriction sites into the pSOL1 vector ( ) to generate pSOL1-nahG1, and this vector was used to transform N. attenuata wild-type plants using Agrobacterium -mediated transformation as previously described ( ). .. DNA samples (10 μg) were digested with Eco RV and Dra I (New England Biolabs) overnight at 37°C according to commercial instructions and separated on a 1% (w/v) agarose gel using standard conditions.

    Article Title: Polymorphisms in thymidylate synthase gene and susceptibility to breast cancer in a Chinese population: a case-control analysis
    Article Snippet: .. For the TS 3'-UTR del6 polymorphism, 152 bp (i.e. del6) or 158 bp fragments (i.e. ins6) were amplified and then digested by Dra I (New England BioLabs, Inc., Beverly, MA). .. The variant (ins6) allele produces two fragments of 88 and 70 bp, while the wild-type (del6) allele produces a single 152-bp fragment.

    Article Title: RsaI but not DraI polymorphism in CYP2E1 gene increases the risk of gastrointestinal cancer in Malaysians: a case-control study
    Article Snippet: For C-1019T SNP, forward (5′-CCAGTCGAGTCTACATTGTCA-3′) and reverse (5′-TTCATTCTGTCTTCTAACTGG-3′) primers were used with PCR conditions set as followed: initial denaturation at 94°C for 5 min; amplification of 35 cycles at 94°C for 30 s, 58°C for 30 s and 72°C for 1 min; final extension at 72°C for 7 min. .. The PCR products were subjected to overnight 2.5 U Rsa I and 5.0 U Dra I (New England BioLabs Inc, Ipswich, Massachusetts, USA restriction enzymes digestion for C-1019T and T7678A SNPs, respectively.

    Positive Control:

    Article Title: Polymorphisms in thymidylate synthase gene and susceptibility to breast cancer in a Chinese population: a case-control analysis
    Article Snippet: For the TS 3'-UTR del6 polymorphism, 152 bp (i.e. del6) or 158 bp fragments (i.e. ins6) were amplified and then digested by Dra I (New England BioLabs, Inc., Beverly, MA). .. Genotyping was performed without knowing the subjects' case or control status, and approximately equal number of cases and controls were assayed in each 96-well PCR plate with a positive control of a DNA sample with a known heterozygous genotype.

    Synthesized:

    Article Title: Colorimetric Assay for Exon 7 SMN1/SMN2 Single Nucleotide Polymorphism Using Gold Nanoprobes
    Article Snippet: All primers and pGEM easy vectors containing exon 7 and exon 8 contigs of SMN 1 and SMN 2 were synthesized by Bioneer Company. .. Dra I and Dde I enzymes were obtained from New England Biolab.

    Lambda DNA Preparation:

    Article Title: Chromosomal Integration of a Cephalosporinase Gene from Acinetobacter baumannii into Oligella urethralis as a Source of Acquired Resistance to ?-Lactams
    Article Snippet: Macrorestriction analysis of whole-cell DNA of O. urethralis COH-1 was done by the pulsed-field gel electrophoresis (PFGE) technique with Xba I, Spe I, Dra I, Apa I, and Sfi I (New England Biolabs), as reported previously ( , ). .. The sizes of the fragments generated with Ceu I fragment I were determined by comparison with those of a bacteriophage lambda DNA molecular weight marker (Bio-Rad).

    Construct:

    Article Title: Smads bind directly to the Jun family of AP-1 transcription factors
    Article Snippet: Full length JunB in pGEM4 was digested with Bsp HI, BssHII, or Dra I (NEB). .. The full length construct and the digested DNAs were used as templates for in vitro transcription and translation (TNT) with [35 S]methionine in rabbit reticulocyte lysates (Promega).

    Electrophoresis:

    Article Title: Tight clustering and hemizygosity of apomixis-linked molecular markers in Pennisetum squamulatum implies genetic control of apospory by a divergent locus that may have no allelic form in sexual genotypes
    Article Snippet: .. DNA (15 μg) was digested overnight with 50 units of Dra I (New England Biolabs) and separated by electrophoresis for 16 hours in 1% GTG agarose (FMC) in 1× TBE buffer. .. DNA was transferred to Genescreen Plus nylon membrane (NEN) and hybridized with labeled insert DNA generated by PCR amplification from RAPD clones using SCAR-specific primers.

    Article Title: Chromosomal Integration of a Cephalosporinase Gene from Acinetobacter baumannii into Oligella urethralis as a Source of Acquired Resistance to ?-Lactams
    Article Snippet: Paragraph title: Endonuclease restriction, electrophoresis, and hybridization experiments. ... Macrorestriction analysis of whole-cell DNA of O. urethralis COH-1 was done by the pulsed-field gel electrophoresis (PFGE) technique with Xba I, Spe I, Dra I, Apa I, and Sfi I (New England Biolabs), as reported previously ( , ).

    Incubation:

    Article Title: Smads bind directly to the Jun family of AP-1 transcription factors
    Article Snippet: Full length JunB in pGEM4 was digested with Bsp HI, BssHII, or Dra I (NEB). .. The TNT–JunB lysates were incubated with an equal amount of bacterially purified glutathione S- transferase (GST), or GST-Smad3 or GST-Smad4 ( ) in B/P (150 mM NaCl/50 mM Tris, pH 7.5/0.1% Tween/1 mM DTT) for 2.5 hours at 4°C.

    Infection:

    Article Title: Chromatin Landscapes of Retroviral and Transposon Integration Profiles
    Article Snippet: By using a primer pair, which was specific to MMTV in Mm5MT and did not amplify endogenous MMTV sequences in NMuMG cells, it was confirmed that NMuMG cells got infected. .. The ligated DNA was cut with Dra-I (New England Biolabs).

    Expressing:

    Article Title: Nicotiana attenuata LECTIN RECEPTOR KINASE1 Suppresses the Insect-Mediated Inhibition of Induced Defense Responses during Manduca sexta Herbivory [C] Herbivory [C] [W]
    Article Snippet: Segregation analysis for hygromycin resistance in T2 seedlings was performed on agar plates supplemented with hygromycin (0.025 mg mL−1 ), and homozygous T2 transformed plants were analyzed for expression of the nahG gene by RT-PCR using the primers NahG1-Fw and NahG1-Rv (see online). .. DNA samples (10 μg) were digested with Eco RV and Dra I (New England Biolabs) overnight at 37°C according to commercial instructions and separated on a 1% (w/v) agarose gel using standard conditions.

