s1 nuclease  (Thermo Fisher)


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    Structured Review

    Thermo Fisher s1 nuclease
    Summary of nuclease sensitivity of the heat-treated Rif1BS-derived duplex DNAs. Portions of the sequences of the Rif1BS I:2663 and Rif1BS II:4255 are shown. Locations of <t>S1</t> nuclease sensitivities and those of protection from DNase I digestion are shown for both strands, as indicated in the key .
    S1 Nuclease, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 103 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/s1 nuclease/product/Thermo Fisher
    Average 95 stars, based on 103 article reviews
    Price from $9.99 to $1999.99
    s1 nuclease - by Bioz Stars, 2020-05
    95/100 stars

    Images

    1) Product Images from "Molecular architecture of G-quadruplex structures generated on duplex Rif1-binding sequences"

    Article Title: Molecular architecture of G-quadruplex structures generated on duplex Rif1-binding sequences

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.RA118.005240

    Summary of nuclease sensitivity of the heat-treated Rif1BS-derived duplex DNAs. Portions of the sequences of the Rif1BS I:2663 and Rif1BS II:4255 are shown. Locations of S1 nuclease sensitivities and those of protection from DNase I digestion are shown for both strands, as indicated in the key .
    Figure Legend Snippet: Summary of nuclease sensitivity of the heat-treated Rif1BS-derived duplex DNAs. Portions of the sequences of the Rif1BS I:2663 and Rif1BS II:4255 are shown. Locations of S1 nuclease sensitivities and those of protection from DNase I digestion are shown for both strands, as indicated in the key .

    Techniques Used: Derivative Assay

    2) Product Images from "Molecular architecture of G-quadruplex structures generated on duplex Rif1-binding sequences"

    Article Title: Molecular architecture of G-quadruplex structures generated on duplex Rif1-binding sequences

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.RA118.005240

    Summary of nuclease sensitivity of the heat-treated Rif1BS-derived duplex DNAs. Portions of the sequences of the Rif1BS I:2663 and Rif1BS II:4255 are shown. Locations of S1 nuclease sensitivities and those of protection from DNase I digestion are shown for both strands, as indicated in the key .
    Figure Legend Snippet: Summary of nuclease sensitivity of the heat-treated Rif1BS-derived duplex DNAs. Portions of the sequences of the Rif1BS I:2663 and Rif1BS II:4255 are shown. Locations of S1 nuclease sensitivities and those of protection from DNase I digestion are shown for both strands, as indicated in the key .

    Techniques Used: Derivative Assay

    Related Articles

    Sequencing:

    Article Title: Bleomycin-induced genome structural variations in normal, non-tumor cells
    Article Snippet: .. Ligation-mediated chimera-free (LCF) libraries were prepared as follows: Fragmentation using NEBNext dsDNA Fragmentase (NEB); End-repair I using S1 nuclease (Thermo Fisher Scientific, Waltham, MA USA); A-tailing using Terminal Transferase (TdT) polymerase (NEB) and dATP (NEB); Ligation of single-stranded sequencing adaptors using Taq DNA Ligase (NEB). .. The sequencing adaptor oligos were: 5′-CCTCTCTATGGGCAGTCGGTGATTTTTTTT-3′ (universal adaptor) and 5′-CCATCTCATCCCTGCGTGTCTCCGACTCAG NNNNNNNNNN TTTTTTTT-3′ (barcoded adaptors, where NNNNNNNNNN represents an IonXpress barcode); End-repair II using T4 DNA polymerase (NEB) and dNTP mix (NEB).

    Incubation:

    Article Title: USP1 is Required for Replication Fork Protection in BRCA1-Deficient Tumors
    Article Snippet: .. For S1 nuclease treatment, S1 nuclease (ThermoFisher Scientific) was added to DNA solution following agarase treatment and incubated at room temperature for 30 min. Nuclease treated samples were then poured into FiberComb wells and combed onto silanized coverslips. .. Cells were transfected with siRNA or plasmid 18–24h before being plated for colony formation assays.

    other:

    Article Title: Molecular architecture of G-quadruplex structures generated on duplex Rif1-binding sequences
    Article Snippet: The amount of DNase I, S1 nuclease, and T7 endonuclease was titrated in each experiment.

