cobra venom rnase v1  (Thermo Fisher)


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    Structured Review

    Thermo Fisher cobra venom rnase v1
    ( A ) Sequence and secondary structure for the 5′ and the 3′ ends of the HCV genome. The 5′ UTR plus domains V and VI located at the core coding sequence are included. The minimum region for IRES activity is shown. The 3′ end of the viral genomic RNA is organized into two structural elements: the CRE region and the 3′X-tail, separated by a hypervariable sequence and the polyU/UC stretch. Numbers refer to the nucleotide positions of the HCV Con1 isolate. Residues accessible to <t>RNase</t> T1, RNase V1, or lead processing under nondenaturing conditions are indicated by an asterisk, an arrow, or underlined, respectively. Start and stop translation codons placed at positions 342 and 9371, respectively, are shown in bold. ( B ) Diagram of the transcripts encompassing different functional domains of both the 5′ and the 3′ ends of the HCV genome used in this study.
    Cobra Venom Rnase V1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    cobra venom rnase v1 - by Bioz Stars, 2020-07
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    1) Product Images from "A long-range RNA–RNA interaction between the 5′ and 3′ ends of the HCV genome"

    Article Title: A long-range RNA–RNA interaction between the 5′ and 3′ ends of the HCV genome

    Journal: RNA

    doi: 10.1261/rna.1680809

    ( A ) Sequence and secondary structure for the 5′ and the 3′ ends of the HCV genome. The 5′ UTR plus domains V and VI located at the core coding sequence are included. The minimum region for IRES activity is shown. The 3′ end of the viral genomic RNA is organized into two structural elements: the CRE region and the 3′X-tail, separated by a hypervariable sequence and the polyU/UC stretch. Numbers refer to the nucleotide positions of the HCV Con1 isolate. Residues accessible to RNase T1, RNase V1, or lead processing under nondenaturing conditions are indicated by an asterisk, an arrow, or underlined, respectively. Start and stop translation codons placed at positions 342 and 9371, respectively, are shown in bold. ( B ) Diagram of the transcripts encompassing different functional domains of both the 5′ and the 3′ ends of the HCV genome used in this study.
    Figure Legend Snippet: ( A ) Sequence and secondary structure for the 5′ and the 3′ ends of the HCV genome. The 5′ UTR plus domains V and VI located at the core coding sequence are included. The minimum region for IRES activity is shown. The 3′ end of the viral genomic RNA is organized into two structural elements: the CRE region and the 3′X-tail, separated by a hypervariable sequence and the polyU/UC stretch. Numbers refer to the nucleotide positions of the HCV Con1 isolate. Residues accessible to RNase T1, RNase V1, or lead processing under nondenaturing conditions are indicated by an asterisk, an arrow, or underlined, respectively. Start and stop translation codons placed at positions 342 and 9371, respectively, are shown in bold. ( B ) Diagram of the transcripts encompassing different functional domains of both the 5′ and the 3′ ends of the HCV genome used in this study.

    Techniques Used: Sequencing, Activity Assay, Functional Assay

    Secondary structure analysis of the 5′ and the 3′ ends of the HCV genome and identification of the interacting residues. ( A ) 32 P-5′-end-labeled 5′HCV-691 was partially digested with RNase T1 or Pb 2+ , either in the absence (−) or presence (+) of the 3′HCV-9181. The right panel shows a different run length aimed to resolve the higher molecular weight cleavage products. The functional subdomains of the IRES region are indicated. C, 5′HCV-691 incubated in binding buffer. T1L, T1 cleavage ladder. ( B ) Primer extension analysis of the 3′HCV-9181 transcript treated with RNase T1 or RNase V1 in the absence (−) or presence (+) of the 5′-end RNA. cDNA products were analyzed in 6% denaturing polyacrylamide gels in parallel with a sequence ladder obtained with the same labeled primer. The autoradiograph shows the results obtained for the CRE region.
    Figure Legend Snippet: Secondary structure analysis of the 5′ and the 3′ ends of the HCV genome and identification of the interacting residues. ( A ) 32 P-5′-end-labeled 5′HCV-691 was partially digested with RNase T1 or Pb 2+ , either in the absence (−) or presence (+) of the 3′HCV-9181. The right panel shows a different run length aimed to resolve the higher molecular weight cleavage products. The functional subdomains of the IRES region are indicated. C, 5′HCV-691 incubated in binding buffer. T1L, T1 cleavage ladder. ( B ) Primer extension analysis of the 3′HCV-9181 transcript treated with RNase T1 or RNase V1 in the absence (−) or presence (+) of the 5′-end RNA. cDNA products were analyzed in 6% denaturing polyacrylamide gels in parallel with a sequence ladder obtained with the same labeled primer. The autoradiograph shows the results obtained for the CRE region.

