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dna cleanup kit  (New England Biolabs)


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    Structured Review

    New England Biolabs dna cleanup kit
    Activity of Cas12a orthologs at varied temperatures. (A) Cas12a/SpCas9 proteins with their <t>respective</t> <t>crRNA/sgRNA</t> and buffer (same as indicated in (B)) were combined to form the ribonucleoprotein (RNPs) for 5 min at the temperatures indicated. The double-stranded <t>DNA</t> (dsDNA) cleavage reactions were initiated by adding the 5′-FAM-labeled dsDNA containing the target site preincubated at the designated incubation temperatures. Digested fragments were resolved by capillary electrophoresis, and peaks corresponding to cleaved and intact substrates were quantified. Data are shown as the mean ± standard deviation (SD) of three experimental replicates. (B) Recombinant crRNA-free Cas proteins or crRNA-loaded RNPs were subjected to thermal melting analysis using Nano differential scanning fluorimetry (Supplementary Figure S1). The melting temperature (Tm) of three experimental replicates are shown, with means ± SD indicated.
    Dna Cleanup Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 509 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/actin+polymerization+depolymerization+kit/Monarch+PCR+%26+DNA+Cleanup+Kit/pmc07898400-63-9-12
    Average 99 stars, based on 509 article reviews
    dna cleanup kit - by Bioz Stars, 2026-10
    99/100 stars

    Images

    1) Product Images from "Development of a Cas12a-Based Genome Editing Tool for Moderate Thermophiles"

    Article Title: Development of a Cas12a-Based Genome Editing Tool for Moderate Thermophiles

    Journal: The CRISPR Journal

    doi: 10.1089/crispr.2020.0086

    Activity of Cas12a orthologs at varied temperatures. (A) Cas12a/SpCas9 proteins with their respective crRNA/sgRNA and buffer (same as indicated in (B)) were combined to form the ribonucleoprotein (RNPs) for 5 min at the temperatures indicated. The double-stranded DNA (dsDNA) cleavage reactions were initiated by adding the 5′-FAM-labeled dsDNA containing the target site preincubated at the designated incubation temperatures. Digested fragments were resolved by capillary electrophoresis, and peaks corresponding to cleaved and intact substrates were quantified. Data are shown as the mean ± standard deviation (SD) of three experimental replicates. (B) Recombinant crRNA-free Cas proteins or crRNA-loaded RNPs were subjected to thermal melting analysis using Nano differential scanning fluorimetry (Supplementary Figure S1). The melting temperature (Tm) of three experimental replicates are shown, with means ± SD indicated.
    Figure Legend Snippet: Activity of Cas12a orthologs at varied temperatures. (A) Cas12a/SpCas9 proteins with their respective crRNA/sgRNA and buffer (same as indicated in (B)) were combined to form the ribonucleoprotein (RNPs) for 5 min at the temperatures indicated. The double-stranded DNA (dsDNA) cleavage reactions were initiated by adding the 5′-FAM-labeled dsDNA containing the target site preincubated at the designated incubation temperatures. Digested fragments were resolved by capillary electrophoresis, and peaks corresponding to cleaved and intact substrates were quantified. Data are shown as the mean ± standard deviation (SD) of three experimental replicates. (B) Recombinant crRNA-free Cas proteins or crRNA-loaded RNPs were subjected to thermal melting analysis using Nano differential scanning fluorimetry (Supplementary Figure S1). The melting temperature (Tm) of three experimental replicates are shown, with means ± SD indicated.

    Techniques Used: Activity Assay, Labeling, Incubation, Electrophoresis, Standard Deviation, Recombinant, Nano Differential Scanning Fluorimetry