    Binding Assay:

    Article Title: Molecular architecture of G-quadruplex structures generated on duplex Rif1-binding sequences
    Article Snippet: .. For DNase I digestion, 32 P-end–labeled DNA (heat-treated in 50 m m KCl and 40% PEG 200 or nontreated) was digested with DNase I (Takara; 5 units/μl; 1 μl of 1:1000 to 1:5000 dilution (0.005–0.001 units) was used per assay) in 10 μl of 1× DNA binding buffer containing 8 m m MgOAc and 0.5 m m CaCl2 at room temperature for 2.5 min. For S1 nuclease mapping, DNA was digested with S1 nuclease (Thermo Fisher Scientific; 1–3 units) in 10 μl of 10× S1 buffer (supplied with the enzyme) at room temperature for 2.5–5 min. For T7 endonuclease mapping, DNA was digested in 50 m m NaCl, 10 m m Tris-HCl (pH 7.9), 10 m m MgCl2 , and 1 m m DTT with T7 endonuclease I (New England Biolabs; 0.5–5 units) for 10 min at 37 °C in 50 μl. ..

    Ligation:

    Article Title: Bleomycin-induced genome structural variations in normal, non-tumor cells
    Article Snippet: .. Ligation-mediated chimera-free (LCF) libraries were prepared as follows: Fragmentation using NEBNext dsDNA Fragmentase (NEB); End-repair I using S1 nuclease (Thermo Fisher Scientific, Waltham, MA USA); A-tailing using Terminal Transferase (TdT) polymerase (NEB) and dATP (NEB); Ligation of single-stranded sequencing adaptors using Taq DNA Ligase (NEB). .. The sequencing adaptor oligos were: 5′-CCTCTCTATGGGCAGTCGGTGATTTTTTTT-3′ (universal adaptor) and 5′-CCATCTCATCCCTGCGTGTCTCCGACTCAG NNNNNNNNNN TTTTTTTT-3′ (barcoded adaptors, where NNNNNNNNNN represents an IonXpress barcode); End-repair II using T4 DNA polymerase (NEB) and dNTP mix (NEB).

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    Thermo Fisher s1 nuclease
    Electrophoresis analysis, enzyme treatment, and genomic characteristics and organization of the eight dsRNA segments extracted from mycelia of Colletotrichum camelliae strain LT-3-1. a Electrophoretic profiles on a 1.2% agarose gel of dsRNA preparations from strain LT-3-1 before (−) and after (+) digestion with DNase I and S1 nuclease, and from strain DP-3-1 after digestion with both enzymes. Nucleic acid sizes are indicated beside the gels. b Electrophoresis analysis of enzyme-treated nucleic acid samples on 1.2% agarose gels. The samples were treated with RNase III, <t>S1</t> nuclease and RNase A (in 2× and 0.1× SSC), respectively. “−” and “+” refer to incubated in the reaction buffer without and with the enzyme, respectively. CEVd and BdCV 1, ssRNA transcripts from dimeric cDNAs of citrus exocortis viroid ( CEVd ), and dsRNA extracts from mycelia of Botryosphaeria dothidea chrysovirus 1 ( BdCV 1 ), respectively. The upper bands on the lane of CEVd sample correspond to the remnant plasmid used for transcription, and the lower bands to the transcripts (two bands due to conformation difference). c Genomic organization of dsRNAs 1–8 showing putative open reading frames ( ORFs ) and untranslated regions ( UTRs ). The dot line refers to the separation of the both gels migrated in separate lanes with treatments in parallel
    S1 Nuclease, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 103 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/s1 nuclease/product/Thermo Fisher
    Average 99 stars, based on 103 article reviews
    Price from $9.99 to $1999.99
    s1 nuclease - by Bioz Stars, 2020-05
    99/100 stars
      Buy from Supplier