    Western Blot:

    Article Title: Nicotiana attenuata LECTIN RECEPTOR KINASE1 Suppresses the Insect-Mediated Inhibition of Induced Defense Responses during Manduca sexta Herbivory [C] Herbivory [C] [W]
    Article Snippet: For DNA gel blot analysis, genomic DNA was isolated as described above. .. DNA samples (10 μg) were digested with Eco RV and Dra I (New England Biolabs) overnight at 37°C according to commercial instructions and separated on a 1% (w/v) agarose gel using standard conditions.

    Transformation Assay:

    Article Title: Nicotiana attenuata LECTIN RECEPTOR KINASE1 Suppresses the Insect-Mediated Inhibition of Induced Defense Responses during Manduca sexta Herbivory [C] Herbivory [C] [W]
    Article Snippet: Segregation analysis for hygromycin resistance in T2 seedlings was performed on agar plates supplemented with hygromycin (0.025 mg mL−1 ), and homozygous T2 transformed plants were analyzed for expression of the nahG gene by RT-PCR using the primers NahG1-Fw and NahG1-Rv (see online). .. DNA samples (10 μg) were digested with Eco RV and Dra I (New England Biolabs) overnight at 37°C according to commercial instructions and separated on a 1% (w/v) agarose gel using standard conditions.

    Hybridization:

    Article Title: Chromosomal Integration of a Cephalosporinase Gene from Acinetobacter baumannii into Oligella urethralis as a Source of Acquired Resistance to ?-Lactams
    Article Snippet: Paragraph title: Endonuclease restriction, electrophoresis, and hybridization experiments. ... Macrorestriction analysis of whole-cell DNA of O. urethralis COH-1 was done by the pulsed-field gel electrophoresis (PFGE) technique with Xba I, Spe I, Dra I, Apa I, and Sfi I (New England Biolabs), as reported previously ( , ).

    Southern Blot:

    Article Title: Atypical 16S rRNA Gene Copies in Ochrobactrum intermedium Strains Reveal a Large Genomic Rearrangement by Recombination between rrn Copies
    Article Snippet: Determination of fragments harboring a 16S rDNA copy was done by Southern blotting (see below). .. Restriction analysis of PCR products was done with 10 U of Dra I (New England Biolabs, Hertfordshire, United Kingdom) by following the supplier's recommendations. ) and with sequences deposited in the Ribosomal Database Project, version 7.0, by using SIMILARITY RANK and SUGGEST TREE ( ).

    Ligation:

    Article Title: Chromatin Landscapes of Retroviral and Transposon Integration Profiles
    Article Snippet: The integration sites were measured by two methods: either shearing the DNA with sonication and blunt end ligation of adapters as described previously or cutting the DNA with Nla-III and ligation of adapters with sticky ends. of genomic DNA was digested with 20 units of Nla-III (New England Biolabs) at C for overnight in a reaction. of purified digested DNA was ligated with of splinkerette adapter using 10 units of T4 DNA ligase (Roche Applied Science) in a reaction. .. The ligated DNA was cut with Dra-I (New England Biolabs).

    Article Title: Occurrence of subdioecy and scarcity of gender-specific markers reveal an ongoing transition to dioecy in Himalayan seabuckthorn (Hippophae rhamnoides ssp. turkestanica)
    Article Snippet: Total genomic DNA (1 µg) was digested with rare DNA restriction enzymes, that is, Dra I, Ssp I, Stu I, and Eco RV (NEB, India). .. The adapter’s (AP1 and AP2) ligation, primary PCR conditions, and secondary PCR conditions were followed as detailed in the Genome Walker™ Universal Kit (Clontech, California, USA).

    Article Title: Gene silencing via DNA methylation in naturally occurring Tragopogon miscellus (Asteraceae) allopolyploids
    Article Snippet: Genomic DNA of Tragopogon dubius (a diploid parental species) was digested with three different restriction enzymes: Eco RV, Dra I and Sca I (New England Biolabs, USA) in separate reaction tubes containing 2.5 μg of genomic DNA, 80 units of restriction enzyme and 10X buffer (New England Biolabs) in a total volume of 100 μl. .. Adapter ligation to the precipitated, digested genomic DNA was performed in a total volume of 8 μl containing 25 μM adapter, 10X ligation buffer, 3 units of T4 DNA ligase (New England Biolabs) and 0.5 μg of purified DNA.

    Cell Culture:

    Article Title: Chromatin Landscapes of Retroviral and Transposon Integration Profiles
    Article Snippet: Three days later the mixed cell culture was treated with of Puromycin to remove Mm5MT cells. .. The ligated DNA was cut with Dra-I (New England Biolabs).

    Generated:

    Article Title: Tight clustering and hemizygosity of apomixis-linked molecular markers in Pennisetum squamulatum implies genetic control of apospory by a divergent locus that may have no allelic form in sexual genotypes
    Article Snippet: DNA (15 μg) was digested overnight with 50 units of Dra I (New England Biolabs) and separated by electrophoresis for 16 hours in 1% GTG agarose (FMC) in 1× TBE buffer. .. DNA was transferred to Genescreen Plus nylon membrane (NEN) and hybridized with labeled insert DNA generated by PCR amplification from RAPD clones using SCAR-specific primers.

    Article Title: Chromosomal Integration of a Cephalosporinase Gene from Acinetobacter baumannii into Oligella urethralis as a Source of Acquired Resistance to ?-Lactams
    Article Snippet: Macrorestriction analysis of whole-cell DNA of O. urethralis COH-1 was done by the pulsed-field gel electrophoresis (PFGE) technique with Xba I, Spe I, Dra I, Apa I, and Sfi I (New England Biolabs), as reported previously ( , ). .. The sizes of the fragments generated with Ceu I fragment I were determined by comparison with those of a bacteriophage lambda DNA molecular weight marker (Bio-Rad).

    Article Title: Nicotiana attenuata LECTIN RECEPTOR KINASE1 Suppresses the Insect-Mediated Inhibition of Induced Defense Responses during Manduca sexta Herbivory [C] Herbivory [C] [W]
    Article Snippet: DNA samples (10 μg) were digested with Eco RV and Dra I (New England Biolabs) overnight at 37°C according to commercial instructions and separated on a 1% (w/v) agarose gel using standard conditions. .. Membranes were hybridized with a nahG-specific radiolabeled probe that was generated by PCR using the primer pairs NahG1 Fw and NahG1 Rv (see online) and [α-32 P]dCTP (Perkin-Elmer) using the Rediprime II kit (Amersham Pharmacia) according to commercial instruction.