    Transformation of HR-FnCas12a mediated editing plasmids in B. smithii ET 138. (A) Schematic representation of the pFnCas12a_Δgene-of-interest (goi)-HR construct. The fncas12a gene was introduced to the pNW33n vector backbone. Homologous recombination (HR) flanks were introduced upstream fncas12a gene and encompassed the 1 kb upstream and 1 kb downstream region of the goi in the B. smithii genome. A crRNA-expressing module was introduced downstream the fncas12a gene. Other elements on the plasmid are origin of replication (ori), replication protein (repB), and chloramphenicol-resistance marker (CmR). (B) Sequential transfer scheme of B. smithii cultures to evaluate FnCas12a editing efficiency; detailed description of the protocol can be found in the Methods section. (C) Agarose gel electrophoresis showing the results from polymerase chain reaction on the genomic DNA of B. smithii cultures transformed with pFnCas12a_ΔpyrF-HR_Sp1 (1), pFnCas12a_ΔpyrF-HR_Sp2 (2), and pFnCas12a_ΔpyrF-HR_NT (NT) in two different selection media (TVMYxgu and LB2xgu). The last two lanes are the negative (wild type) and positive (ΔpyrF) controls that correspond to DNA fragments 2.9 and 2.2 kb long, respectively. (D) Representative image of the sequence verification of the desired pyrF gene deletion by Sanger sequencing.
    Figure Legend Snippet: Transformation of HR-FnCas12a mediated editing plasmids in B. smithii ET 138. (A) Schematic representation of the pFnCas12a_Δgene-of-interest (goi)-HR construct. The fncas12a gene was introduced to the pNW33n vector backbone. Homologous recombination (HR) flanks were introduced upstream fncas12a gene and encompassed the 1 kb upstream and 1 kb downstream region of the goi in the B. smithii genome. A crRNA-expressing module was introduced downstream the fncas12a gene. Other elements on the plasmid are origin of replication (ori), replication protein (repB), and chloramphenicol-resistance marker (CmR). (B) Sequential transfer scheme of B. smithii cultures to evaluate FnCas12a editing efficiency; detailed description of the protocol can be found in the Methods section. (C) Agarose gel electrophoresis showing the results from polymerase chain reaction on the genomic DNA of B. smithii cultures transformed with pFnCas12a_ΔpyrF-HR_Sp1 (1), pFnCas12a_ΔpyrF-HR_Sp2 (2), and pFnCas12a_ΔpyrF-HR_NT (NT) in two different selection media (TVMYxgu and LB2xgu). The last two lanes are the negative (wild type) and positive (ΔpyrF) controls that correspond to DNA fragments 2.9 and 2.2 kb long, respectively. (D) Representative image of the sequence verification of the desired pyrF gene deletion by Sanger sequencing.

    Techniques Used: Transformation Assay, Construct, Plasmid Preparation, Homologous Recombination, Expressing, Marker, Agarose Gel Electrophoresis, Polymerase Chain Reaction, Selection, Sequencing

    Related Articles

    Polymerase Chain Reaction:

    Article Title: Phylogenomics and morphology of Celmisiinae (Asteraceae: Astereae): Taxonomic and evolutionary implications.
    Article Snippet: Hybridisation was done at 65 ◦C for 22 h, and 13 cycles of amplification were carried out using NEBNext Ultra II Q5 Master Mix. .. Enriched PCR pools were cleaned with the Monarch PCR and DNA Cleanup Kit (New England Biolabs, Ipswich, MA, USA). ..

    Article Title: Genetic variation is a key determinant of chromatin accessibility and drives differences in the regulatory landscape of C57BL/6J and 129S1/SvImJ mice
    Article Snippet: .. The proteins were decrosslinked by adding Proteinase K (New England BioLabs, #T2002) and incubating at 65°C for 4 h and DNA purified using the Monarch PCR & DNA Cleanup Kit (New England BioLabs, #T1030), and eluting in 50 μl of Monarch DNA Elution Buffer. qPCRs were carried out as individual biological replicates for each of the immunoprecipitated and input DNA samples. qPCR analysis was carried out with LightCycler 480 SYBR Green I Master (Roche Diagnostics Gmbh). ..

    Article Title: Genome-Wide CRISPR-Cas9 Screening Identifies a Synergy between Hypomethylating Agents and SUMOylation Blockade in MDS/AML
    Article Snippet: Genomic regions flanking the expected cut sites for the indicated sgRNAs were PCR amplified using Q5 PCR Master Mix (NEB, #M0541L). .. PCR products were purified using the Monarch PCR and DNA Cleanup Kit (NEB, #T1030L) prior to Sanger sequencing. ..