    88
    Thermo Fisher rnase s1
    Enzymatic probing analysis of hmtRNA Thr , -G30A and -G30A/C40U. ( A ) Probing was performed using various <t>RNase</t> S1 concentrations. Lane C, control; lane G, ladder digested by RNase T1 under denaturing conditions; lane OH − , alkaline digestion. ( B ) Structure analysis by enzymatic probing. The red stars indicate the main RNase S1 cleavage sites.
    Rnase S1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rnase s1/product/Thermo Fisher
    Average 88 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    rnase s1 - by Bioz Stars, 2020-05
    88/100 stars
      Buy from Supplier

    Image Search Results


    Electrophoresis analysis, enzyme treatment, and genomic characteristics and organization of the eight dsRNA segments extracted from mycelia of Colletotrichum camelliae strain LT-3-1. a Electrophoretic profiles on a 1.2% agarose gel of dsRNA preparations from strain LT-3-1 before (−) and after (+) digestion with DNase I and S1 nuclease, and from strain DP-3-1 after digestion with both enzymes. Nucleic acid sizes are indicated beside the gels. b Electrophoresis analysis of enzyme-treated nucleic acid samples on 1.2% agarose gels. The samples were treated with RNase III, S1 nuclease and RNase A (in 2× and 0.1× SSC), respectively. “−” and “+” refer to incubated in the reaction buffer without and with the enzyme, respectively. CEVd and BdCV 1, ssRNA transcripts from dimeric cDNAs of citrus exocortis viroid ( CEVd ), and dsRNA extracts from mycelia of Botryosphaeria dothidea chrysovirus 1 ( BdCV 1 ), respectively. The upper bands on the lane of CEVd sample correspond to the remnant plasmid used for transcription, and the lower bands to the transcripts (two bands due to conformation difference). c Genomic organization of dsRNAs 1–8 showing putative open reading frames ( ORFs ) and untranslated regions ( UTRs ). The dot line refers to the separation of the both gels migrated in separate lanes with treatments in parallel

    Journal: Nature Communications

    Article Title: A dsRNA virus with filamentous viral particles

    doi: 10.1038/s41467-017-00237-9

    Figure Lengend Snippet: Electrophoresis analysis, enzyme treatment, and genomic characteristics and organization of the eight dsRNA segments extracted from mycelia of Colletotrichum camelliae strain LT-3-1. a Electrophoretic profiles on a 1.2% agarose gel of dsRNA preparations from strain LT-3-1 before (−) and after (+) digestion with DNase I and S1 nuclease, and from strain DP-3-1 after digestion with both enzymes. Nucleic acid sizes are indicated beside the gels. b Electrophoresis analysis of enzyme-treated nucleic acid samples on 1.2% agarose gels. The samples were treated with RNase III, S1 nuclease and RNase A (in 2× and 0.1× SSC), respectively. “−” and “+” refer to incubated in the reaction buffer without and with the enzyme, respectively. CEVd and BdCV 1, ssRNA transcripts from dimeric cDNAs of citrus exocortis viroid ( CEVd ), and dsRNA extracts from mycelia of Botryosphaeria dothidea chrysovirus 1 ( BdCV 1 ), respectively. The upper bands on the lane of CEVd sample correspond to the remnant plasmid used for transcription, and the lower bands to the transcripts (two bands due to conformation difference). c Genomic organization of dsRNAs 1–8 showing putative open reading frames ( ORFs ) and untranslated regions ( UTRs ). The dot line refers to the separation of the both gels migrated in separate lanes with treatments in parallel

    Article Snippet: Briefly, aliquots of 200 ng of total dsRNA were digested with 2 U DNase I (New England Biolabs) at 37 °C for 1 h, treated with phenol/chloroform/isoamyl alcohol (25:24:1) (phenol saturated with water, pH 5.2), precipitated with ethanol, dissolved in diethylpyrocarbonate (DEPC)-treated water, and treated with 10 U S1 nuclease (Thermo Scientific) at 37 °C for 1 h. The purified RNAs were analyzed by 1.2% agarose gel electrophoresis and visualized by staining with ethidium bromide.