    Article Title: Occurrence of subdioecy and scarcity of gender-specific markers reveal an ongoing transition to dioecy in Himalayan seabuckthorn (Hippophae rhamnoides ssp. turkestanica)
    Article Snippet: Total genomic DNA (1 µg) was digested with rare DNA restriction enzymes, that is, Dra I, Ssp I, Stu I, and Eco RV (NEB, India). .. Primary PCR was done using the AP1-specific primers provided in the kit and the primer designed based on sequence generated from the locus.

    Polymerase Chain Reaction:

    Article Title: Chromatin Landscapes of Retroviral and Transposon Integration Profiles
    Article Snippet: The ligated DNA was cut with Dra-I (New England Biolabs). .. The ligation reactions were amplified in two rounds of PCR to generate high throughput sequencing libraries (for details see ).

    Article Title: Atypical 16S rRNA Gene Copies in Ochrobactrum intermedium Strains Reveal a Large Genomic Rearrangement by Recombination between rrn Copies
    Article Snippet: .. Restriction analysis of PCR products was done with 10 U of Dra I (New England Biolabs, Hertfordshire, United Kingdom) by following the supplier's recommendations. ) and with sequences deposited in the Ribosomal Database Project, version 7.0, by using SIMILARITY RANK and SUGGEST TREE ( ). ..

    Article Title: Association between folate metabolism-related polymorphisms and colorectal cancer risk
    Article Snippet: For the 677C > T polymorphism, an undigested PCR product (203 bp) indicated the homozygous wild-type genotype, while three bands of 203, 173 and 30 bp indicated the heterozygous genotype and two bands of 173 and 30 bp indicated the homozygous minor variant genotype. .. The TS 1494del6 polymorphism was characterized using Dra I (New England BioLabs, Ipswich, MA, USA) digestion.

    Article Title: Tight clustering and hemizygosity of apomixis-linked molecular markers in Pennisetum squamulatum implies genetic control of apospory by a divergent locus that may have no allelic form in sexual genotypes
    Article Snippet: DNA (15 μg) was digested overnight with 50 units of Dra I (New England Biolabs) and separated by electrophoresis for 16 hours in 1% GTG agarose (FMC) in 1× TBE buffer. .. DNA was transferred to Genescreen Plus nylon membrane (NEN) and hybridized with labeled insert DNA generated by PCR amplification from RAPD clones using SCAR-specific primers.

    Article Title: Colorimetric Assay for Exon 7 SMN1/SMN2 Single Nucleotide Polymorphism Using Gold Nanoprobes
    Article Snippet: Dra I and Dde I enzymes were obtained from New England Biolab. .. Nap-5 column, OliGreen ssDNA Quantitation kit, and QIAquick PCR Purification Kit were bought from GE Healthcare, Invitrogen, and QIAGEN, respectively.

    Article Title: Nicotiana attenuata LECTIN RECEPTOR KINASE1 Suppresses the Insect-Mediated Inhibition of Induced Defense Responses during Manduca sexta Herbivory [C] Herbivory [C] [W]
    Article Snippet: DNA samples (10 μg) were digested with Eco RV and Dra I (New England Biolabs) overnight at 37°C according to commercial instructions and separated on a 1% (w/v) agarose gel using standard conditions. .. Membranes were hybridized with a nahG-specific radiolabeled probe that was generated by PCR using the primer pairs NahG1 Fw and NahG1 Rv (see online) and [α-32 P]dCTP (Perkin-Elmer) using the Rediprime II kit (Amersham Pharmacia) according to commercial instruction.

    Article Title: Polymorphisms in thymidylate synthase gene and susceptibility to breast cancer in a Chinese population: a case-control analysis
    Article Snippet: For the TS 3'-UTR del6 polymorphism, 152 bp (i.e. del6) or 158 bp fragments (i.e. ins6) were amplified and then digested by Dra I (New England BioLabs, Inc., Beverly, MA). .. Genotyping was performed without knowing the subjects' case or control status, and approximately equal number of cases and controls were assayed in each 96-well PCR plate with a positive control of a DNA sample with a known heterozygous genotype.

    Article Title: Occurrence of subdioecy and scarcity of gender-specific markers reveal an ongoing transition to dioecy in Himalayan seabuckthorn (Hippophae rhamnoides ssp. turkestanica)
    Article Snippet: Total genomic DNA (1 µg) was digested with rare DNA restriction enzymes, that is, Dra I, Ssp I, Stu I, and Eco RV (NEB, India). .. The adapter’s (AP1 and AP2) ligation, primary PCR conditions, and secondary PCR conditions were followed as detailed in the Genome Walker™ Universal Kit (Clontech, California, USA).

    Article Title: RsaI but not DraI polymorphism in CYP2E1 gene increases the risk of gastrointestinal cancer in Malaysians: a case-control study
    Article Snippet: .. The PCR products were subjected to overnight 2.5 U Rsa I and 5.0 U Dra I (New England BioLabs Inc, Ipswich, Massachusetts, USA restriction enzymes digestion for C-1019T and T7678A SNPs, respectively. .. The digested fragments were electrophoresed and analysed on 2% agarose gel stained with ethidium bromide in 1×TAE buffer.

    Article Title: Gene silencing via DNA methylation in naturally occurring Tragopogon miscellus (Asteraceae) allopolyploids
    Article Snippet: Genomic DNA of Tragopogon dubius (a diploid parental species) was digested with three different restriction enzymes: Eco RV, Dra I and Sca I (New England Biolabs, USA) in separate reaction tubes containing 2.5 μg of genomic DNA, 80 units of restriction enzyme and 10X buffer (New England Biolabs) in a total volume of 100 μl. .. Primary PCR was performed in 50-μl total volume using 10 mM dNTPs, 10X PCR buffer (Takara Biotechnology, Japan), 10 μM of adapter primer AP1 (Forward) and gene-specific primer (Reverse) (gene-specific reverse primers for all the genes S2, S3, S8, S18 and TDF-44 are listed in Additional file : Table S1) and 1 unit of Takara Ex Taq polymerase (Takara Biotechnology, Japan).

    Sequencing:

    Article Title: Chromatin Landscapes of Retroviral and Transposon Integration Profiles
    Article Snippet: The ligated DNA was cut with Dra-I (New England Biolabs). .. Sequencing was done on an Illumina HiSeq 2000 instrument to obtain single 100 bp reads.

    Article Title: Atypical 16S rRNA Gene Copies in Ochrobactrum intermedium Strains Reveal a Large Genomic Rearrangement by Recombination between rrn Copies
    Article Snippet: Paragraph title: rDNA amplification, sequencing, and analysis. ... Restriction analysis of PCR products was done with 10 U of Dra I (New England Biolabs, Hertfordshire, United Kingdom) by following the supplier's recommendations. ) and with sequences deposited in the Ribosomal Database Project, version 7.0, by using SIMILARITY RANK and SUGGEST TREE ( ).

    Article Title: Chromosomal Integration of a Cephalosporinase Gene from Acinetobacter baumannii into Oligella urethralis as a Source of Acquired Resistance to ?-Lactams
    Article Snippet: Macrorestriction analysis of whole-cell DNA of O. urethralis COH-1 was done by the pulsed-field gel electrophoresis (PFGE) technique with Xba I, Spe I, Dra I, Apa I, and Sfi I (New England Biolabs), as reported previously ( , ). .. To search for the chromosomal integration of the β-lactamase genes, whole-cell DNA of O. urethralis COH-1 was restricted with Ceu I fragment (New England Biolabs), which recognizes a 26-bp sequence in rrn genes coding for the 23S large-subunit rRNA ( ).

    Article Title: Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome
    Article Snippet: Paragraph title: Library construction and sequencing ... Extracted DNA was pooled (60 ng) and digested with Dra I (100 units; New England Biolabs, Ipswich, MA, USA) at 37°C for 16 hours.

    Article Title: Occurrence of subdioecy and scarcity of gender-specific markers reveal an ongoing transition to dioecy in Himalayan seabuckthorn (Hippophae rhamnoides ssp. turkestanica)
    Article Snippet: Total genomic DNA (1 µg) was digested with rare DNA restriction enzymes, that is, Dra I, Ssp I, Stu I, and Eco RV (NEB, India). .. Primary PCR was done using the AP1-specific primers provided in the kit and the primer designed based on sequence generated from the locus.

    Sonication:

    Article Title: Chromatin Landscapes of Retroviral and Transposon Integration Profiles
    Article Snippet: The integration sites were measured by two methods: either shearing the DNA with sonication and blunt end ligation of adapters as described previously or cutting the DNA with Nla-III and ligation of adapters with sticky ends. of genomic DNA was digested with 20 units of Nla-III (New England Biolabs) at C for overnight in a reaction. of purified digested DNA was ligated with of splinkerette adapter using 10 units of T4 DNA ligase (Roche Applied Science) in a reaction. .. The ligated DNA was cut with Dra-I (New England Biolabs).

    Binding Assay:

    Article Title: Smads bind directly to the Jun family of AP-1 transcription factors
    Article Snippet: Paragraph title: Binding Studies. ... Full length JunB in pGEM4 was digested with Bsp HI, BssHII, or Dra I (NEB).

    Pulsed-Field Gel:

    Article Title: Chromosomal Integration of a Cephalosporinase Gene from Acinetobacter baumannii into Oligella urethralis as a Source of Acquired Resistance to ?-Lactams
    Article Snippet: .. Macrorestriction analysis of whole-cell DNA of O. urethralis COH-1 was done by the pulsed-field gel electrophoresis (PFGE) technique with Xba I, Spe I, Dra I, Apa I, and Sfi I (New England Biolabs), as reported previously ( , ). .. To search for the chromosomal integration of the β-lactamase genes, whole-cell DNA of O. urethralis COH-1 was restricted with Ceu I fragment (New England Biolabs), which recognizes a 26-bp sequence in rrn genes coding for the 23S large-subunit rRNA ( ).

    Methylation:

    Article Title: Gene silencing via DNA methylation in naturally occurring Tragopogon miscellus (Asteraceae) allopolyploids
    Article Snippet: Genome walking In order to determine the methylation status of the promoter region, 5’genome walking was performed following the GenomeWalker manual (Clontech Laboratories, USA) [ ]. .. Genomic DNA of Tragopogon dubius (a diploid parental species) was digested with three different restriction enzymes: Eco RV, Dra I and Sca I (New England Biolabs, USA) in separate reaction tubes containing 2.5 μg of genomic DNA, 80 units of restriction enzyme and 10X buffer (New England Biolabs) in a total volume of 100 μl.

    Mutagenesis:

    Article Title: Nature of guanine oxidation in RNA via the flash-quench technique versus direct oxidation by a metal oxo complex
    Article Snippet: Dra I, T4 RNA ligase, and T4 RNA ligase buffer were purchased from New England Biolabs. .. QuikChange mutagenesis kit was purchased from Stratagene.

    Isolation:

    Article Title: Chromatin Landscapes of Retroviral and Transposon Integration Profiles
    Article Snippet: The remaining cells (NMuMG) were grown till passage 8 before the isolation of genomic DNA for integration site mapping ( ). .. The ligated DNA was cut with Dra-I (New England Biolabs).

    Article Title: Nicotiana attenuata LECTIN RECEPTOR KINASE1 Suppresses the Insect-Mediated Inhibition of Induced Defense Responses during Manduca sexta Herbivory [C] Herbivory [C] [W]
    Article Snippet: For DNA gel blot analysis, genomic DNA was isolated as described above. .. DNA samples (10 μg) were digested with Eco RV and Dra I (New England Biolabs) overnight at 37°C according to commercial instructions and separated on a 1% (w/v) agarose gel using standard conditions.

    Article Title: Occurrence of subdioecy and scarcity of gender-specific markers reveal an ongoing transition to dioecy in Himalayan seabuckthorn (Hippophae rhamnoides ssp. turkestanica)
    Article Snippet: The genomic region around SCAR was explored through genome walking (both 5′ and 3′) in the plant from which the SCAR was originally isolated. .. Total genomic DNA (1 µg) was digested with rare DNA restriction enzymes, that is, Dra I, Ssp I, Stu I, and Eco RV (NEB, India).

    Labeling:

    Article Title: Tight clustering and hemizygosity of apomixis-linked molecular markers in Pennisetum squamulatum implies genetic control of apospory by a divergent locus that may have no allelic form in sexual genotypes
    Article Snippet: DNA (15 μg) was digested overnight with 50 units of Dra I (New England Biolabs) and separated by electrophoresis for 16 hours in 1% GTG agarose (FMC) in 1× TBE buffer. .. DNA was transferred to Genescreen Plus nylon membrane (NEN) and hybridized with labeled insert DNA generated by PCR amplification from RAPD clones using SCAR-specific primers.

    Article Title: Nicotiana attenuata LECTIN RECEPTOR KINASE1 Suppresses the Insect-Mediated Inhibition of Induced Defense Responses during Manduca sexta Herbivory [C] Herbivory [C] [W]
    Article Snippet: The probe was labeled with [α-32 P]dCTP (Perkin-Elmer) using the Rediprime II kit (Amersham Pharmacia) according to commercial instruction. .. DNA samples (10 μg) were digested with Eco RV and Dra I (New England Biolabs) overnight at 37°C according to commercial instructions and separated on a 1% (w/v) agarose gel using standard conditions.

    Purification:

    Article Title: Chromatin Landscapes of Retroviral and Transposon Integration Profiles
    Article Snippet: The integration sites were measured by two methods: either shearing the DNA with sonication and blunt end ligation of adapters as described previously or cutting the DNA with Nla-III and ligation of adapters with sticky ends. of genomic DNA was digested with 20 units of Nla-III (New England Biolabs) at C for overnight in a reaction. of purified digested DNA was ligated with of splinkerette adapter using 10 units of T4 DNA ligase (Roche Applied Science) in a reaction. .. The ligated DNA was cut with Dra-I (New England Biolabs).

    Article Title: Nature of guanine oxidation in RNA via the flash-quench technique versus direct oxidation by a metal oxo complex
    Article Snippet: Plasmid purification kits were purchased from Qiagen. .. Dra I, T4 RNA ligase, and T4 RNA ligase buffer were purchased from New England Biolabs.

    Article Title: Smads bind directly to the Jun family of AP-1 transcription factors
    Article Snippet: Full length JunB in pGEM4 was digested with Bsp HI, BssHII, or Dra I (NEB). .. The TNT–JunB lysates were incubated with an equal amount of bacterially purified glutathione S- transferase (GST), or GST-Smad3 or GST-Smad4 ( ) in B/P (150 mM NaCl/50 mM Tris, pH 7.5/0.1% Tween/1 mM DTT) for 2.5 hours at 4°C.

    Article Title: Colorimetric Assay for Exon 7 SMN1/SMN2 Single Nucleotide Polymorphism Using Gold Nanoprobes
    Article Snippet: Dra I and Dde I enzymes were obtained from New England Biolab. .. Nap-5 column, OliGreen ssDNA Quantitation kit, and QIAquick PCR Purification Kit were bought from GE Healthcare, Invitrogen, and QIAGEN, respectively.

    Article Title: Characterization of DNA synthesis catalyzed by bacteriophage T4 replication complexes reconstituted on synthetic circular substrates
    Article Snippet: T4 DNA ligase, Dra I and polynucleotide kinase were from New England Biolabs. .. Gp43, gp43D219A, gp44/gp62, gp45, gp32, gp41, gp61 and gp59 were purified and their concentrations were estimated as described ( ).

    Article Title: Gene silencing via DNA methylation in naturally occurring Tragopogon miscellus (Asteraceae) allopolyploids
    Article Snippet: Genomic DNA of Tragopogon dubius (a diploid parental species) was digested with three different restriction enzymes: Eco RV, Dra I and Sca I (New England Biolabs, USA) in separate reaction tubes containing 2.5 μg of genomic DNA, 80 units of restriction enzyme and 10X buffer (New England Biolabs) in a total volume of 100 μl. .. Adapter ligation to the precipitated, digested genomic DNA was performed in a total volume of 8 μl containing 25 μM adapter, 10X ligation buffer, 3 units of T4 DNA ligase (New England Biolabs) and 0.5 μg of purified DNA.

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Nicotiana attenuata LECTIN RECEPTOR KINASE1 Suppresses the Insect-Mediated Inhibition of Induced Defense Responses during Manduca sexta Herbivory [C] Herbivory [C] [W]
    Article Snippet: Segregation analysis for hygromycin resistance in T2 seedlings was performed on agar plates supplemented with hygromycin (0.025 mg mL−1 ), and homozygous T2 transformed plants were analyzed for expression of the nahG gene by RT-PCR using the primers NahG1-Fw and NahG1-Rv (see online). .. DNA samples (10 μg) were digested with Eco RV and Dra I (New England Biolabs) overnight at 37°C according to commercial instructions and separated on a 1% (w/v) agarose gel using standard conditions.

    Concentration Assay:

    Article Title: Nature of guanine oxidation in RNA via the flash-quench technique versus direct oxidation by a metal oxo complex
    Article Snippet: Dra I, T4 RNA ligase, and T4 RNA ligase buffer were purchased from New England Biolabs. .. Proteinase K, phenol/chloroform, linear acrylamide, GlycoBlue, Superase-In, MEGAshortscript T7 Kit, RNase A (1 μg/ml), RNase T1 (1 U/μl), alkaline hydrolysis buffer, 10% SDS, 10 × phosphate buffered saline (PBS) buffer and high concentration T7 RNA polymerase were obtained from Applied Biosystems.

    Plasmid Preparation:

    Article Title: Nature of guanine oxidation in RNA via the flash-quench technique versus direct oxidation by a metal oxo complex
    Article Snippet: Plasmid purification kits were purchased from Qiagen. .. Dra I, T4 RNA ligase, and T4 RNA ligase buffer were purchased from New England Biolabs.

    Article Title: Nicotiana attenuata LECTIN RECEPTOR KINASE1 Suppresses the Insect-Mediated Inhibition of Induced Defense Responses during Manduca sexta Herbivory [C] Herbivory [C] [W]
    Article Snippet: For the generation of N. attenuata plants ectopically expressing the bacterial salicylate hydroxylase gene ( nahG ) from Pseudomonas putida , a 690-bp fragment corresponding to this gene was amplified with primers NahG1-33 and NahG1-34 (see online) using P. putida genomic DNA as template and subcloned using Xho I and Bst EII (New England Biolabs) restriction sites into the pSOL1 vector ( ) to generate pSOL1-nahG1, and this vector was used to transform N. attenuata wild-type plants using Agrobacterium -mediated transformation as previously described ( ). .. DNA samples (10 μg) were digested with Eco RV and Dra I (New England Biolabs) overnight at 37°C according to commercial instructions and separated on a 1% (w/v) agarose gel using standard conditions.

    Real-time Polymerase Chain Reaction:

    Article Title: Nicotiana attenuata LECTIN RECEPTOR KINASE1 Suppresses the Insect-Mediated Inhibition of Induced Defense Responses during Manduca sexta Herbivory [C] Herbivory [C] [W]
    Article Snippet: Efficiency of gene silencing was evaluated by qPCR (see below) after 1 h of wounding and 18:3-Glu treatment using the primers 5358 Fw and 5358 Rv (see online). .. DNA samples (10 μg) were digested with Eco RV and Dra I (New England Biolabs) overnight at 37°C according to commercial instructions and separated on a 1% (w/v) agarose gel using standard conditions.

    Agarose Gel Electrophoresis:

    Article Title: Atypical 16S rRNA Gene Copies in Ochrobactrum intermedium Strains Reveal a Large Genomic Rearrangement by Recombination between rrn Copies
    Article Snippet: Amplification of a single 16S rDNA copy was performed by cutting a restriction fragment from agarose gel and using 2 μl of the melted agarose as the PCR template. .. Restriction analysis of PCR products was done with 10 U of Dra I (New England Biolabs, Hertfordshire, United Kingdom) by following the supplier's recommendations. ) and with sequences deposited in the Ribosomal Database Project, version 7.0, by using SIMILARITY RANK and SUGGEST TREE ( ).

    Article Title: Nature of guanine oxidation in RNA via the flash-quench technique versus direct oxidation by a metal oxo complex
    Article Snippet: Dra I, T4 RNA ligase, and T4 RNA ligase buffer were purchased from New England Biolabs. .. Reliant fast-lane agarose gel systems were purchased from Lonza.

    Article Title: Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome
    Article Snippet: Extracted DNA was pooled (60 ng) and digested with Dra I (100 units; New England Biolabs, Ipswich, MA, USA) at 37°C for 16 hours. .. The fragments were separated by 1.2% agarose gel electrophoresis (2 hours; 60 volts), and 150–250 bp-fragments were eluted (yielding 1069 ng), end-repaired, and ligated to Illumina's oligonucleotide adapters.

    Article Title: Nicotiana attenuata LECTIN RECEPTOR KINASE1 Suppresses the Insect-Mediated Inhibition of Induced Defense Responses during Manduca sexta Herbivory [C] Herbivory [C] [W]
    Article Snippet: .. DNA samples (10 μg) were digested with Eco RV and Dra I (New England Biolabs) overnight at 37°C according to commercial instructions and separated on a 1% (w/v) agarose gel using standard conditions. ..

    Article Title: RsaI but not DraI polymorphism in CYP2E1 gene increases the risk of gastrointestinal cancer in Malaysians: a case-control study
    Article Snippet: The PCR products were subjected to overnight 2.5 U Rsa I and 5.0 U Dra I (New England BioLabs Inc, Ipswich, Massachusetts, USA restriction enzymes digestion for C-1019T and T7678A SNPs, respectively. .. The digested fragments were electrophoresed and analysed on 2% agarose gel stained with ethidium bromide in 1×TAE buffer.

    In Vitro:

    Article Title: Smads bind directly to the Jun family of AP-1 transcription factors
    Article Snippet: Full length JunB in pGEM4 was digested with Bsp HI, BssHII, or Dra I (NEB). .. The full length construct and the digested DNAs were used as templates for in vitro transcription and translation (TNT) with [35 S]methionine in rabbit reticulocyte lysates (Promega).

    Next-Generation Sequencing:

    Article Title: Chromatin Landscapes of Retroviral and Transposon Integration Profiles
    Article Snippet: The ligated DNA was cut with Dra-I (New England Biolabs). .. The ligation reactions were amplified in two rounds of PCR to generate high throughput sequencing libraries (for details see ).

    Quantitation Assay:

    Article Title: Colorimetric Assay for Exon 7 SMN1/SMN2 Single Nucleotide Polymorphism Using Gold Nanoprobes
    Article Snippet: Dra I and Dde I enzymes were obtained from New England Biolab. .. Nap-5 column, OliGreen ssDNA Quantitation kit, and QIAquick PCR Purification Kit were bought from GE Healthcare, Invitrogen, and QIAGEN, respectively.

    Produced:

    Article Title: Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome
    Article Snippet: Library construction and sequencing DNA was extracted from five individual boars produced from a cross between Landrace and Pietrain. .. Extracted DNA was pooled (60 ng) and digested with Dra I (100 units; New England Biolabs, Ipswich, MA, USA) at 37°C for 16 hours.

    Activation Assay:

    Article Title: RsaI but not DraI polymorphism in CYP2E1 gene increases the risk of gastrointestinal cancer in Malaysians: a case-control study
    Article Snippet: In contrast, primers 5′-TCGTCAGTTCCTGAAAGCAGG-3′ (forward) and 5′-GAGCTCTGATGCAAGTATCGCA-3′ (reverse) were used to amplify the T7678A SNP and the PCR conditions were as followed: initial activation for 5 min at 94°C, 35 cycles at 94°C for 1 min, 60°C for 1 min and 72°C for 2 min, followed by a final extension for 7 min at 72°C. .. The PCR products were subjected to overnight 2.5 U Rsa I and 5.0 U Dra I (New England BioLabs Inc, Ipswich, Massachusetts, USA restriction enzymes digestion for C-1019T and T7678A SNPs, respectively.

    Molecular Weight:

    Article Title: Chromosomal Integration of a Cephalosporinase Gene from Acinetobacter baumannii into Oligella urethralis as a Source of Acquired Resistance to ?-Lactams
    Article Snippet: Macrorestriction analysis of whole-cell DNA of O. urethralis COH-1 was done by the pulsed-field gel electrophoresis (PFGE) technique with Xba I, Spe I, Dra I, Apa I, and Sfi I (New England Biolabs), as reported previously ( , ). .. The sizes of the fragments generated with Ceu I fragment I were determined by comparison with those of a bacteriophage lambda DNA molecular weight marker (Bio-Rad).

    Marker:

    Article Title: Chromosomal Integration of a Cephalosporinase Gene from Acinetobacter baumannii into Oligella urethralis as a Source of Acquired Resistance to ?-Lactams
    Article Snippet: Macrorestriction analysis of whole-cell DNA of O. urethralis COH-1 was done by the pulsed-field gel electrophoresis (PFGE) technique with Xba I, Spe I, Dra I, Apa I, and Sfi I (New England Biolabs), as reported previously ( , ). .. The sizes of the fragments generated with Ceu I fragment I were determined by comparison with those of a bacteriophage lambda DNA molecular weight marker (Bio-Rad).

    Staining:

    Article Title: RsaI but not DraI polymorphism in CYP2E1 gene increases the risk of gastrointestinal cancer in Malaysians: a case-control study
    Article Snippet: The PCR products were subjected to overnight 2.5 U Rsa I and 5.0 U Dra I (New England BioLabs Inc, Ipswich, Massachusetts, USA restriction enzymes digestion for C-1019T and T7678A SNPs, respectively. .. The digested fragments were electrophoresed and analysed on 2% agarose gel stained with ethidium bromide in 1×TAE buffer.

    Variant Assay:

    Article Title: Association between folate metabolism-related polymorphisms and colorectal cancer risk
    Article Snippet: For the 1298A > C polymorphism, a single band of 138 bp indicated the homozygous wild-type genotype and two fragments of 119 and 19 bp indicated the homozygous minor variant genotype. .. The TS 1494del6 polymorphism was characterized using Dra I (New England BioLabs, Ipswich, MA, USA) digestion.

    Article Title: Polymorphisms in thymidylate synthase gene and susceptibility to breast cancer in a Chinese population: a case-control analysis
    Article Snippet: For the TS 3'-UTR del6 polymorphism, 152 bp (i.e. del6) or 158 bp fragments (i.e. ins6) were amplified and then digested by Dra I (New England BioLabs, Inc., Beverly, MA). .. The variant (ins6) allele produces two fragments of 88 and 70 bp, while the wild-type (del6) allele produces a single 152-bp fragment.

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    New England Biolabs dra i
    Expression of the 46-bp insertion and detection of the two types of 16S rRNA by <t>RT-PCR.</t> The strains analyzed are indicated at the top. (A) Lanes +, use of consensual primer pair 27f and 590r; lanes ins, use of an insertion-specific pair of primers, ins1 and 590r. (B) Lanes +, RT-PCR products obtained with the primers 27f and 590r; lanes Dra I, RT-PCR products obtained in + lanes digested by Dra I. Lanes − (A and B), negative controls performed on the RNA of strain PR17/sat without reverse transcription and with the primers 27f and 590r (negative controls were also obtained for other strains and for the primers ins1 and 590r but are not shown); lane M, 100-bp DNA ladder (Promega) as a molecular weight marker.
    Dra I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dra i/product/New England Biolabs
    Average 95 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    dra i - by Bioz Stars, 2020-02
    95/100 stars
      Buy from Supplier

    85
    New England Biolabs restriction enzyme dra i
    Examples of genomic DNA macrorestriction profiles of S. maltophilia produced by PFGE after <t>Dra</t> I digestion. Lane 1, c12; lane 2, c1; lane 3, c7; lane 4, c17; lane 5, c5; lane 6, e1; lane 7, e2; lane 8, lambda ladder marker (size range, 225 to 1,900 kb); lane 9, e9; lane 10, e10; lane 11, t20; lane 12, e18; lane 13, e5.
    Restriction Enzyme Dra I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/restriction enzyme dra i/product/New England Biolabs
    Average 85 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    restriction enzyme dra i - by Bioz Stars, 2020-02
    85/100 stars
      Buy from Supplier

    Image Search Results


    Expression of the 46-bp insertion and detection of the two types of 16S rRNA by RT-PCR. The strains analyzed are indicated at the top. (A) Lanes +, use of consensual primer pair 27f and 590r; lanes ins, use of an insertion-specific pair of primers, ins1 and 590r. (B) Lanes +, RT-PCR products obtained with the primers 27f and 590r; lanes Dra I, RT-PCR products obtained in + lanes digested by Dra I. Lanes − (A and B), negative controls performed on the RNA of strain PR17/sat without reverse transcription and with the primers 27f and 590r (negative controls were also obtained for other strains and for the primers ins1 and 590r but are not shown); lane M, 100-bp DNA ladder (Promega) as a molecular weight marker.

    Journal: Journal of Bacteriology

    Article Title: Atypical 16S rRNA Gene Copies in Ochrobactrum intermedium Strains Reveal a Large Genomic Rearrangement by Recombination between rrn Copies

    doi: 10.1128/JB.185.9.2901-2909.2003

    Figure Lengend Snippet: Expression of the 46-bp insertion and detection of the two types of 16S rRNA by RT-PCR. The strains analyzed are indicated at the top. (A) Lanes +, use of consensual primer pair 27f and 590r; lanes ins, use of an insertion-specific pair of primers, ins1 and 590r. (B) Lanes +, RT-PCR products obtained with the primers 27f and 590r; lanes Dra I, RT-PCR products obtained in + lanes digested by Dra I. Lanes − (A and B), negative controls performed on the RNA of strain PR17/sat without reverse transcription and with the primers 27f and 590r (negative controls were also obtained for other strains and for the primers ins1 and 590r but are not shown); lane M, 100-bp DNA ladder (Promega) as a molecular weight marker.

    Article Snippet: Restriction analysis of PCR products was done with 10 U of Dra I (New England Biolabs, Hertfordshire, United Kingdom) by following the supplier's recommendations. ) and with sequences deposited in the Ribosomal Database Project, version 7.0, by using SIMILARITY RANK and SUGGEST TREE ( ).

    Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Molecular Weight, Marker

    Effect of an abasic site on DNA synthesis by reconstituted phage T4 replication complexes. ( A ) An abasic site blocks DNA synthesis by T4 DNA polymerase holoenzyme. 32 P-end-labeled 21mer #7 annealed with 120mer #3 (lanes 1, 3, 5, 7, 9, 11, 13 and 15) or with the same oligomer containing an abasic site at position 99 (120mer #4) (lanes 2, 4, 6, 8, 10, 12, 14 and 16) was incubated with either T4 gp43 (lanes 5, 6, 13 and 14) or the exonuclease-deficient gp43D219A (lanes 7, 8, 15 and 16) in the presence of gp44/62, gp45 and gp32 for the indicated times, and the products were separated in a 10% polyacrylamide gel + 6 M urea. Note that in the substrate with an abasic site, the first nucleotide to be incorporated into the 32 P-end-labeled 21mer is opposite the abasic site. ( B ) Block to lagging-strand synthesis imposed by the abasic site. Products of DNA synthesized by reconstituted T4 replication complexes in the presence of [α- 32 P]dCTP and 240mer circular ssDNA annealed with the 120mer ssDNA without (lanes 1 and 2) or with (lanes 3 and 4) abasic site were digested (lanes 2 and 4) or not (lanes 1 and 3) by Dra I and separated in a 6% polyacrylamide gel + 6 M urea along with marker DNA. Note that the 240mer circular ssDNA has a unique Dra I site. Upon Dra I cleavage of the replication products, the major 240mer fragment is formed along with other fragments that are located between the Dra I site and either the 3′ or 5′ ends of Okazaki fragments. Arrows show positions of the major 240-nt Dra I fragment and the 126-nt fragment located between the Dra I site and the 3′ end of the nascent fragment terminated by the abasic site. ( C ) DNA products were synthesized by reconstituted T4 replication complexes in the presence of [α- 32 P]dTTP and of 240mer circular ssDNA annealed with 120mer ssDNA without (lanes 1–3) or with (lanes 4–6) an abasic site, and separated in a 0.6% alkali gel.

    Journal: Nucleic Acids Research

    Article Title: Characterization of DNA synthesis catalyzed by bacteriophage T4 replication complexes reconstituted on synthetic circular substrates

    doi:

    Figure Lengend Snippet: Effect of an abasic site on DNA synthesis by reconstituted phage T4 replication complexes. ( A ) An abasic site blocks DNA synthesis by T4 DNA polymerase holoenzyme. 32 P-end-labeled 21mer #7 annealed with 120mer #3 (lanes 1, 3, 5, 7, 9, 11, 13 and 15) or with the same oligomer containing an abasic site at position 99 (120mer #4) (lanes 2, 4, 6, 8, 10, 12, 14 and 16) was incubated with either T4 gp43 (lanes 5, 6, 13 and 14) or the exonuclease-deficient gp43D219A (lanes 7, 8, 15 and 16) in the presence of gp44/62, gp45 and gp32 for the indicated times, and the products were separated in a 10% polyacrylamide gel + 6 M urea. Note that in the substrate with an abasic site, the first nucleotide to be incorporated into the 32 P-end-labeled 21mer is opposite the abasic site. ( B ) Block to lagging-strand synthesis imposed by the abasic site. Products of DNA synthesized by reconstituted T4 replication complexes in the presence of [α- 32 P]dCTP and 240mer circular ssDNA annealed with the 120mer ssDNA without (lanes 1 and 2) or with (lanes 3 and 4) abasic site were digested (lanes 2 and 4) or not (lanes 1 and 3) by Dra I and separated in a 6% polyacrylamide gel + 6 M urea along with marker DNA. Note that the 240mer circular ssDNA has a unique Dra I site. Upon Dra I cleavage of the replication products, the major 240mer fragment is formed along with other fragments that are located between the Dra I site and either the 3′ or 5′ ends of Okazaki fragments. Arrows show positions of the major 240-nt Dra I fragment and the 126-nt fragment located between the Dra I site and the 3′ end of the nascent fragment terminated by the abasic site. ( C ) DNA products were synthesized by reconstituted T4 replication complexes in the presence of [α- 32 P]dTTP and of 240mer circular ssDNA annealed with 120mer ssDNA without (lanes 1–3) or with (lanes 4–6) an abasic site, and separated in a 0.6% alkali gel.

    Article Snippet: T4 DNA ligase, Dra I and polynucleotide kinase were from New England Biolabs.

    Techniques: DNA Synthesis, Labeling, Incubation, Blocking Assay, Synthesized, Marker

    PFGE profiles of Sfi I-, Apa I-, Dra I-, Spe I-, and Xba I-digested whole-cell DNA of O. urethralis COH-1 (A; lanes 1 to 5) and their Southern transfer, followed by hybridization with internal probes specific for bla ABA-1 (B) and bla CARB-8 (C). Lanes M, molecular size markers

    Journal: Antimicrobial Agents and Chemotherapy

    Article Title: Chromosomal Integration of a Cephalosporinase Gene from Acinetobacter baumannii into Oligella urethralis as a Source of Acquired Resistance to ?-Lactams

    doi: 10.1128/AAC.47.5.1536-1542.2003

    Figure Lengend Snippet: PFGE profiles of Sfi I-, Apa I-, Dra I-, Spe I-, and Xba I-digested whole-cell DNA of O. urethralis COH-1 (A; lanes 1 to 5) and their Southern transfer, followed by hybridization with internal probes specific for bla ABA-1 (B) and bla CARB-8 (C). Lanes M, molecular size markers

    Article Snippet: Macrorestriction analysis of whole-cell DNA of O. urethralis COH-1 was done by the pulsed-field gel electrophoresis (PFGE) technique with Xba I, Spe I, Dra I, Apa I, and Sfi I (New England Biolabs), as reported previously ( , ).

    Techniques: Hybridization

    Examples of genomic DNA macrorestriction profiles of S. maltophilia produced by PFGE after Dra I digestion. Lane 1, c12; lane 2, c1; lane 3, c7; lane 4, c17; lane 5, c5; lane 6, e1; lane 7, e2; lane 8, lambda ladder marker (size range, 225 to 1,900 kb); lane 9, e9; lane 10, e10; lane 11, t20; lane 12, e18; lane 13, e5.

    Journal: Journal of Clinical Microbiology

    Article Title: Genotypic and Phenotypic Relationships between Clinical and Environmental Isolates of Stenotrophomonas maltophilia

    doi:

    Figure Lengend Snippet: Examples of genomic DNA macrorestriction profiles of S. maltophilia produced by PFGE after Dra I digestion. Lane 1, c12; lane 2, c1; lane 3, c7; lane 4, c17; lane 5, c5; lane 6, e1; lane 7, e2; lane 8, lambda ladder marker (size range, 225 to 1,900 kb); lane 9, e9; lane 10, e10; lane 11, t20; lane 12, e18; lane 13, e5.

    Article Snippet: Agarose plugs were digested with restriction enzyme Dra I (New England Biolabs, Schalbach, Germany) for 20 h at 35°C according to the manufacturer's recommendations.

    Techniques: Produced, Marker