    Techniques Used: Labeling, Molecular Weight, Functional Assay, Incubation, Binding Assay, Sequencing, Autoradiography

    Related Articles

    Combined Bisulfite Restriction Analysis Assay:

    Article Title: A long-range RNA–RNA interaction between the 5′ and 3′ ends of the HCV genome
    Article Snippet: .. Briefly, complex formation was accomplished as noted above and subjected to partial digestion with 0.1 units of cobra venom RNase V1 (Pierce Biotechnology) or 0.1 units of RNase T1 (Industrial Research) at 4°C for 10 and 5 min, respectively. .. Cleavage reactions were stopped as above and the RNA extracted using phenol-chloroform followed by ethanol precipitation.

    Article Title: Trypanosoma brucei 20 S Editosomes Have One RNA Substrate-binding Site and Execute RNA Unwinding Activity *
    Article Snippet: .. RNA cleavage was performed with 60 units/ml RNase T1 (Fermentas) or 3 units/ml cobra venom RNase V1 (Ambion) for 2 min at room temperature. ..

    Article Title: A cis-Acting Replication Element in the Sequence Encoding the NS5B RNA-Dependent RNA Polymerase Is Required for Hepatitis C Virus RNA Replication
    Article Snippet: .. One microgram of transcript RNA was treated with cobra venom RNase V1 (Ambion) or RNase T1 (U.S. Biochemicals) at 0°C for 30 min as described elsewhere ( ). ..

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    Thermo Fisher rnase v1
    Addition of CA-repeats does not change the secondary structure of the coat RBS stem–loop. ( A ) Enzymatic and chemical structure probing was conducted on control mRNA (00) or mRNAs with tails of 4, 6 or 8 (CA)-repeats, (see Materials and Methods), as indicated. The mRNAs were mock-treated (lanes ‘–’), partially digested with double-strand-specific <t>RNase</t> V1 (V1), or treated with lead(II) acetate (Pb 2+ ). UCGA: sequencing reactions on (CA)8 mRNA. The position of the SD and AUG start codon are indicated by red boxes. Regions of reactivity toward RNase V1 (red solid line) and lead(II) acetate (red dashed line) are indicated on the autoradiogram. ( B ) The localization of RNase V1 (filled triangles) and lead(II) acetate (black dots) cuts are shown on the secondary structure of the 5′-segment of (CA)8 mRNA. Black boxes: SD and AUG.
    Rnase V1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 123 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Addition of CA-repeats does not change the secondary structure of the coat RBS stem–loop. ( A ) Enzymatic and chemical structure probing was conducted on control mRNA (00) or mRNAs with tails of 4, 6 or 8 (CA)-repeats, (see Materials and Methods), as indicated. The mRNAs were mock-treated (lanes ‘–’), partially digested with double-strand-specific RNase V1 (V1), or treated with lead(II) acetate (Pb 2+ ). UCGA: sequencing reactions on (CA)8 mRNA. The position of the SD and AUG start codon are indicated by red boxes. Regions of reactivity toward RNase V1 (red solid line) and lead(II) acetate (red dashed line) are indicated on the autoradiogram. ( B ) The localization of RNase V1 (filled triangles) and lead(II) acetate (black dots) cuts are shown on the secondary structure of the 5′-segment of (CA)8 mRNA. Black boxes: SD and AUG.

    Journal: Nucleic Acids Research

    Article Title: Unstructured 5′-tails act through ribosome standby to override inhibitory structure at ribosome binding sites

    doi: 10.1093/nar/gky073

    Figure Lengend Snippet: Addition of CA-repeats does not change the secondary structure of the coat RBS stem–loop. ( A ) Enzymatic and chemical structure probing was conducted on control mRNA (00) or mRNAs with tails of 4, 6 or 8 (CA)-repeats, (see Materials and Methods), as indicated. The mRNAs were mock-treated (lanes ‘–’), partially digested with double-strand-specific RNase V1 (V1), or treated with lead(II) acetate (Pb 2+ ). UCGA: sequencing reactions on (CA)8 mRNA. The position of the SD and AUG start codon are indicated by red boxes. Regions of reactivity toward RNase V1 (red solid line) and lead(II) acetate (red dashed line) are indicated on the autoradiogram. ( B ) The localization of RNase V1 (filled triangles) and lead(II) acetate (black dots) cuts are shown on the secondary structure of the 5′-segment of (CA)8 mRNA. Black boxes: SD and AUG.

    Article Snippet: RNase V1 probing used a final concentration of 0.01 U/μl (ThermoFisher Scientific, #AM2275) for 5 min at 37°C.

    Techniques: Sequencing

    Addition of CA-repeats does not change the secondary structure of the coat RBS stem–loop. ( A ) Enzymatic and chemical structure probing was conducted on control mRNA (00) or mRNAs with tails of 4, 6 or 8 (CA)-repeats, (see Materials and Methods), as indicated. The mRNAs were mock-treated (lanes ‘–’), partially digested with double-strand-specific RNase V1 (V1), or treated with lead(II) acetate (Pb 2+ ). UCGA: sequencing reactions on (CA)8 mRNA. The position of the SD and AUG start codon are indicated by red boxes. Regions of reactivity toward RNase V1 (red solid line) and lead(II) acetate (red dashed line) are indicated on the autoradiogram. ( B ) The localization of RNase V1 (filled triangles) and lead(II) acetate (black dots) cuts are shown on the secondary structure of the 5′-segment of (CA)8 mRNA. Black boxes: SD and AUG.

    Journal: Nucleic Acids Research

    Article Title: Unstructured 5′-tails act through ribosome standby to override inhibitory structure at ribosome binding sites

    doi: 10.1093/nar/gky073

    Figure Lengend Snippet: Addition of CA-repeats does not change the secondary structure of the coat RBS stem–loop. ( A ) Enzymatic and chemical structure probing was conducted on control mRNA (00) or mRNAs with tails of 4, 6 or 8 (CA)-repeats, (see Materials and Methods), as indicated. The mRNAs were mock-treated (lanes ‘–’), partially digested with double-strand-specific RNase V1 (V1), or treated with lead(II) acetate (Pb 2+ ). UCGA: sequencing reactions on (CA)8 mRNA. The position of the SD and AUG start codon are indicated by red boxes. Regions of reactivity toward RNase V1 (red solid line) and lead(II) acetate (red dashed line) are indicated on the autoradiogram. ( B ) The localization of RNase V1 (filled triangles) and lead(II) acetate (black dots) cuts are shown on the secondary structure of the 5′-segment of (CA)8 mRNA. Black boxes: SD and AUG.

    Article Snippet: RNase V1 probing used a final concentration of 0.01 U/μl (ThermoFisher Scientific, #AM2275) for 5 min at 37°C.

    Techniques: Sequencing

    Enzymatic degradation of RNA causes protein aggregation. a Diagram showing the experimental design. b SDS-PAGE analysis of soluble (Supernatant) and insoluble proteins (Pellet) from human neurons after treatment with a mixture of RNase A and RNase T1 (A/T1), or vehicle (Ve-). c Protein aggregation (Pellet) after incubation with different ribonucleases or DNase I in the presence of either EDTA or Mg 2+ . Ribonucleases used were RNase A (A), RNase T1 (T1), a mixture of RNase A and RNase T1 (A/T1), RNase 1f (1f), and RNase V1 (V1),