    Techniques: Electrophoresis, Agarose Gel Electrophoresis, Incubation, Plasmid Preparation

    Summary of nuclease sensitivity of the heat-treated Rif1BS-derived duplex DNAs. Portions of the sequences of the Rif1BS I:2663 and Rif1BS II:4255 are shown. Locations of S1 nuclease sensitivities and those of protection from DNase I digestion are shown for both strands, as indicated in the key .

    Journal: The Journal of Biological Chemistry

    Article Title: Molecular architecture of G-quadruplex structures generated on duplex Rif1-binding sequences

    doi: 10.1074/jbc.RA118.005240

    Figure Lengend Snippet: Summary of nuclease sensitivity of the heat-treated Rif1BS-derived duplex DNAs. Portions of the sequences of the Rif1BS I:2663 and Rif1BS II:4255 are shown. Locations of S1 nuclease sensitivities and those of protection from DNase I digestion are shown for both strands, as indicated in the key .

    Article Snippet: For DNase I digestion, 32 P-end–labeled DNA (heat-treated in 50 m m KCl and 40% PEG 200 or nontreated) was digested with DNase I (Takara; 5 units/μl; 1 μl of 1:1000 to 1:5000 dilution (0.005–0.001 units) was used per assay) in 10 μl of 1× DNA binding buffer containing 8 m m MgOAc and 0.5 m m CaCl2 at room temperature for 2.5 min. For S1 nuclease mapping, DNA was digested with S1 nuclease (Thermo Fisher Scientific; 1–3 units) in 10 μl of 10× S1 buffer (supplied with the enzyme) at room temperature for 2.5–5 min. For T7 endonuclease mapping, DNA was digested in 50 m m NaCl, 10 m m Tris-HCl (pH 7.9), 10 m m MgCl2 , and 1 m m DTT with T7 endonuclease I (New England Biolabs; 0.5–5 units) for 10 min at 37 °C in 50 μl.

    Techniques: Derivative Assay

    Schematic of RNA structure probing by PARS in zebrafish. Poly-A RNA from zebrafish is folded in-vitro. The folded RNA is cleaved by RNase V1 and S1 nuclease separately. The enzyme cut sites generate 5’P ends and 3’ OH ends at the cleaved sites. Long fragments generated by single-hit kinetics are further fragmented by alkaline hydrolysis, which blocks the 3′ site of the enzyme-cut fragments. Sequencing adapters are ligated to the 5′ end followed by alkaline phosphatase treatment to 3’ P group. Adapters are ligated to 3’ends followed cDNA synthesis and PCR purification of the library. Appropriate size of the library is maintained by purification by nucleic acid beads. Sequenced reads are aligned back to the genome and only unique reads with the correct read start positions are considered for PARS score calculation

    Journal: BMC Genomics

    Article Title: RNA secondary structure profiling in zebrafish reveals unique regulatory features

    doi: 10.1186/s12864-018-4497-0

    Figure Lengend Snippet: Schematic of RNA structure probing by PARS in zebrafish. Poly-A RNA from zebrafish is folded in-vitro. The folded RNA is cleaved by RNase V1 and S1 nuclease separately. The enzyme cut sites generate 5’P ends and 3’ OH ends at the cleaved sites. Long fragments generated by single-hit kinetics are further fragmented by alkaline hydrolysis, which blocks the 3′ site of the enzyme-cut fragments. Sequencing adapters are ligated to the 5′ end followed by alkaline phosphatase treatment to 3’ P group. Adapters are ligated to 3’ends followed cDNA synthesis and PCR purification of the library. Appropriate size of the library is maintained by purification by nucleic acid beads. Sequenced reads are aligned back to the genome and only unique reads with the correct read start positions are considered for PARS score calculation

    Article Snippet: Further, the poly-A pool was folded in RNA Structure Buffer (Life Technologies, USA) containing 10 mM Tris pH 7, 100 mM KCl, and 10 mM MgCl2 slowly from 4 °C to 28 °C for 25 min. Each 2 μg of Poly-A RNA was digested with 10 μl (0.000125 U) of RNase V1 (Life Technologies, USA) for 45 s and 10 μl (10,000 U) of S1 Nuclease (Thermo Fisher Scientific, USA) for 10 min to achieve single hit kinetics.

    Techniques: In Vitro, Generated, Sequencing, Polymerase Chain Reaction, Purification

    Comparison of RNA structures of ubc 3’UTR as determined by PARS based pairing probability and enzymatic footprinting using RNase V1 and S1 Nuclease. a . Bar plot represents PARS scores of 3’UTR region of ubiquitin c (ubc) . Out of 105 positions, 87 positions are captured by PARS. b . Enzymatic footprinting of ubc 3’UTR probed by S1 Nuclease and RNase V1. Nucleotide positions are correlated with alkaline hydrolysis (AH) ladder and RNase T1 (G) ladder. Positions with similar structural pattern with PARS scores are highlighted. Red dots indicate unpaired positions; green indicates paired positions while yellow represents ambiguous regions. c . Heatmap representing secondary structure of 68 positions of ubc 3’UTR as determined by PARS and enzymatic footprinting (FP). Top panel represents PARS pairing probability; bottom panel indicates enzymatic footprinting pairing probability; middle panel represents the consensus between the two (PARS: FP). Red represents unpaired, green represents paired and yellow represents ambiguous regions

    Journal: BMC Genomics

    Article Title: RNA secondary structure profiling in zebrafish reveals unique regulatory features

    doi: 10.1186/s12864-018-4497-0

    Figure Lengend Snippet: Comparison of RNA structures of ubc 3’UTR as determined by PARS based pairing probability and enzymatic footprinting using RNase V1 and S1 Nuclease. a . Bar plot represents PARS scores of 3’UTR region of ubiquitin c (ubc) . Out of 105 positions, 87 positions are captured by PARS. b . Enzymatic footprinting of ubc 3’UTR probed by S1 Nuclease and RNase V1. Nucleotide positions are correlated with alkaline hydrolysis (AH) ladder and RNase T1 (G) ladder. Positions with similar structural pattern with PARS scores are highlighted. Red dots indicate unpaired positions; green indicates paired positions while yellow represents ambiguous regions. c . Heatmap representing secondary structure of 68 positions of ubc 3’UTR as determined by PARS and enzymatic footprinting (FP). Top panel represents PARS pairing probability; bottom panel indicates enzymatic footprinting pairing probability; middle panel represents the consensus between the two (PARS: FP). Red represents unpaired, green represents paired and yellow represents ambiguous regions

    Article Snippet: Further, the poly-A pool was folded in RNA Structure Buffer (Life Technologies, USA) containing 10 mM Tris pH 7, 100 mM KCl, and 10 mM MgCl2 slowly from 4 °C to 28 °C for 25 min. Each 2 μg of Poly-A RNA was digested with 10 μl (0.000125 U) of RNase V1 (Life Technologies, USA) for 45 s and 10 μl (10,000 U) of S1 Nuclease (Thermo Fisher Scientific, USA) for 10 min to achieve single hit kinetics.

    Techniques: Footprinting

    Enzymatic probing analysis of hmtRNA Thr , -G30A and -G30A/C40U. ( A ) Probing was performed using various RNase S1 concentrations. Lane C, control; lane G, ladder digested by RNase T1 under denaturing conditions; lane OH − , alkaline digestion. ( B ) Structure analysis by enzymatic probing. The red stars indicate the main RNase S1 cleavage sites.

    Journal: Nucleic Acids Research

    Article Title: A natural non-Watson–Crick base pair in human mitochondrial tRNAThr causes structural and functional susceptibility to local mutations

    doi: 10.1093/nar/gky243

    Figure Lengend Snippet: Enzymatic probing analysis of hmtRNA Thr , -G30A and -G30A/C40U. ( A ) Probing was performed using various RNase S1 concentrations. Lane C, control; lane G, ladder digested by RNase T1 under denaturing conditions; lane OH − , alkaline digestion. ( B ) Structure analysis by enzymatic probing. The red stars indicate the main RNase S1 cleavage sites.

    Article Snippet: T4 DNA ligase, T4 PNK (polynucleotide kinase), RNase T1, RNase S1, and restriction endonucleases were obtained from Thermo Scientific (Pittsburgh, PA, USA).

    Techniques: