dnase i reaction buffer  (New England Biolabs)


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    Name:
    DNase I Reaction Buffer
    Description:
    DNase I Reaction Buffer 6 0 ml
    Catalog Number:
    b0303s
    Price:
    23
    Size:
    6 0 ml
    Category:
    Buffers
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    New England Biolabs dnase i reaction buffer
    DNase I Reaction Buffer
    DNase I Reaction Buffer 6 0 ml
    https://www.bioz.com/result/dnase i reaction buffer/product/New England Biolabs
    Average 90 stars, based on 23 article reviews
    Price from $9.99 to $1999.99
    dnase i reaction buffer - by Bioz Stars, 2020-01
    90/100 stars

    Images

    1) Product Images from "Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA"

    Article Title: Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA

    Journal: Molecular Microbiology

    doi: 10.1111/j.1365-2958.2010.07292.x

    CbpA protects plasmid DNA from degradation by nucleases. A. The panel shows naked plasmid and complexes with CbpA run on a 1% agarose gel. Plasmid (30 ng) was pre-incubated with 0, 0.5, 1.0, or 2.0 µM CbpA. Note that only every other lane has been loaded on the gel. B. The panel shows plasmid run on a 1% agarose gel. Plasmids (77 ng) were treated with different combinations of DNase I, BSA (1, 2 or 3 µM) and CbpA (1, 2 or 3 µM).
    Figure Legend Snippet: CbpA protects plasmid DNA from degradation by nucleases. A. The panel shows naked plasmid and complexes with CbpA run on a 1% agarose gel. Plasmid (30 ng) was pre-incubated with 0, 0.5, 1.0, or 2.0 µM CbpA. Note that only every other lane has been loaded on the gel. B. The panel shows plasmid run on a 1% agarose gel. Plasmids (77 ng) were treated with different combinations of DNase I, BSA (1, 2 or 3 µM) and CbpA (1, 2 or 3 µM).

    Techniques Used: Plasmid Preparation, Agarose Gel Electrophoresis, Incubation

    2) Product Images from "A Thermonuclease of Neisseria gonorrhoeae Enhances Bacterial Escape From Killing by Neutrophil Extracellular Traps"

    Article Title: A Thermonuclease of Neisseria gonorrhoeae Enhances Bacterial Escape From Killing by Neutrophil Extracellular Traps

    Journal: The Journal of Infectious Diseases

    doi: 10.1093/infdis/jiv031

    Nuc cleaves human neutrophil and neutrophil extracellular trap DNA. A , Human neutrophil DNA was incubated with increasing amounts of Nuc or DNAse I and separated on ethidium bromide–stained agarose gels. B , Phorbol 12-myristate 13-acetate–stimulated
    Figure Legend Snippet: Nuc cleaves human neutrophil and neutrophil extracellular trap DNA. A , Human neutrophil DNA was incubated with increasing amounts of Nuc or DNAse I and separated on ethidium bromide–stained agarose gels. B , Phorbol 12-myristate 13-acetate–stimulated

    Techniques Used: Incubation, Staining

    3) Product Images from "Glucose-Dependent Activation of Bacillus anthracis Toxin Gene Expression and Virulence Requires the Carbon Catabolite Protein CcpA ▿ Toxin Gene Expression and Virulence Requires the Carbon Catabolite Protein CcpA ▿ †"

    Article Title: Glucose-Dependent Activation of Bacillus anthracis Toxin Gene Expression and Virulence Requires the Carbon Catabolite Protein CcpA ▿ Toxin Gene Expression and Virulence Requires the Carbon Catabolite Protein CcpA ▿ †

    Journal: Journal of Bacteriology

    doi: 10.1128/JB.01656-09

    DNase I footprinting analysis of CcpA binding to the atxA (A and B) and BAS3893 (C and D) promoters. Fragments labeled with γ- 32 P at the 5′ end (coding strand) (A and C) or at the 3′ end (noncoding strand) (B and D) were incubated
    Figure Legend Snippet: DNase I footprinting analysis of CcpA binding to the atxA (A and B) and BAS3893 (C and D) promoters. Fragments labeled with γ- 32 P at the 5′ end (coding strand) (A and C) or at the 3′ end (noncoding strand) (B and D) were incubated

    Techniques Used: Footprinting, Binding Assay, Labeling, Incubation

    4) Product Images from "Enterococcus faecalis Virulence Regulator FsrA Binding to Target Promoters ▿"

    Article Title: Enterococcus faecalis Virulence Regulator FsrA Binding to Target Promoters ▿

    Journal: Journal of Bacteriology

    doi: 10.1128/JB.01522-10

    DNase I footprinting analysis of the promoter-regulatory regions of fsrB (A) and gelE (B). The labeled DNA fragments were obtained as described in Materials and Methods. The fragments were incubated with different amounts of FsrA-His6 before DNase I treatment.
    Figure Legend Snippet: DNase I footprinting analysis of the promoter-regulatory regions of fsrB (A) and gelE (B). The labeled DNA fragments were obtained as described in Materials and Methods. The fragments were incubated with different amounts of FsrA-His6 before DNase I treatment.

    Techniques Used: Footprinting, Labeling, Incubation

    5) Product Images from "Structure and decoy-mediated inhibition of the SOX18/Prox1-DNA interaction"

    Article Title: Structure and decoy-mediated inhibition of the SOX18/Prox1-DNA interaction

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkw130

    Modified SOX decoys show enhanced stability and repress reporter gene transactivation. ( A ) Decoys were incubated in mouse serum and their integrity was assessed by urea-PAGE and SYBR gold nucleic acid staining as a function of incubation time. The ‘0’ lane marks a sample taken immediately after mixing with serum and numbers denote time in hours. UD: undigested decoys. SO: serum only. ( B ) Decoys were incubated with DNase I and analysed as in (A). ( C ) The melting of decoys was monitored by heating 1 μM DNA to 90°C at 1°C/min and recording the absorbance at 260 nm. ( D ) SOX18 exogenously expressed in COS-7 cells activates the expression of a luciferase reporter under control of a regulatory region derived from the VCAM-1 gene ( 38 ) in a dose-dependent manner. The inlet illustrates the assay set-up. ( E ) The effect of decoys at 1000 nM on the VCAM-1 reporter activity was compared 48 h post-transfection using 50 ng of SOX18 plasmid. ( F ) Effects of the PSCIRC on luciferase expression at different concentrations. ( G ) Expression of selected genes detected by RT-qPCR in the absence or presence of the PSCIRC. The mean and standard deviation from three experiments each carried out in triplicates is shown. The asterisks (**) denote P
    Figure Legend Snippet: Modified SOX decoys show enhanced stability and repress reporter gene transactivation. ( A ) Decoys were incubated in mouse serum and their integrity was assessed by urea-PAGE and SYBR gold nucleic acid staining as a function of incubation time. The ‘0’ lane marks a sample taken immediately after mixing with serum and numbers denote time in hours. UD: undigested decoys. SO: serum only. ( B ) Decoys were incubated with DNase I and analysed as in (A). ( C ) The melting of decoys was monitored by heating 1 μM DNA to 90°C at 1°C/min and recording the absorbance at 260 nm. ( D ) SOX18 exogenously expressed in COS-7 cells activates the expression of a luciferase reporter under control of a regulatory region derived from the VCAM-1 gene ( 38 ) in a dose-dependent manner. The inlet illustrates the assay set-up. ( E ) The effect of decoys at 1000 nM on the VCAM-1 reporter activity was compared 48 h post-transfection using 50 ng of SOX18 plasmid. ( F ) Effects of the PSCIRC on luciferase expression at different concentrations. ( G ) Expression of selected genes detected by RT-qPCR in the absence or presence of the PSCIRC. The mean and standard deviation from three experiments each carried out in triplicates is shown. The asterisks (**) denote P

    Techniques Used: Modification, Incubation, Polyacrylamide Gel Electrophoresis, Staining, Expressing, Luciferase, Derivative Assay, Activity Assay, Transfection, Plasmid Preparation, Quantitative RT-PCR, Standard Deviation

    6) Product Images from "A peculiar IclR family transcription factor regulates para-hydroxybenzoate catabolism in Streptomyces coelicolor"

    Article Title: A peculiar IclR family transcription factor regulates para-hydroxybenzoate catabolism in Streptomyces coelicolor

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkx1234

    Biochemical and bioinformatic analyses of PobR, a negative regulator of pobA . ( A ) Predicted domains organization of PobR protein. Both N-terminal domain and C-terminal domains of PobR are homologous to intact IclR family transcription factors. ( B ) The overall view of the region upstream of the pobA open reading frame (ORF), highlighting the transcription start site of pobA (turquoise), putative -35 and -10 pobA promoter elements (underlined and highlighted in orange) and the PobR regulator binding site sequence (in bold and boxed). ( C ) DNA binding of PobR was assessed using agarose electrophoretic mobility shift assays (EMSAs). A PCR-amplified DNA fragment spanning the entire region between the transcription and translation start sites (5′-untranslated region) was titrated with PobR. In comparison with the unbound DNA probe in the electrophoresis, retarded migration of the DNA probe was observed upon addition of PobR. Bands representing the PobR-DNA probe complex and the unbound DNA probe are highlighted by arrows. For a negative control, a 486-bp fragment amplified from hrdB ORF, which does not contain the PobR binding site, was used. ( D ) The PobR binding site upstream of the pobA ORF was mapped using DNase I footprinting analysis. A 5′- 32 P end-labeled 118-bp DNA fragment was digested with DNase I in the absence and presence of heterologously produced and purified PobR. In comparison with the DNA digest in the absence of PobR, a protected region was observed when DNA was incubated with PobR before digestion. Sequencing ladders indicated by lanes C/T and A/G were generated via Maxam-Gilbert reactions. The reactions were performed in duplicate. ( E ) Sequence alignment of the regions upstream of the pobA ORFs in various streptomycetes. Putative –35 and –10 pobA promoter elements and PobR binding site sequence (boxed) identified in DNase I footprinting reaction are conserved in several members of the Streptomyces genus. A conserved PobR binding site was also identified using the Gibbs Motif Sampler ( 47 ). Sequence logo images ( 51 ) depict the sequence conservation of PobR binding site.
    Figure Legend Snippet: Biochemical and bioinformatic analyses of PobR, a negative regulator of pobA . ( A ) Predicted domains organization of PobR protein. Both N-terminal domain and C-terminal domains of PobR are homologous to intact IclR family transcription factors. ( B ) The overall view of the region upstream of the pobA open reading frame (ORF), highlighting the transcription start site of pobA (turquoise), putative -35 and -10 pobA promoter elements (underlined and highlighted in orange) and the PobR regulator binding site sequence (in bold and boxed). ( C ) DNA binding of PobR was assessed using agarose electrophoretic mobility shift assays (EMSAs). A PCR-amplified DNA fragment spanning the entire region between the transcription and translation start sites (5′-untranslated region) was titrated with PobR. In comparison with the unbound DNA probe in the electrophoresis, retarded migration of the DNA probe was observed upon addition of PobR. Bands representing the PobR-DNA probe complex and the unbound DNA probe are highlighted by arrows. For a negative control, a 486-bp fragment amplified from hrdB ORF, which does not contain the PobR binding site, was used. ( D ) The PobR binding site upstream of the pobA ORF was mapped using DNase I footprinting analysis. A 5′- 32 P end-labeled 118-bp DNA fragment was digested with DNase I in the absence and presence of heterologously produced and purified PobR. In comparison with the DNA digest in the absence of PobR, a protected region was observed when DNA was incubated with PobR before digestion. Sequencing ladders indicated by lanes C/T and A/G were generated via Maxam-Gilbert reactions. The reactions were performed in duplicate. ( E ) Sequence alignment of the regions upstream of the pobA ORFs in various streptomycetes. Putative –35 and –10 pobA promoter elements and PobR binding site sequence (boxed) identified in DNase I footprinting reaction are conserved in several members of the Streptomyces genus. A conserved PobR binding site was also identified using the Gibbs Motif Sampler ( 47 ). Sequence logo images ( 51 ) depict the sequence conservation of PobR binding site.

    Techniques Used: Binding Assay, Sequencing, Electrophoretic Mobility Shift Assay, Polymerase Chain Reaction, Amplification, Electrophoresis, Migration, Negative Control, Footprinting, Labeling, Produced, Purification, Incubation, Generated

    7) Product Images from "Transcriptional Regulation of the Vanillate Utilization Genes (vanABK Operon) of Corynebacterium glutamicum by VanR, a PadR-Like Repressor"

    Article Title: Transcriptional Regulation of the Vanillate Utilization Genes (vanABK Operon) of Corynebacterium glutamicum by VanR, a PadR-Like Repressor

    Journal: Journal of Bacteriology

    doi: 10.1128/JB.02431-14

    Identification of the VanR binding site at the promoter region of the vanABK operon (P vanABK ). The coding strand of P vanABK DNA (amplified from pJOE7658.1) was sequenced using oligonucleotide primer s8821 (A), while the noncoding strand was sequenced using oligonucleotide primer s8753 (B) according to Sanger's dideoxy chain termination method. A, C, G, and T correspond to ddATP, ddCTP, ddGTP, and ddTTP, respectively, used in the sequencing reactions. DNase I digestion of the coding or noncoding strands was carried out in the presence (+) or absence (−) of purified VanR. (C) Promoter sequence of the vanABK operon, including the −35 and −10 boxes (rectangles) and the transcription start site (+1; rectangle). The VanR binding site is indicated by a boldfaced line. The probable GlxR operator sequence is underlined. The start codon of VanA is depicted by an arrow.
    Figure Legend Snippet: Identification of the VanR binding site at the promoter region of the vanABK operon (P vanABK ). The coding strand of P vanABK DNA (amplified from pJOE7658.1) was sequenced using oligonucleotide primer s8821 (A), while the noncoding strand was sequenced using oligonucleotide primer s8753 (B) according to Sanger's dideoxy chain termination method. A, C, G, and T correspond to ddATP, ddCTP, ddGTP, and ddTTP, respectively, used in the sequencing reactions. DNase I digestion of the coding or noncoding strands was carried out in the presence (+) or absence (−) of purified VanR. (C) Promoter sequence of the vanABK operon, including the −35 and −10 boxes (rectangles) and the transcription start site (+1; rectangle). The VanR binding site is indicated by a boldfaced line. The probable GlxR operator sequence is underlined. The start codon of VanA is depicted by an arrow.

    Techniques Used: Binding Assay, Amplification, Sequencing, Purification

    Studying the VanR binding site at P vanABK and the properties of VanR-DNA complex. (A) Mutation of the VanR binding site at P vanABK . The VanR binding site determined by DNase I footprinting is shown by boldface lines. Transcription start sites of the P vanABK wild-type sequence and the mutants thereof are enclosed by a rectangle. The start codon for eGFP is highlighted in gray. Two inverted repeats (IR1 and IR2) inside the VanR binding site are indicated by arrows. The inducibility of P vanABK and its mutants was investigated in CGXII medium with the addition of 2 mM vanillate as the inducer. Production of eGFP was measured after 6 h of induction. (B) Binding of VanR to the Cy5-labeled P vanABK wild type and its derivatives. The 2.5 nM Cy5-labeled P vanABK DNA fragment was incubated with (+) or without (−) 49.5 nM purified VanR. Cy5-labeled DNA fragments were generated by PCR using oligonucleotides s9177 and s9071. (C) The migration pattern of the Cy5-P vanABK DNA-VanR complex at the equilibrium point of reaction was studied by gel mobility shift assay. The migration of the Cy5-labeled DNA (2.5 nM) without VanR (−) was compared to the same sample with 49.5 nM VanR (+). The amount of VanR added to the gel mobility shift reactions were 29.5 nM (pJOE8297.6) and 17.4 nM (pJOE8077.1 and pJOE8300.2) according to the determined K D values.
    Figure Legend Snippet: Studying the VanR binding site at P vanABK and the properties of VanR-DNA complex. (A) Mutation of the VanR binding site at P vanABK . The VanR binding site determined by DNase I footprinting is shown by boldface lines. Transcription start sites of the P vanABK wild-type sequence and the mutants thereof are enclosed by a rectangle. The start codon for eGFP is highlighted in gray. Two inverted repeats (IR1 and IR2) inside the VanR binding site are indicated by arrows. The inducibility of P vanABK and its mutants was investigated in CGXII medium with the addition of 2 mM vanillate as the inducer. Production of eGFP was measured after 6 h of induction. (B) Binding of VanR to the Cy5-labeled P vanABK wild type and its derivatives. The 2.5 nM Cy5-labeled P vanABK DNA fragment was incubated with (+) or without (−) 49.5 nM purified VanR. Cy5-labeled DNA fragments were generated by PCR using oligonucleotides s9177 and s9071. (C) The migration pattern of the Cy5-P vanABK DNA-VanR complex at the equilibrium point of reaction was studied by gel mobility shift assay. The migration of the Cy5-labeled DNA (2.5 nM) without VanR (−) was compared to the same sample with 49.5 nM VanR (+). The amount of VanR added to the gel mobility shift reactions were 29.5 nM (pJOE8297.6) and 17.4 nM (pJOE8077.1 and pJOE8300.2) according to the determined K D values.

    Techniques Used: Binding Assay, Mutagenesis, Footprinting, Sequencing, Labeling, Incubation, Purification, Generated, Polymerase Chain Reaction, Migration, Mobility Shift

    8) Product Images from "A novel method for the efficient and selective identification of 5-hydroxymethylcytosine in genomic DNA"

    Article Title: A novel method for the efficient and selective identification of 5-hydroxymethylcytosine in genomic DNA

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkr051

    The β-gt can specifically modify 5hmC residues at a high efficiency. ( a ) Oligonucleotides that were either incubated in the presence or absence of the β-gt were digested with Taq I, treated with alkaline phosphatase, 5′-end labeled using T4 polynucleotide kinase and digested to 5′-mononucleotides using DNase I and Snake Venom Phosphodiesterase. Radiolabeled mononucleotides were analyzed by two-dimensional TLC. C, 3′-deoxyribocytosine-5′-monophosphate; T, 3′-deoxyribothymidine-5′-monophosphate; 5meC, 3′-deoxyribo-N5-methylcytosine-5′-monophosphate; 5hmC, 3′-deoxyribo-N5-hydroxymethylcytosine-5′-monophosphate. ( b ) HPLC coupled to tandem mass spectrometry was used to measure the efficiency of the β-gt reaction. Substrates analyzed were 2.7 kb linear PCR products of pUC18: the dC substrate contained only cytosine residues; the 5meC substrate was created by methylating the CpG dinucleotide of the cytosine substrate; the 5hmC substrate was created by using d5hmC in place of dCTP in the PCR reactions; the β-glu-5hmC substrate was created by incubating the 5hmC substrate with the β-gt in the presence of UDP-glucose. Control DNA was prepared from salmon sperm. LC/MS/MS chromatograms of the cytosine residues from each of the substrates are presented. Abbreviations: dC, 3′-deoxyribocytosine; 5me(dC), 3′-deoxyribo-N5-methylcytosine; 5hm(dC), 3′-deoxyribo-N5-hydroxymethylcytosine; 5-glu-hm(dC), 3′-deoxyribo-N5-(β- d -glucosyl(hydroxymethyl))cytosine. Asterisks indictes that cytosines are only 5meC modified at CpG sequences.
    Figure Legend Snippet: The β-gt can specifically modify 5hmC residues at a high efficiency. ( a ) Oligonucleotides that were either incubated in the presence or absence of the β-gt were digested with Taq I, treated with alkaline phosphatase, 5′-end labeled using T4 polynucleotide kinase and digested to 5′-mononucleotides using DNase I and Snake Venom Phosphodiesterase. Radiolabeled mononucleotides were analyzed by two-dimensional TLC. C, 3′-deoxyribocytosine-5′-monophosphate; T, 3′-deoxyribothymidine-5′-monophosphate; 5meC, 3′-deoxyribo-N5-methylcytosine-5′-monophosphate; 5hmC, 3′-deoxyribo-N5-hydroxymethylcytosine-5′-monophosphate. ( b ) HPLC coupled to tandem mass spectrometry was used to measure the efficiency of the β-gt reaction. Substrates analyzed were 2.7 kb linear PCR products of pUC18: the dC substrate contained only cytosine residues; the 5meC substrate was created by methylating the CpG dinucleotide of the cytosine substrate; the 5hmC substrate was created by using d5hmC in place of dCTP in the PCR reactions; the β-glu-5hmC substrate was created by incubating the 5hmC substrate with the β-gt in the presence of UDP-glucose. Control DNA was prepared from salmon sperm. LC/MS/MS chromatograms of the cytosine residues from each of the substrates are presented. Abbreviations: dC, 3′-deoxyribocytosine; 5me(dC), 3′-deoxyribo-N5-methylcytosine; 5hm(dC), 3′-deoxyribo-N5-hydroxymethylcytosine; 5-glu-hm(dC), 3′-deoxyribo-N5-(β- d -glucosyl(hydroxymethyl))cytosine. Asterisks indictes that cytosines are only 5meC modified at CpG sequences.

    Techniques Used: Incubation, Labeling, Thin Layer Chromatography, High Performance Liquid Chromatography, Mass Spectrometry, Polymerase Chain Reaction, Liquid Chromatography with Mass Spectroscopy, Modification

    Related Articles

    Clone Assay:

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: The PCR products were subcloned using the TOPO TA Cloning® Kit with pCR®2.1-TOPO® vector and TOP 10 cells (Invitrogen Corporation), and cloned DNA fragments were reamplified by direct PCR of the colony with M13f and M13r primers, and sequenced using ABI BigDye® Terminator reaction mixture and an ABI PRISM® 3730 DNA Analyzer (Applied Biosystems). .. Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25 –50 bp.

    Article Title: Highly stable hexitol based XNA aptamers targeting the vascular endothelial growth factor
    Article Snippet: Materials Deoxyribonucleoside triphosphates (dNTPs), Taq DNA polymerase, 10× ThermoPol buffer, MgSO4 , Lambda exonuclease, 10× Lambda exonuclease reaction buffer, 10× DNase I reaction buffer and 6× purple gel loading dye were purchased from New England Biolabs. .. Turbo DNase I, magnetic beads (Dynabeads M-280 Streptavidin), SYBR Gold nucleic acid gel stain, CloneJet PCR cloning kit, Micro BCA protein assay kit, the biotinylation reagent EZ-Link Sulfo-NHS-LC-Biotin, Biotin Quantitation Kit (HABA, Pierce) as well as the chemiluminescent (SuperSignal West Pico or Femto) and calorimetric (1-Step Ultra TMB ELISA) HRP substrates were also purchased from ThermoFisher Scientific.

    Centrifugation:

    Article Title: R‐loop formation during S phase is restricted by PrimPol‐mediated repriming
    Article Snippet: Sheared nucleic acids were supplemented with 1× DNase I Reaction Buffer (New England Biolabs), denatured for 5 min at 95°C and snap‐cooled on ice to release RNA moiety of DNA:RNA hybrids. .. RNA was collected by centrifugation, washed with 70% ethanol and resuspended in 217 μl of RNase‐free water.

    Article Title: Integrating chemical mutagenesis and whole genome sequencing as a platform for forward and reverse genetic analysis of Chlamydia
    Article Snippet: .. At time of harvest, EBs were concentrated from cell lysates by centrifugation (21,000 × g, 15 minutes, 4 °C), and resuspended in DNAse I reaction buffer (NEB Labs). .. Residual host DNA was digested with 8 Units of DNAse I (NEB) for 1 hour at 37 °C and EBs washed with PBS, pelleted, and resuspended in 180 μl of ATL buffer (Qiagen).

    Amplification:

    Article Title: Digital MDA for enumeration of total nucleic acid contamination
    Article Snippet: The crude products were also analyzed by agarose gel electrophoresis to assess the presence of high molecular weight amplified DNA. .. Endonuclease activity was tested by incubation of enzyme samples with 1 μg ϕ × 174 virion (ss, closed circular) DNA (New England Biolabs) at 37°C for 4 h in DNAse I reaction buffer (New England Biolabs).

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: Oligonucleotide primers were designed from the DNA sequences of CDC36, CCA1, DST1, UIP5 and RRP15 in S. paradoxus using P rimer 3 software and fragments of these genes were amplified by PCR in total volumes of 20 μl containing 0.5 μM of each primer (see ), 1 U Taq DNA polymerase, 10 mM Tris-HCl pH 9, 15 mM MgCl2 , 50 mM KCl, 200 μM of all four dNTPs and approximately 2 ng of genomic DNA template. .. Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25 –50 bp.

    Whole Genome Amplification:

    Article Title: Microarray-based method for detection of unknown genetic modifications
    Article Snippet: .. DNA fragmentation, labeling and hybridization For each experiment, 90 μg of DNA was fragmented using 4 units (8 units for the WGA DNA) of DNase I (New England Biolabs, Ipswich, MA, USA) in a total volume of 500 μl 1× DNase I Reaction Buffer (New England Biolabs). .. The fragmentation reaction was incubated for 5 minutes at 37°C, followed by 10 minutes at 95°C to inactivate the enzyme.

    Polymerase Chain Reaction:

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: The PCR products were subcloned using the TOPO TA Cloning® Kit with pCR®2.1-TOPO® vector and TOP 10 cells (Invitrogen Corporation), and cloned DNA fragments were reamplified by direct PCR of the colony with M13f and M13r primers, and sequenced using ABI BigDye® Terminator reaction mixture and an ABI PRISM® 3730 DNA Analyzer (Applied Biosystems). .. Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25 –50 bp.

    Article Title: Highly stable hexitol based XNA aptamers targeting the vascular endothelial growth factor
    Article Snippet: Materials Deoxyribonucleoside triphosphates (dNTPs), Taq DNA polymerase, 10× ThermoPol buffer, MgSO4 , Lambda exonuclease, 10× Lambda exonuclease reaction buffer, 10× DNase I reaction buffer and 6× purple gel loading dye were purchased from New England Biolabs. .. Turbo DNase I, magnetic beads (Dynabeads M-280 Streptavidin), SYBR Gold nucleic acid gel stain, CloneJet PCR cloning kit, Micro BCA protein assay kit, the biotinylation reagent EZ-Link Sulfo-NHS-LC-Biotin, Biotin Quantitation Kit (HABA, Pierce) as well as the chemiluminescent (SuperSignal West Pico or Femto) and calorimetric (1-Step Ultra TMB ELISA) HRP substrates were also purchased from ThermoFisher Scientific.

    TA Cloning:

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: The PCR products were subcloned using the TOPO TA Cloning® Kit with pCR®2.1-TOPO® vector and TOP 10 cells (Invitrogen Corporation), and cloned DNA fragments were reamplified by direct PCR of the colony with M13f and M13r primers, and sequenced using ABI BigDye® Terminator reaction mixture and an ABI PRISM® 3730 DNA Analyzer (Applied Biosystems). .. Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25 –50 bp.

    SYBR Green Assay:

    Article Title: Digital MDA for enumeration of total nucleic acid contamination
    Article Snippet: Reaction master mixes were made up according to the manufacturers’ instructions, omitting any chemical or thermal template denaturation steps and supplementing 0.3% Tween-20 and 1× SYBR GREEN I (Invitrogen), used to follow the reactions in real time during a 16 h, 30°C incubation on the MX3005-P thermocycler (Stratagene). .. Endonuclease activity was tested by incubation of enzyme samples with 1 μg ϕ × 174 virion (ss, closed circular) DNA (New England Biolabs) at 37°C for 4 h in DNAse I reaction buffer (New England Biolabs).

    Article Title: Modulation of inflammatory cytokines and mitogen-activated protein kinases by acetate in primary astrocytes
    Article Snippet: Reverse and forward IL-1β, IL-6, TNF-α, IL-4, IL-10, TGF-β1 and β-actin primers from SA Biosciences (Frederick, MD), FastStart Universal SYBR Green Master from Roche Applied Science (Indianapolis, IN), TRIzol® reagent from Life Technologies (Grand Island, NY), DMEM–F-12 media from Invitrogen (Grand Island, NY), and buffering reagents and other chemicals from EMD Biosciences (Gibbstown, NJ). .. DNase I and DNase I reaction buffer were purchased from New England Biolabs (Ipswich, MA), and a DeadEnd™ fluorometric TUNEL assay kit was from Promega (Madison, WI).

    Microarray:

    Article Title: GENOME-WIDE ASSOCIATION ANALYSIS OF CLINICAL VERSUS NON-CLINICAL ORIGIN PROVIDES INSIGHTS INTO SACCHAROMYCES CEREVISIAE PATHOGENESIS
    Article Snippet: Paragraph title: DNA extraction and microarray hybridization ... Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 min at 37 °C in 1× DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25-50 bp.

    Article Title: Nature and distribution of large sequence polymorphisms in Saccharomyces cerevisiae
    Article Snippet: Paragraph title: DNA extraction and microarray hybridization ... DNA fragments of 25–50 bp were obtained by incubation of the extracted DNA with 1U of DNaseI (New England Biolabs) for 2 min at 37 °C in 1× DNase I Reaction Buffer (New England Biolabs).

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: Paragraph title: DNA extraction and microarray hybridization ... Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 1.5 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 50 – 100 bp.

    Incubation:

    Article Title: R‐loop formation during S phase is restricted by PrimPol‐mediated repriming
    Article Snippet: Any soluble ssRNA was degraded by treating the nucleic acids with 25 U of RNase I (Ambion) in TNE buffer (10 mM Tris–HCl (pH 7.4), 100 mM NaCl, 1 mM EDTA) for 30 min at 37°C; to remove RNase I (Ambion, AM2294), 5 μg of Proteinase K was added and reaction incubated for a further 2 h, after which the nucleic acids were purified with phenol:chloroform:isoamyl alcohol (25:24:1) and precipitated with 0.3 M NaCl. .. Sheared nucleic acids were supplemented with 1× DNase I Reaction Buffer (New England Biolabs), denatured for 5 min at 95°C and snap‐cooled on ice to release RNA moiety of DNA:RNA hybrids.

    Article Title: GENOME-WIDE ASSOCIATION ANALYSIS OF CLINICAL VERSUS NON-CLINICAL ORIGIN PROVIDES INSIGHTS INTO SACCHAROMYCES CEREVISIAE PATHOGENESIS
    Article Snippet: Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 min at 37 °C in 1× DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25-50 bp. .. The fragmented DNA was end-labeled by incubation at 37 °C for 1 h with 20 U of terminal deoxynucleotidyl transferase (New England Biolabs) and 1 nmol of biotin-11-ddATP (Perkin Elmer) in 1× NEBuffer 4 (New England Biolabs), and the labeling reaction was terminated by heat inactivation of the terminal transferase at 75 °C for 25 min.

    Article Title: Digital MDA for enumeration of total nucleic acid contamination
    Article Snippet: .. Endonuclease activity was tested by incubation of enzyme samples with 1 μg ϕ × 174 virion (ss, closed circular) DNA (New England Biolabs) at 37°C for 4 h in DNAse I reaction buffer (New England Biolabs). .. DNA shearing Twenty nanograms E. coli K12 genomic DNA [again prepared by the DNeasy method (Qiagen) for Gram-negative cells] was diluted in 200 μl 20 mM Tris, pH 7.5, containing 0.05% Tween-20.

    Article Title: Optimization of a Nucleic Acid-Based Reporter System To Detect Mycobacterium tuberculosis Antibiotic Sensitivity
    Article Snippet: .. The reaction mixture was incubated at 40°C for 1 h. DNA was then digested by adding RNase-free DNase I and DNase I reaction buffer (New England BioLabs), followed by incubation at 37°C for 2 h. EDTA was then added to a final concentration of 18 mM, and the sample was heat inactivated at 75°C for 10 min. .. Finally, duplicate 10-fold serial dilutions of in vitro -transcribed cSML were made in RNase-free water and added to a one-step RT-PCR.

    Article Title: Microarray-based method for detection of unknown genetic modifications
    Article Snippet: DNA fragmentation, labeling and hybridization For each experiment, 90 μg of DNA was fragmented using 4 units (8 units for the WGA DNA) of DNase I (New England Biolabs, Ipswich, MA, USA) in a total volume of 500 μl 1× DNase I Reaction Buffer (New England Biolabs). .. The fragmentation reaction was incubated for 5 minutes at 37°C, followed by 10 minutes at 95°C to inactivate the enzyme.

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25 –50 bp. .. Fragmented DNA was end-labeled by incubation at 37°C for 1 hour with 20 U terminal deoxynucleotidyl transferase (New England Biolabs) and 1 nmol of biotin-11-ddATP (Perkin Elmer) in 1x NEBuffer 4 (New England Biolabs), and the labeling reaction was terminated by heat inactivation of the terminal transferase at 75°C for 25 minutes.

    Article Title: A Thermonuclease of Neisseria gonorrhoeae Enhances Bacterial Escape From Killing by Neutrophil Extracellular Traps
    Article Snippet: .. Neutrophil genomic DNA (3 μg) was incubated for 30 minutes at 37°C in molecular biology–grade water (Thermo Scientific) and DNAse I reaction buffer alone, with 0.5 U of DNAse I (recombinant bovine pancreatic DNAse I ; New England Biolabs), or with recombinant Nuc that was boiled for 10 minutes or left unboiled. .. Nuc was expressed in Escherichia coli and purified as described by Steichen et al [ ].

    Article Title: A High-Throughput RNA Extraction for Sprouted Single-Seed Barley (Hordeum vulgare L.) Rich in Polysaccharides
    Article Snippet: Then, 6 μL 10× DNase I reaction buffer and 10 units total of DNase I (NEB Inc., Ipswich, MA, USA) were added. .. An amount of 60 μL of 5 M lithium chloride solution was added prior to incubation for 1 h to overnight at −20 °C.

    Article Title: Nature and distribution of large sequence polymorphisms in Saccharomyces cerevisiae
    Article Snippet: .. DNA fragments of 25–50 bp were obtained by incubation of the extracted DNA with 1U of DNaseI (New England Biolabs) for 2 min at 37 °C in 1× DNase I Reaction Buffer (New England Biolabs). .. After heat inactivation of the DNase I by incubation of the digestion mixture at 95 °C for 20 min, the digested DNA was analyzed on a 2% agarose gel.

    Article Title: Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA
    Article Snippet: DNase I protection assays Purified plasmid DNA (77 ng) was pre-incubated with CbpA or BSA, at 37°C, in DNase I reaction buffer (NEB) in a final volume of 10 µl. .. The reactions were stopped by adding 2 µl of 10% SDS and by incubation at 75°C for 5 min. Gel-loading dye was then added and reactions were analysed by electrophoresis on 1% agarose gels.

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 1.5 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 50 – 100 bp. .. Fragmented DNA was end-labeled by incubation at 37°C for 1 hour with 20 U terminal deoxynucleotidyl transferase (New England Biolabs) and 1 nmol of biotin-11-ddATP (Perkin Elmer) in 1x NEBuffer 4 (New England Biolabs), and the labeling reaction was terminated by heat inactivation of the terminal transferase at 75°C for 25 minutes.

    Activity Assay:

    Article Title: Digital MDA for enumeration of total nucleic acid contamination
    Article Snippet: .. Endonuclease activity was tested by incubation of enzyme samples with 1 μg ϕ × 174 virion (ss, closed circular) DNA (New England Biolabs) at 37°C for 4 h in DNAse I reaction buffer (New England Biolabs). .. DNA shearing Twenty nanograms E. coli K12 genomic DNA [again prepared by the DNeasy method (Qiagen) for Gram-negative cells] was diluted in 200 μl 20 mM Tris, pH 7.5, containing 0.05% Tween-20.

    BIA-KA:

    Article Title: Highly stable hexitol based XNA aptamers targeting the vascular endothelial growth factor
    Article Snippet: Materials Deoxyribonucleoside triphosphates (dNTPs), Taq DNA polymerase, 10× ThermoPol buffer, MgSO4 , Lambda exonuclease, 10× Lambda exonuclease reaction buffer, 10× DNase I reaction buffer and 6× purple gel loading dye were purchased from New England Biolabs. .. Turbo DNase I, magnetic beads (Dynabeads M-280 Streptavidin), SYBR Gold nucleic acid gel stain, CloneJet PCR cloning kit, Micro BCA protein assay kit, the biotinylation reagent EZ-Link Sulfo-NHS-LC-Biotin, Biotin Quantitation Kit (HABA, Pierce) as well as the chemiluminescent (SuperSignal West Pico or Femto) and calorimetric (1-Step Ultra TMB ELISA) HRP substrates were also purchased from ThermoFisher Scientific.

    Western Blot:

    Article Title: Modulation of inflammatory cytokines and mitogen-activated protein kinases by acetate in primary astrocytes
    Article Snippet: All Western blot supplies and a goat anti-rabbit horse radish peroxidase (HRP)-linked antibody and iScript cDNA synthesis kits were purchased from Bio-Rad Laboratories (Hercules, CA). .. DNase I and DNase I reaction buffer were purchased from New England Biolabs (Ipswich, MA), and a DeadEnd™ fluorometric TUNEL assay kit was from Promega (Madison, WI).

    Hybridization:

    Article Title: GENOME-WIDE ASSOCIATION ANALYSIS OF CLINICAL VERSUS NON-CLINICAL ORIGIN PROVIDES INSIGHTS INTO SACCHAROMYCES CEREVISIAE PATHOGENESIS
    Article Snippet: Paragraph title: DNA extraction and microarray hybridization ... Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 min at 37 °C in 1× DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25-50 bp.

    Article Title: Microarray-based method for detection of unknown genetic modifications
    Article Snippet: .. DNA fragmentation, labeling and hybridization For each experiment, 90 μg of DNA was fragmented using 4 units (8 units for the WGA DNA) of DNase I (New England Biolabs, Ipswich, MA, USA) in a total volume of 500 μl 1× DNase I Reaction Buffer (New England Biolabs). .. The fragmentation reaction was incubated for 5 minutes at 37°C, followed by 10 minutes at 95°C to inactivate the enzyme.

    Article Title: Nature and distribution of large sequence polymorphisms in Saccharomyces cerevisiae
    Article Snippet: Paragraph title: DNA extraction and microarray hybridization ... DNA fragments of 25–50 bp were obtained by incubation of the extracted DNA with 1U of DNaseI (New England Biolabs) for 2 min at 37 °C in 1× DNase I Reaction Buffer (New England Biolabs).

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: Paragraph title: DNA extraction and microarray hybridization ... Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 1.5 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 50 – 100 bp.

    TUNEL Assay:

    Article Title: Modulation of inflammatory cytokines and mitogen-activated protein kinases by acetate in primary astrocytes
    Article Snippet: .. DNase I and DNase I reaction buffer were purchased from New England Biolabs (Ipswich, MA), and a DeadEnd™ fluorometric TUNEL assay kit was from Promega (Madison, WI). .. Astrocyte cultures were derived from C57BL/6 mouse brains as described previously ( ).

    Infection:

    Article Title: Integrating chemical mutagenesis and whole genome sequencing as a platform for forward and reverse genetic analysis of Chlamydia
    Article Snippet: Vero cells in T25 flasks were infected with each mutant strain. .. At time of harvest, EBs were concentrated from cell lysates by centrifugation (21,000 × g, 15 minutes, 4 °C), and resuspended in DNAse I reaction buffer (NEB Labs).

    Multiple Displacement Amplification:

    Article Title: Digital MDA for enumeration of total nucleic acid contamination
    Article Snippet: Activity assays The commercial and high-purity ϕ29 DNAP reagents were tested for activity in 50 μl MDA reactions. .. Endonuclease activity was tested by incubation of enzyme samples with 1 μg ϕ × 174 virion (ss, closed circular) DNA (New England Biolabs) at 37°C for 4 h in DNAse I reaction buffer (New England Biolabs).

    Generated:

    Article Title: Optimization of a Nucleic Acid-Based Reporter System To Detect Mycobacterium tuberculosis Antibiotic Sensitivity
    Article Snippet: In vitro -transcribed cSML was generated by linearizing 100 ng of plasmid pSP6Pro-Cyc with HindIII, followed by addition to an in vitro transcription reaction mixture containing 1 U/μl purified SP6 RNA polymerase (New England BioLabs), 40 mM Tris-HCl (pH 7.9), 10 mM dithiothreitol, 2 mM spermidine, 4 mM concentrations of each nucleotide triphosphate, 8 mM MgCl2 , and 0.8 U/μl RNaseOUT. .. The reaction mixture was incubated at 40°C for 1 h. DNA was then digested by adding RNase-free DNase I and DNase I reaction buffer (New England BioLabs), followed by incubation at 37°C for 2 h. EDTA was then added to a final concentration of 18 mM, and the sample was heat inactivated at 75°C for 10 min.

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Optimization of a Nucleic Acid-Based Reporter System To Detect Mycobacterium tuberculosis Antibiotic Sensitivity
    Article Snippet: Paragraph title: Determining the dynamic range of cSML detection by one-step RT-PCR. ... The reaction mixture was incubated at 40°C for 1 h. DNA was then digested by adding RNase-free DNase I and DNase I reaction buffer (New England BioLabs), followed by incubation at 37°C for 2 h. EDTA was then added to a final concentration of 18 mM, and the sample was heat inactivated at 75°C for 10 min.

    Recombinant:

    Article Title: A Thermonuclease of Neisseria gonorrhoeae Enhances Bacterial Escape From Killing by Neutrophil Extracellular Traps
    Article Snippet: .. Neutrophil genomic DNA (3 μg) was incubated for 30 minutes at 37°C in molecular biology–grade water (Thermo Scientific) and DNAse I reaction buffer alone, with 0.5 U of DNAse I (recombinant bovine pancreatic DNAse I ; New England Biolabs), or with recombinant Nuc that was boiled for 10 minutes or left unboiled. .. Nuc was expressed in Escherichia coli and purified as described by Steichen et al [ ].

    Molecular Weight:

    Article Title: Digital MDA for enumeration of total nucleic acid contamination
    Article Snippet: The crude products were also analyzed by agarose gel electrophoresis to assess the presence of high molecular weight amplified DNA. .. Endonuclease activity was tested by incubation of enzyme samples with 1 μg ϕ × 174 virion (ss, closed circular) DNA (New England Biolabs) at 37°C for 4 h in DNAse I reaction buffer (New England Biolabs).

    DNA Extraction:

    Article Title: GENOME-WIDE ASSOCIATION ANALYSIS OF CLINICAL VERSUS NON-CLINICAL ORIGIN PROVIDES INSIGHTS INTO SACCHAROMYCES CEREVISIAE PATHOGENESIS
    Article Snippet: Paragraph title: DNA extraction and microarray hybridization ... Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 min at 37 °C in 1× DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25-50 bp.

    Article Title: Nature and distribution of large sequence polymorphisms in Saccharomyces cerevisiae
    Article Snippet: Paragraph title: DNA extraction and microarray hybridization ... DNA fragments of 25–50 bp were obtained by incubation of the extracted DNA with 1U of DNaseI (New England Biolabs) for 2 min at 37 °C in 1× DNase I Reaction Buffer (New England Biolabs).

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: Paragraph title: DNA extraction and microarray hybridization ... Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 1.5 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 50 – 100 bp.

    Magnetic Beads:

    Article Title: Highly stable hexitol based XNA aptamers targeting the vascular endothelial growth factor
    Article Snippet: Materials Deoxyribonucleoside triphosphates (dNTPs), Taq DNA polymerase, 10× ThermoPol buffer, MgSO4 , Lambda exonuclease, 10× Lambda exonuclease reaction buffer, 10× DNase I reaction buffer and 6× purple gel loading dye were purchased from New England Biolabs. .. Turbo DNase I, magnetic beads (Dynabeads M-280 Streptavidin), SYBR Gold nucleic acid gel stain, CloneJet PCR cloning kit, Micro BCA protein assay kit, the biotinylation reagent EZ-Link Sulfo-NHS-LC-Biotin, Biotin Quantitation Kit (HABA, Pierce) as well as the chemiluminescent (SuperSignal West Pico or Femto) and calorimetric (1-Step Ultra TMB ELISA) HRP substrates were also purchased from ThermoFisher Scientific.

    Mutagenesis:

    Article Title: Integrating chemical mutagenesis and whole genome sequencing as a platform for forward and reverse genetic analysis of Chlamydia
    Article Snippet: Vero cells in T25 flasks were infected with each mutant strain. .. At time of harvest, EBs were concentrated from cell lysates by centrifugation (21,000 × g, 15 minutes, 4 °C), and resuspended in DNAse I reaction buffer (NEB Labs).

    Isolation:

    Article Title: Integrating chemical mutagenesis and whole genome sequencing as a platform for forward and reverse genetic analysis of Chlamydia
    Article Snippet: At time of harvest, EBs were concentrated from cell lysates by centrifugation (21,000 × g, 15 minutes, 4 °C), and resuspended in DNAse I reaction buffer (NEB Labs). .. Total DNA was isolated with a Qiagen DNeasy Blood and Tissue Kit (Qiagen).

    Detection Assay:

    Article Title: Optimization of a Nucleic Acid-Based Reporter System To Detect Mycobacterium tuberculosis Antibiotic Sensitivity
    Article Snippet: The reaction mixture was incubated at 40°C for 1 h. DNA was then digested by adding RNase-free DNase I and DNase I reaction buffer (New England BioLabs), followed by incubation at 37°C for 2 h. EDTA was then added to a final concentration of 18 mM, and the sample was heat inactivated at 75°C for 10 min. .. The average cycle detection threshold for each dilution was plotted to determine the dynamic range of the one-step RT-PCR cSML detection assay, which is described by the equation y = (109 )−0.557x , where x is the cycle detection threshold, and y is the relative level of cSML in a sample.

    Immunodetection:

    Article Title: Highly stable hexitol based XNA aptamers targeting the vascular endothelial growth factor
    Article Snippet: Materials Deoxyribonucleoside triphosphates (dNTPs), Taq DNA polymerase, 10× ThermoPol buffer, MgSO4 , Lambda exonuclease, 10× Lambda exonuclease reaction buffer, 10× DNase I reaction buffer and 6× purple gel loading dye were purchased from New England Biolabs. .. Antibodies used in the immunodetection assays were a polyclonal rabbit anti-VEGFA antibody (Abcam), HRP-conjugated polyclonal anti-FITC antibody (ThermoFisher Scientific), HRP-conjugated streptavidin, and HRP-conjugated polyclonal anti-rabbit IgG (Jackson Immuno Research).

    Labeling:

    Article Title: GENOME-WIDE ASSOCIATION ANALYSIS OF CLINICAL VERSUS NON-CLINICAL ORIGIN PROVIDES INSIGHTS INTO SACCHAROMYCES CEREVISIAE PATHOGENESIS
    Article Snippet: Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 min at 37 °C in 1× DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25-50 bp. .. The fragmented DNA was end-labeled by incubation at 37 °C for 1 h with 20 U of terminal deoxynucleotidyl transferase (New England Biolabs) and 1 nmol of biotin-11-ddATP (Perkin Elmer) in 1× NEBuffer 4 (New England Biolabs), and the labeling reaction was terminated by heat inactivation of the terminal transferase at 75 °C for 25 min.

    Article Title: Microarray-based method for detection of unknown genetic modifications
    Article Snippet: .. DNA fragmentation, labeling and hybridization For each experiment, 90 μg of DNA was fragmented using 4 units (8 units for the WGA DNA) of DNase I (New England Biolabs, Ipswich, MA, USA) in a total volume of 500 μl 1× DNase I Reaction Buffer (New England Biolabs). .. The fragmentation reaction was incubated for 5 minutes at 37°C, followed by 10 minutes at 95°C to inactivate the enzyme.

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25 –50 bp. .. Fragmented DNA was end-labeled by incubation at 37°C for 1 hour with 20 U terminal deoxynucleotidyl transferase (New England Biolabs) and 1 nmol of biotin-11-ddATP (Perkin Elmer) in 1x NEBuffer 4 (New England Biolabs), and the labeling reaction was terminated by heat inactivation of the terminal transferase at 75°C for 25 minutes.

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 1.5 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 50 – 100 bp. .. Fragmented DNA was end-labeled by incubation at 37°C for 1 hour with 20 U terminal deoxynucleotidyl transferase (New England Biolabs) and 1 nmol of biotin-11-ddATP (Perkin Elmer) in 1x NEBuffer 4 (New England Biolabs), and the labeling reaction was terminated by heat inactivation of the terminal transferase at 75°C for 25 minutes.

    Purification:

    Article Title: R‐loop formation during S phase is restricted by PrimPol‐mediated repriming
    Article Snippet: Any soluble ssRNA was degraded by treating the nucleic acids with 25 U of RNase I (Ambion) in TNE buffer (10 mM Tris–HCl (pH 7.4), 100 mM NaCl, 1 mM EDTA) for 30 min at 37°C; to remove RNase I (Ambion, AM2294), 5 μg of Proteinase K was added and reaction incubated for a further 2 h, after which the nucleic acids were purified with phenol:chloroform:isoamyl alcohol (25:24:1) and precipitated with 0.3 M NaCl. .. Sheared nucleic acids were supplemented with 1× DNase I Reaction Buffer (New England Biolabs), denatured for 5 min at 95°C and snap‐cooled on ice to release RNA moiety of DNA:RNA hybrids.

    Article Title: GENOME-WIDE ASSOCIATION ANALYSIS OF CLINICAL VERSUS NON-CLINICAL ORIGIN PROVIDES INSIGHTS INTO SACCHAROMYCES CEREVISIAE PATHOGENESIS
    Article Snippet: .. Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 min at 37 °C in 1× DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25-50 bp. .. DNase I was heat inactivated at 95 °C for 20 min, and the digestion products were analyzed on a 2% agarose gel.

    Article Title: Optimization of a Nucleic Acid-Based Reporter System To Detect Mycobacterium tuberculosis Antibiotic Sensitivity
    Article Snippet: In vitro -transcribed cSML was generated by linearizing 100 ng of plasmid pSP6Pro-Cyc with HindIII, followed by addition to an in vitro transcription reaction mixture containing 1 U/μl purified SP6 RNA polymerase (New England BioLabs), 40 mM Tris-HCl (pH 7.9), 10 mM dithiothreitol, 2 mM spermidine, 4 mM concentrations of each nucleotide triphosphate, 8 mM MgCl2 , and 0.8 U/μl RNaseOUT. .. The reaction mixture was incubated at 40°C for 1 h. DNA was then digested by adding RNase-free DNase I and DNase I reaction buffer (New England BioLabs), followed by incubation at 37°C for 2 h. EDTA was then added to a final concentration of 18 mM, and the sample was heat inactivated at 75°C for 10 min.

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: .. Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25 –50 bp. .. DNase I was heat inactivated at 95°C for 20 minutes, and the digestion products were analyzed on a 2% agarose gel.

    Article Title: A Thermonuclease of Neisseria gonorrhoeae Enhances Bacterial Escape From Killing by Neutrophil Extracellular Traps
    Article Snippet: Neutrophil genomic DNA (3 μg) was incubated for 30 minutes at 37°C in molecular biology–grade water (Thermo Scientific) and DNAse I reaction buffer alone, with 0.5 U of DNAse I (recombinant bovine pancreatic DNAse I ; New England Biolabs), or with recombinant Nuc that was boiled for 10 minutes or left unboiled. .. Nuc was expressed in Escherichia coli and purified as described by Steichen et al [ ].

    Article Title: Highly stable hexitol based XNA aptamers targeting the vascular endothelial growth factor
    Article Snippet: Materials Deoxyribonucleoside triphosphates (dNTPs), Taq DNA polymerase, 10× ThermoPol buffer, MgSO4 , Lambda exonuclease, 10× Lambda exonuclease reaction buffer, 10× DNase I reaction buffer and 6× purple gel loading dye were purchased from New England Biolabs. .. The PCR purification kit was obtained from Macherey-Nagel (NucleoSpin Gel and PCR clean-up kit).

    Article Title: Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA
    Article Snippet: .. DNase I protection assays Purified plasmid DNA (77 ng) was pre-incubated with CbpA or BSA, at 37°C, in DNase I reaction buffer (NEB) in a final volume of 10 µl. ..

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: .. Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 1.5 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 50 – 100 bp. .. DNase I was heat inactivated at 75°C for 25 minutes, and the digestion products were analyzed on a 2% agarose gel.

    Sequencing:

    Article Title: Integrating chemical mutagenesis and whole genome sequencing as a platform for forward and reverse genetic analysis of Chlamydia
    Article Snippet: Paragraph title: Genome sequencing of C. trachomatis LGV-L2 mutants ... At time of harvest, EBs were concentrated from cell lysates by centrifugation (21,000 × g, 15 minutes, 4 °C), and resuspended in DNAse I reaction buffer (NEB Labs).

    Staining:

    Article Title: GENOME-WIDE ASSOCIATION ANALYSIS OF CLINICAL VERSUS NON-CLINICAL ORIGIN PROVIDES INSIGHTS INTO SACCHAROMYCES CEREVISIAE PATHOGENESIS
    Article Snippet: Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 min at 37 °C in 1× DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25-50 bp. .. The target DNA was hybridized onto GeneChip® S. cerevisiae Tiling 1.0R Arrays (Affymetrix) following standard Affymetrix protocols for DNA hybridization, washing and staining (see ), and the arrays were scanned using the Affymetrix scanner at 0.7 μm resolution.

    Article Title: Highly stable hexitol based XNA aptamers targeting the vascular endothelial growth factor
    Article Snippet: Materials Deoxyribonucleoside triphosphates (dNTPs), Taq DNA polymerase, 10× ThermoPol buffer, MgSO4 , Lambda exonuclease, 10× Lambda exonuclease reaction buffer, 10× DNase I reaction buffer and 6× purple gel loading dye were purchased from New England Biolabs. .. Turbo DNase I, magnetic beads (Dynabeads M-280 Streptavidin), SYBR Gold nucleic acid gel stain, CloneJet PCR cloning kit, Micro BCA protein assay kit, the biotinylation reagent EZ-Link Sulfo-NHS-LC-Biotin, Biotin Quantitation Kit (HABA, Pierce) as well as the chemiluminescent (SuperSignal West Pico or Femto) and calorimetric (1-Step Ultra TMB ELISA) HRP substrates were also purchased from ThermoFisher Scientific.

    Article Title: Nature and distribution of large sequence polymorphisms in Saccharomyces cerevisiae
    Article Snippet: DNA fragments of 25–50 bp were obtained by incubation of the extracted DNA with 1U of DNaseI (New England Biolabs) for 2 min at 37 °C in 1× DNase I Reaction Buffer (New England Biolabs). .. The DNA fragments were 3′ end-labeled by incubation with 1 nmol of biotin-11-ddATP (Perkin Elmer) and 20 U of terminal deoxynucleotidyl transferase (New England Biolabs) in 1× NEBuffer 4 (New England Biolabs) for 1 h at 37 °C, and the terminal transferase was subsequently heat inactivated at 75 °C for 25 min. Hybridization of the target DNA onto Affymetrix GeneChip® S. cerevisiae Tiling 1.0R Arrays followed standard Affymetrix protocols for hybridization, washing and staining , and the arrays were scanned using the Affymetrix scanner at 0.7 μm resolution.

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 1.5 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 50 – 100 bp. .. The digested and labeled DNA was hybridized to custom-made CustomArray™ 4x2K microarrays (Combimatrix) following standard protocols from Combimatrix for hybridization, washing, and staining.

    Integrity Assay:

    Article Title: A Thermonuclease of Neisseria gonorrhoeae Enhances Bacterial Escape From Killing by Neutrophil Extracellular Traps
    Article Snippet: Paragraph title: Neutrophil DNA Integrity Assay ... Neutrophil genomic DNA (3 μg) was incubated for 30 minutes at 37°C in molecular biology–grade water (Thermo Scientific) and DNAse I reaction buffer alone, with 0.5 U of DNAse I (recombinant bovine pancreatic DNAse I ; New England Biolabs), or with recombinant Nuc that was boiled for 10 minutes or left unboiled.

    Plasmid Preparation:

    Article Title: Optimization of a Nucleic Acid-Based Reporter System To Detect Mycobacterium tuberculosis Antibiotic Sensitivity
    Article Snippet: In vitro -transcribed cSML was generated by linearizing 100 ng of plasmid pSP6Pro-Cyc with HindIII, followed by addition to an in vitro transcription reaction mixture containing 1 U/μl purified SP6 RNA polymerase (New England BioLabs), 40 mM Tris-HCl (pH 7.9), 10 mM dithiothreitol, 2 mM spermidine, 4 mM concentrations of each nucleotide triphosphate, 8 mM MgCl2 , and 0.8 U/μl RNaseOUT. .. The reaction mixture was incubated at 40°C for 1 h. DNA was then digested by adding RNase-free DNase I and DNase I reaction buffer (New England BioLabs), followed by incubation at 37°C for 2 h. EDTA was then added to a final concentration of 18 mM, and the sample was heat inactivated at 75°C for 10 min.

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: The PCR products were subcloned using the TOPO TA Cloning® Kit with pCR®2.1-TOPO® vector and TOP 10 cells (Invitrogen Corporation), and cloned DNA fragments were reamplified by direct PCR of the colony with M13f and M13r primers, and sequenced using ABI BigDye® Terminator reaction mixture and an ABI PRISM® 3730 DNA Analyzer (Applied Biosystems). .. Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25 –50 bp.

    Article Title: Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA
    Article Snippet: .. DNase I protection assays Purified plasmid DNA (77 ng) was pre-incubated with CbpA or BSA, at 37°C, in DNase I reaction buffer (NEB) in a final volume of 10 µl. ..

    Article Title: Modulation of inflammatory cytokines and mitogen-activated protein kinases by acetate in primary astrocytes
    Article Snippet: Rabbit polyclonal antibodies to IL-1β, IL-6, TNF-α, TGF-β1, IL-4, IL-10 and acetyl-CoA synthetase were from Abcam (Cambridge, MA), anti-GFAP rabbit antibody was from Sigma (St. Louis, MO), a biotinylated anti-rabbit antibody, Vectasheild mounting medium containing propidium iodide, Elite Vectastain ABC Avidin and Vector VIP chromogen were purchased from Vector Laboratories (Burlingame, CA). .. DNase I and DNase I reaction buffer were purchased from New England Biolabs (Ipswich, MA), and a DeadEnd™ fluorometric TUNEL assay kit was from Promega (Madison, WI).

    Software:

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: Oligonucleotide primers were designed from the DNA sequences of CDC36, CCA1, DST1, UIP5 and RRP15 in S. paradoxus using P rimer 3 software and fragments of these genes were amplified by PCR in total volumes of 20 μl containing 0.5 μM of each primer (see ), 1 U Taq DNA polymerase, 10 mM Tris-HCl pH 9, 15 mM MgCl2 , 50 mM KCl, 200 μM of all four dNTPs and approximately 2 ng of genomic DNA template. .. Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25 –50 bp.

    Article Title: Nature and distribution of large sequence polymorphisms in Saccharomyces cerevisiae
    Article Snippet: DNA fragments of 25–50 bp were obtained by incubation of the extracted DNA with 1U of DNaseI (New England Biolabs) for 2 min at 37 °C in 1× DNase I Reaction Buffer (New England Biolabs). .. Average hybridization intensities were computed for each oligonucleotide feature with the GeneChip® Operating Software (Affymetrix) using the hybridization intensities of the 9 central pixels.

    DNA Hybridization:

    Article Title: GENOME-WIDE ASSOCIATION ANALYSIS OF CLINICAL VERSUS NON-CLINICAL ORIGIN PROVIDES INSIGHTS INTO SACCHAROMYCES CEREVISIAE PATHOGENESIS
    Article Snippet: Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 min at 37 °C in 1× DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25-50 bp. .. The target DNA was hybridized onto GeneChip® S. cerevisiae Tiling 1.0R Arrays (Affymetrix) following standard Affymetrix protocols for DNA hybridization, washing and staining (see ), and the arrays were scanned using the Affymetrix scanner at 0.7 μm resolution.

    Enzyme-linked Immunosorbent Assay:

    Article Title: Highly stable hexitol based XNA aptamers targeting the vascular endothelial growth factor
    Article Snippet: Materials Deoxyribonucleoside triphosphates (dNTPs), Taq DNA polymerase, 10× ThermoPol buffer, MgSO4 , Lambda exonuclease, 10× Lambda exonuclease reaction buffer, 10× DNase I reaction buffer and 6× purple gel loading dye were purchased from New England Biolabs. .. Turbo DNase I, magnetic beads (Dynabeads M-280 Streptavidin), SYBR Gold nucleic acid gel stain, CloneJet PCR cloning kit, Micro BCA protein assay kit, the biotinylation reagent EZ-Link Sulfo-NHS-LC-Biotin, Biotin Quantitation Kit (HABA, Pierce) as well as the chemiluminescent (SuperSignal West Pico or Femto) and calorimetric (1-Step Ultra TMB ELISA) HRP substrates were also purchased from ThermoFisher Scientific.

    Avidin-Biotin Assay:

    Article Title: Modulation of inflammatory cytokines and mitogen-activated protein kinases by acetate in primary astrocytes
    Article Snippet: Rabbit polyclonal antibodies to IL-1β, IL-6, TNF-α, TGF-β1, IL-4, IL-10 and acetyl-CoA synthetase were from Abcam (Cambridge, MA), anti-GFAP rabbit antibody was from Sigma (St. Louis, MO), a biotinylated anti-rabbit antibody, Vectasheild mounting medium containing propidium iodide, Elite Vectastain ABC Avidin and Vector VIP chromogen were purchased from Vector Laboratories (Burlingame, CA). .. DNase I and DNase I reaction buffer were purchased from New England Biolabs (Ipswich, MA), and a DeadEnd™ fluorometric TUNEL assay kit was from Promega (Madison, WI).

    Agarose Gel Electrophoresis:

    Article Title: GENOME-WIDE ASSOCIATION ANALYSIS OF CLINICAL VERSUS NON-CLINICAL ORIGIN PROVIDES INSIGHTS INTO SACCHAROMYCES CEREVISIAE PATHOGENESIS
    Article Snippet: Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 min at 37 °C in 1× DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25-50 bp. .. DNase I was heat inactivated at 95 °C for 20 min, and the digestion products were analyzed on a 2% agarose gel.

    Article Title: Digital MDA for enumeration of total nucleic acid contamination
    Article Snippet: The crude products were also analyzed by agarose gel electrophoresis to assess the presence of high molecular weight amplified DNA. .. Endonuclease activity was tested by incubation of enzyme samples with 1 μg ϕ × 174 virion (ss, closed circular) DNA (New England Biolabs) at 37°C for 4 h in DNAse I reaction buffer (New England Biolabs).

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 2 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 25 –50 bp. .. DNase I was heat inactivated at 95°C for 20 minutes, and the digestion products were analyzed on a 2% agarose gel.

    Article Title: A Thermonuclease of Neisseria gonorrhoeae Enhances Bacterial Escape From Killing by Neutrophil Extracellular Traps
    Article Snippet: Neutrophil genomic DNA (3 μg) was incubated for 30 minutes at 37°C in molecular biology–grade water (Thermo Scientific) and DNAse I reaction buffer alone, with 0.5 U of DNAse I (recombinant bovine pancreatic DNAse I ; New England Biolabs), or with recombinant Nuc that was boiled for 10 minutes or left unboiled. .. Samples were separated on a 1% agarose gel run at 4°C.

    Article Title: A High-Throughput RNA Extraction for Sprouted Single-Seed Barley (Hordeum vulgare L.) Rich in Polysaccharides
    Article Snippet: Then, 6 μL 10× DNase I reaction buffer and 10 units total of DNase I (NEB Inc., Ipswich, MA, USA) were added. .. RNA was subjected to spectrophotometric measurements and agarose gel electrophoresis both before and after DNA-free treatments.

    Article Title: Nature and distribution of large sequence polymorphisms in Saccharomyces cerevisiae
    Article Snippet: DNA fragments of 25–50 bp were obtained by incubation of the extracted DNA with 1U of DNaseI (New England Biolabs) for 2 min at 37 °C in 1× DNase I Reaction Buffer (New England Biolabs). .. After heat inactivation of the DNase I by incubation of the digestion mixture at 95 °C for 20 min, the digested DNA was analyzed on a 2% agarose gel.

    Article Title: A multi-species based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    Article Snippet: Ten micrograms of purified DNA were digested with 1 U of DNase I (New England Biolabs) for 1.5 minutes at 37°C in 1x DNase I Reaction buffer (New England Biolabs) to obtain fragments of 50 – 100 bp. .. DNase I was heat inactivated at 75°C for 25 minutes, and the digestion products were analyzed on a 2% agarose gel.

    In Vitro:

    Article Title: Optimization of a Nucleic Acid-Based Reporter System To Detect Mycobacterium tuberculosis Antibiotic Sensitivity
    Article Snippet: In vitro -transcribed cSML was generated by linearizing 100 ng of plasmid pSP6Pro-Cyc with HindIII, followed by addition to an in vitro transcription reaction mixture containing 1 U/μl purified SP6 RNA polymerase (New England BioLabs), 40 mM Tris-HCl (pH 7.9), 10 mM dithiothreitol, 2 mM spermidine, 4 mM concentrations of each nucleotide triphosphate, 8 mM MgCl2 , and 0.8 U/μl RNaseOUT. .. The reaction mixture was incubated at 40°C for 1 h. DNA was then digested by adding RNase-free DNase I and DNase I reaction buffer (New England BioLabs), followed by incubation at 37°C for 2 h. EDTA was then added to a final concentration of 18 mM, and the sample was heat inactivated at 75°C for 10 min.

    Electrophoresis:

    Article Title: Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA
    Article Snippet: DNase I protection assays Purified plasmid DNA (77 ng) was pre-incubated with CbpA or BSA, at 37°C, in DNase I reaction buffer (NEB) in a final volume of 10 µl. .. The reactions were stopped by adding 2 µl of 10% SDS and by incubation at 75°C for 5 min. Gel-loading dye was then added and reactions were analysed by electrophoresis on 1% agarose gels.

    Quantitation Assay:

    Article Title: Highly stable hexitol based XNA aptamers targeting the vascular endothelial growth factor
    Article Snippet: Materials Deoxyribonucleoside triphosphates (dNTPs), Taq DNA polymerase, 10× ThermoPol buffer, MgSO4 , Lambda exonuclease, 10× Lambda exonuclease reaction buffer, 10× DNase I reaction buffer and 6× purple gel loading dye were purchased from New England Biolabs. .. Turbo DNase I, magnetic beads (Dynabeads M-280 Streptavidin), SYBR Gold nucleic acid gel stain, CloneJet PCR cloning kit, Micro BCA protein assay kit, the biotinylation reagent EZ-Link Sulfo-NHS-LC-Biotin, Biotin Quantitation Kit (HABA, Pierce) as well as the chemiluminescent (SuperSignal West Pico or Femto) and calorimetric (1-Step Ultra TMB ELISA) HRP substrates were also purchased from ThermoFisher Scientific.

    Spectrophotometry:

    Article Title: A High-Throughput RNA Extraction for Sprouted Single-Seed Barley (Hordeum vulgare L.) Rich in Polysaccharides
    Article Snippet: RNA Analysis and Preparation For spectrophotometric measurements, RNA concentration and purity were determined using a Take3 Micro-Volume PlateMicroplate with an Epoch UV-VIS spectrophotometer (BioTek Instruments, Inc., Winooski, VT, USA). .. Then, 6 μL 10× DNase I reaction buffer and 10 units total of DNase I (NEB Inc., Ipswich, MA, USA) were added.

    Concentration Assay:

    Article Title: Optimization of a Nucleic Acid-Based Reporter System To Detect Mycobacterium tuberculosis Antibiotic Sensitivity
    Article Snippet: .. The reaction mixture was incubated at 40°C for 1 h. DNA was then digested by adding RNase-free DNase I and DNase I reaction buffer (New England BioLabs), followed by incubation at 37°C for 2 h. EDTA was then added to a final concentration of 18 mM, and the sample was heat inactivated at 75°C for 10 min. .. Finally, duplicate 10-fold serial dilutions of in vitro -transcribed cSML were made in RNase-free water and added to a one-step RT-PCR.

    Article Title: A High-Throughput RNA Extraction for Sprouted Single-Seed Barley (Hordeum vulgare L.) Rich in Polysaccharides
    Article Snippet: For DNase digestion of RNA samples to remove contaminating gDNA and subsequent LiCl precipitation, the concentration was adjusted to 20–25 μg of total RNA in 50 μL nuclease-free water. .. Then, 6 μL 10× DNase I reaction buffer and 10 units total of DNase I (NEB Inc., Ipswich, MA, USA) were added.

    Lysis:

    Article Title: R‐loop formation during S phase is restricted by PrimPol‐mediated repriming
    Article Snippet: The nuclear pellet was divided, and equivalent of 20–50 million nuclei were lysed in 700 μl of nuclear lysis buffer (25 mM Tris–HCl (pH 7.4), 1% SDS, 5 mM EDTA and 0.125 mg/ml Proteinase K) overnight at 37°C with agitation. .. Sheared nucleic acids were supplemented with 1× DNase I Reaction Buffer (New England Biolabs), denatured for 5 min at 95°C and snap‐cooled on ice to release RNA moiety of DNA:RNA hybrids.

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    New England Biolabs dnase i reaction buffer
    Dnase I Reaction Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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