    Journal: bioRxiv

    Article Title: Enzymatic degradation of RNA causes widespread protein aggregation in cell and tissue lysates

    doi: 10.1101/841577

    Figure Lengend Snippet: Enzymatic degradation of RNA causes protein aggregation. a Diagram showing the experimental design. b SDS-PAGE analysis of soluble (Supernatant) and insoluble proteins (Pellet) from human neurons after treatment with a mixture of RNase A and RNase T1 (A/T1), or vehicle (Ve-). c Protein aggregation (Pellet) after incubation with different ribonucleases or DNase I in the presence of either EDTA or Mg 2+ . Ribonucleases used were RNase A (A), RNase T1 (T1), a mixture of RNase A and RNase T1 (A/T1), RNase 1f (1f), and RNase V1 (V1),

    Article Snippet: Enzymes and reagents RNase T1 (AM2280), RNase V1 (AM2275), RNase A/T1 cocktail (EN0551), DNase I (2222), and Yeast t-RNA (15401-011) were from Thermo Fisher Scientific.

    Techniques: SDS Page, Incubation

    Representative probing experiments using 5′-endlabeled aptamer A011 RNA and analyzed by ( A ) 20% or ( B ) 10% denaturing PAGE. Lanes 1 and 13, undigested RNA control (con.); lanes 2 and 14, limited alkaline hydrolysis; lanes 3, 12, 15 and 24, partial digestion with RNase T1 under denaturing (denat.) conditions; lanes 4, 5, 16 and 17, with two concentrations of RNase T1 under native conditions; lanes 6, 7, 18 and 19, with two concentrations of RNase V1; lanes 8, 9, 20 and 21, with two concentrations of nuclease P1; lane 10 and 22, with nuclease S1; lanes 11 and 23, Pb2+-induced hydrolysis. For experimental details, see Materials and Methods. Alkaline hydrolysis bands and the corresponding structure elements are indicated at the left and right margins, respectively, according to the numbering system presented in Figure 2 (A011, center). ( C , D ) Illustration of prominent cleavage sites in the context of the secondary structure of A011, derived from probing experiments such as those shown in panels A and B . Symbol sizes suggests the relative intensity of cleavage bands based on visual inspection.

    Journal: International Journal of Molecular Sciences

    Article Title: 2′-Fluoro-Pyrimidine-Modified RNA Aptamers Specific for Lipopolysaccharide Binding Protein (LBP)

    doi: 10.3390/ijms19123883

    Figure Lengend Snippet: Representative probing experiments using 5′-endlabeled aptamer A011 RNA and analyzed by ( A ) 20% or ( B ) 10% denaturing PAGE. Lanes 1 and 13, undigested RNA control (con.); lanes 2 and 14, limited alkaline hydrolysis; lanes 3, 12, 15 and 24, partial digestion with RNase T1 under denaturing (denat.) conditions; lanes 4, 5, 16 and 17, with two concentrations of RNase T1 under native conditions; lanes 6, 7, 18 and 19, with two concentrations of RNase V1; lanes 8, 9, 20 and 21, with two concentrations of nuclease P1; lane 10 and 22, with nuclease S1; lanes 11 and 23, Pb2+-induced hydrolysis. For experimental details, see Materials and Methods. Alkaline hydrolysis bands and the corresponding structure elements are indicated at the left and right margins, respectively, according to the numbering system presented in Figure 2 (A011, center). ( C , D ) Illustration of prominent cleavage sites in the context of the secondary structure of A011, derived from probing experiments such as those shown in panels A and B . Symbol sizes suggests the relative intensity of cleavage bands based on visual inspection.

    Article Snippet: Enzymatic digestions were performed as follows: RNase T1 (Thermo Fisher Scientific, Waltham, MA, USA) either in 20 mM sodium citrat (pH 5.0), 7 mM urea, 1 mM EDTA and 1 unit RNase T1 for 30 min at 55 °C (denaturing conditions) or in binding buffer (see above) with 0.5 or 0.05 units for 20 min at room temperature (RT); 0.01 or 0.05 units RNase V1 (Thermo Fisher Scientific Pierce) in binding buffer for 20 min at RT; 1 unit RNase S1 (Thermo Fisher Scientific, Waltham, MA, USA) in binding buffer containing 4.5 mM ZnSO4 for 20 min at RT; 0.01 or 0.05 units nuclease P1 (Sigma-Aldrich, St. Louis, MO, USA) in binding buffer containing 0.4 mM ZnSO4 for 20 min at RT.

    Techniques: Polyacrylamide Gel Electrophoresis, Derivative Assay