    Article Title: TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons
    Article Snippet: .. Solubilized chromatin was then released using CUT&RUN stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg ml–1 RNase A, 50 μg ml–1 glycogen and 0.2 μg fly genomic DNA) and DNA purification was carried out using a PCR cleanup kit (NEB, Monarch PCR & DNA Cleanup kit, T1030). .. Next, 10 ng of the purified CUT&RUN DNA was used for preparation of multiplexed libraries with a NEB Ultra II DNA Library Prep kit per the manufacturer’s instruction (NEB, E7103).

    Purification:

    Article Title: TAD boundary deletion causes PITX2 -related cardiac electrical and structural defects
    Article Snippet: Antibodies mAb against acetyl H3K27 (H3K27ac,1:100, CST#39133), Monomethylated H3K4 (H3K4me1, 1:50, CST#39297) and CTCF (1:50, CST#61311) were also used. .. DNA was purified using a DNA purification kit (New England Biolabs#T1030). .. CUT&RUN libraries were prepared using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (E7645, NEB) according to the manufacturer’s instructions except for the End Prep step which took place for 30 min at 20 °C followed by 1 h at 50 °C in order not to denature the small fragments.

    Article Title: Genetic variation is a key determinant of chromatin accessibility and drives differences in the regulatory landscape of C57BL/6J and 129S1/SvImJ mice
    Article Snippet: .. The proteins were decrosslinked by adding Proteinase K (New England BioLabs, #T2002) and incubating at 65°C for 4 h and DNA purified using the Monarch PCR & DNA Cleanup Kit (New England BioLabs, #T1030), and eluting in 50 μl of Monarch DNA Elution Buffer. qPCRs were carried out as individual biological replicates for each of the immunoprecipitated and input DNA samples. qPCR analysis was carried out with LightCycler 480 SYBR Green I Master (Roche Diagnostics Gmbh). ..

    Article Title: Genome-Wide CRISPR-Cas9 Screening Identifies a Synergy between Hypomethylating Agents and SUMOylation Blockade in MDS/AML
    Article Snippet: Genomic regions flanking the expected cut sites for the indicated sgRNAs were PCR amplified using Q5 PCR Master Mix (NEB, #M0541L). .. PCR products were purified using the Monarch PCR and DNA Cleanup Kit (NEB, #T1030L) prior to Sanger sequencing. ..

    Article Title: TAD boundary deletion causes PITX2-related cardiac electrical and structural defects.
    Article Snippet: AntibodiesmAb against acetyl H3K27 (H3K27ac,1:100, CST#39133), Monomethylated H3K4 (H3K4me1, 1:50, CST#39297) and CTCF (1:50, CST#61311) were also used. .. DNA was purified using a DNA purification kit (New England Biolabs#T1030). .. CUT&RUN libraries were prepared using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (E7645, NEB) according to the manufacturer’s instructions except for the End Prep step which took place for 30min at 20 °C followed by 1 h at 50 °C in order not to denature the small fragments.The adapter-ligatedDNAwas cleanedup with Beckman CoulterTM Agencourt AMPure XP without size selection.

    DNA Purification:

    Article Title: TAD boundary deletion causes PITX2 -related cardiac electrical and structural defects
    Article Snippet: Antibodies mAb against acetyl H3K27 (H3K27ac,1:100, CST#39133), Monomethylated H3K4 (H3K4me1, 1:50, CST#39297) and CTCF (1:50, CST#61311) were also used. .. DNA was purified using a DNA purification kit (New England Biolabs#T1030). .. CUT&RUN libraries were prepared using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (E7645, NEB) according to the manufacturer’s instructions except for the End Prep step which took place for 30 min at 20 °C followed by 1 h at 50 °C in order not to denature the small fragments.

    Article Title: TAD boundary deletion causes PITX2-related cardiac electrical and structural defects.
    Article Snippet: AntibodiesmAb against acetyl H3K27 (H3K27ac,1:100, CST#39133), Monomethylated H3K4 (H3K4me1, 1:50, CST#39297) and CTCF (1:50, CST#61311) were also used. .. DNA was purified using a DNA purification kit (New England Biolabs#T1030). .. CUT&RUN libraries were prepared using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (E7645, NEB) according to the manufacturer’s instructions except for the End Prep step which took place for 30min at 20 °C followed by 1 h at 50 °C in order not to denature the small fragments.The adapter-ligatedDNAwas cleanedup with Beckman CoulterTM Agencourt AMPure XP without size selection.

    Article Title: TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons
    Article Snippet: .. Solubilized chromatin was then released using CUT&RUN stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg ml–1 RNase A, 50 μg ml–1 glycogen and 0.2 μg fly genomic DNA) and DNA purification was carried out using a PCR cleanup kit (NEB, Monarch PCR & DNA Cleanup kit, T1030). .. Next, 10 ng of the purified CUT&RUN DNA was used for preparation of multiplexed libraries with a NEB Ultra II DNA Library Prep kit per the manufacturer’s instruction (NEB, E7103).

    Immunoprecipitation:

    Article Title: Genetic variation is a key determinant of chromatin accessibility and drives differences in the regulatory landscape of C57BL/6J and 129S1/SvImJ mice
    Article Snippet: .. The proteins were decrosslinked by adding Proteinase K (New England BioLabs, #T2002) and incubating at 65°C for 4 h and DNA purified using the Monarch PCR & DNA Cleanup Kit (New England BioLabs, #T1030), and eluting in 50 μl of Monarch DNA Elution Buffer. qPCRs were carried out as individual biological replicates for each of the immunoprecipitated and input DNA samples. qPCR analysis was carried out with LightCycler 480 SYBR Green I Master (Roche Diagnostics Gmbh). ..

    Real-time Polymerase Chain Reaction:

    Article Title: Genetic variation is a key determinant of chromatin accessibility and drives differences in the regulatory landscape of C57BL/6J and 129S1/SvImJ mice
    Article Snippet: .. The proteins were decrosslinked by adding Proteinase K (New England BioLabs, #T2002) and incubating at 65°C for 4 h and DNA purified using the Monarch PCR & DNA Cleanup Kit (New England BioLabs, #T1030), and eluting in 50 μl of Monarch DNA Elution Buffer. qPCRs were carried out as individual biological replicates for each of the immunoprecipitated and input DNA samples. qPCR analysis was carried out with LightCycler 480 SYBR Green I Master (Roche Diagnostics Gmbh). ..

    SYBR Green Assay:

    Article Title: Genetic variation is a key determinant of chromatin accessibility and drives differences in the regulatory landscape of C57BL/6J and 129S1/SvImJ mice
    Article Snippet: .. The proteins were decrosslinked by adding Proteinase K (New England BioLabs, #T2002) and incubating at 65°C for 4 h and DNA purified using the Monarch PCR & DNA Cleanup Kit (New England BioLabs, #T1030), and eluting in 50 μl of Monarch DNA Elution Buffer. qPCRs were carried out as individual biological replicates for each of the immunoprecipitated and input DNA samples. qPCR analysis was carried out with LightCycler 480 SYBR Green I Master (Roche Diagnostics Gmbh). ..

    Gel Extraction:

    Article Title: A sensitive and scalable fluorescence anisotropy single stranded RNA targeting approach for monitoring riboswitch conformational states.
    Article Snippet: .. The following reagents were used for RNA production: Phusion HF Polymerase (#M0530S; New England Biolabs; Ipswich, MA, USA); Monarch DNA Cleanup and gel extraction kit (#T1030L; New England Biolabs; Ipswich, MA, USA); MEGAshortscript T7 Transcription Kit (#AM1354; Thermo Fisher; Waltham, MA, USA); RNA Clean & Concentrator kit (#R1018; Zymo Research; Irvine, C A, US A); and 0.025 μm MCE membrane filter disks (#VSWP02500; MF-Millipore; Burlington, MA, USA). .. For the surface plasmon resonance, a Biacore X100 (Cytiva Lifesciences; Marlborough, MA, USA) was used with CM5 chips (#BR100012; Cytiva Lifesciences; Marlborough, MA, USA) and HBS-N buffer 10 × (#BR100828; Cytiva Lifesciences; Marlborough, MA, USA).

    Article Title: A sensitive and scalable fluorescence anisotropy single stranded RNA targeting approach for monitoring riboswitch conformational states
    Article Snippet: .. The following reagents were used for RNA production: Phusion HF Polymerase (#M0530S; New England Biolabs; Ipswich, MA, USA); Monarch DNA Cleanup and gel extraction kit (#T1030L; New England Biolabs; Ipswich, MA, USA); MEGAshortscript T7 Transcription Kit (#AM1354; Thermo Fisher; Waltham, MA, USA); RNA Clean & Concentrator kit (#R1018; Zymo Research; Irvine, CA, USA); and 0.025 μm MCE membrane filter disks (#VSWP02500; MF-Millipore; Burlington, MA, USA). .. For the surface plasmon resonance, a Biacore X100 (Cytiva Lifesciences; Marlborough, MA, USA) was used with CM5 chips (#BR100012; Cytiva Lifesciences; Marlborough, MA, USA) and HBS-N buffer 10× (#BR100828; Cytiva Lifesciences; Marlborough, MA, USA).

    Membrane:

    Article Title: A sensitive and scalable fluorescence anisotropy single stranded RNA targeting approach for monitoring riboswitch conformational states.
    Article Snippet: .. The following reagents were used for RNA production: Phusion HF Polymerase (#M0530S; New England Biolabs; Ipswich, MA, USA); Monarch DNA Cleanup and gel extraction kit (#T1030L; New England Biolabs; Ipswich, MA, USA); MEGAshortscript T7 Transcription Kit (#AM1354; Thermo Fisher; Waltham, MA, USA); RNA Clean & Concentrator kit (#R1018; Zymo Research; Irvine, C A, US A); and 0.025 μm MCE membrane filter disks (#VSWP02500; MF-Millipore; Burlington, MA, USA). .. For the surface plasmon resonance, a Biacore X100 (Cytiva Lifesciences; Marlborough, MA, USA) was used with CM5 chips (#BR100012; Cytiva Lifesciences; Marlborough, MA, USA) and HBS-N buffer 10 × (#BR100828; Cytiva Lifesciences; Marlborough, MA, USA).

    Article Title: A sensitive and scalable fluorescence anisotropy single stranded RNA targeting approach for monitoring riboswitch conformational states
    Article Snippet: .. The following reagents were used for RNA production: Phusion HF Polymerase (#M0530S; New England Biolabs; Ipswich, MA, USA); Monarch DNA Cleanup and gel extraction kit (#T1030L; New England Biolabs; Ipswich, MA, USA); MEGAshortscript T7 Transcription Kit (#AM1354; Thermo Fisher; Waltham, MA, USA); RNA Clean & Concentrator kit (#R1018; Zymo Research; Irvine, CA, USA); and 0.025 μm MCE membrane filter disks (#VSWP02500; MF-Millipore; Burlington, MA, USA). .. For the surface plasmon resonance, a Biacore X100 (Cytiva Lifesciences; Marlborough, MA, USA) was used with CM5 chips (#BR100012; Cytiva Lifesciences; Marlborough, MA, USA) and HBS-N buffer 10× (#BR100828; Cytiva Lifesciences; Marlborough, MA, USA).

    Sequencing:

    Article Title: Genome-Wide CRISPR-Cas9 Screening Identifies a Synergy between Hypomethylating Agents and SUMOylation Blockade in MDS/AML
    Article Snippet: Genomic regions flanking the expected cut sites for the indicated sgRNAs were PCR amplified using Q5 PCR Master Mix (NEB, #M0541L). .. PCR products were purified using the Monarch PCR and DNA Cleanup Kit (NEB, #T1030L) prior to Sanger sequencing. ..



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    Image Search Results


    List of differentially expressed salt stress responsive ggenes selected by the MapMan program.

    Journal: PeerJ

    Article Title: Identification and transcriptomic profiling of salinity stress response genes in colored wheat mutant

    doi: 10.7717/peerj.17043

    Figure Lengend Snippet: List of differentially expressed salt stress responsive ggenes selected by the MapMan program.

    Article Snippet: TraesCS5D02G492300 , Actin depolymerization factor-like protein , 147 , 6.3E−105 , 87.63 , 0.55 , 0.09 , 0.38 , −3 . 25 , 2.08E−11 , 5.07E−10 , Cytoskeleton organization.

    Techniques: