Structured Review

Roche ribonuclease rnase v1
Ribonuclease Rnase V1, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/ribonuclease rnase v1/product/Roche
Average 85 stars, based on 1 article reviews
Price from $9.99 to $1999.99
ribonuclease rnase v1 - by Bioz Stars, 2020-07
85/100 stars

Related Products / Commonly Used Together

ha3g-3 ′
ha3g-5
vif
enzymatic footprinting

Images

Related Articles

other:

Article Title: Structure and function analysis of the poliovirus cis-acting replication element (CRE)
Article Snippet: Ribonuclease (RNAse) V1, T1, and T2 were obtained from US Biochemicals, Roche, and Sigma, respectively.

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 88
    Roche v1 rnase
    Secondary structure analysis of the HIV-1/BRU RNA region from positions 5303 to 5559. ( A ) Schematic representation of the HIV-1 genome and of the RNAs used for secondary structure analysis. In the HIV-1 genome, the 5′ss (D) and 3′ss (A) are shown; boxes, open reading frames. In the four RNA transcripts (L3 to A3C), numbering of HIV-1/BRU RNA sequences is according to Ratner et al. (25), exon sequences are represented by rectangles, introns by thin lines, the thick horizontal lines at the beginning of the transcripts correspond to sequences generated by plasmid pBluescriptKSII + . The 5′ss, 3′ss and ESS2 are indicated. In transcripts C3 and L3, the junction between the two HIV-1 RNA regions within the intron is indicated by a vertical broken line. ( B ) Examples of primer extension analyses of enzymatically digested and chemically modified L3 transcript. Lanes marked by V, S and CMCT correspond to <t>V1</t> RNase digestion, S1 nuclease digestion and CMCT modification, respectively. Conditions for digestion and modification are given in Materials and Methods. Lanes marked by c correspond to control experiments with the untreated RNA transcript, lanes UGCA to the sequencing ladders. Numbering of nucleotides in the HIV-1/BRU RNA is on the right of the autoradiogram, as well as the positions of the 3′ss (A3, A4c, A4a, A4b and A5). Positions of the various stem–loop structures identified on the basis of this analysis (Fig. 1C) and of ESS2 are shown on the left. The primers used for extension with reverse transcriptase are indicated below each autoradiogram. ( C ) The results of enzymatic probing are schematically represented on the proposed secondary structure model. Cleavages by enzymes are shown by arrows surmounted with circles for S1 nuclease and squares for V1 RNase. Three red circles or squares indicate a strong cleavage, two orange circles or squares a medium cleavage, one green circle or square a low cleavage. The free energy of the proposed stem–loop structures at 37°C, in 1 M NaCl were calculated with the MFold software. Positions of nucleotides in the HIV-1/BRU RNA are given. Stem–loop structures are designated as SLS1–5. The various 3′ss are indicated by blue arrows. The ESS2 inhibitory element is squared. Results of CMCT modification of SLS1 and SLS2 are shown in the inset. Red circles indicate a strong, orange a medium and green a low level of modification. Squared nucleotides were not modified.
    V1 Rnase, supplied by Roche, 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/v1 rnase/product/Roche
    Average 88 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    v1 rnase - by Bioz Stars, 2020-07
    88/100 stars
      Buy from Supplier

    85
    Roche mu rnase v1
    Secondary structure analysis of the HIV-1/BRU RNA region from positions 5303 to 5559. ( A ) Schematic representation of the HIV-1 genome and of the RNAs used for secondary structure analysis. In the HIV-1 genome, the 5′ss (D) and 3′ss (A) are shown; boxes, open reading frames. In the four RNA transcripts (L3 to A3C), numbering of HIV-1/BRU RNA sequences is according to Ratner et al. (25), exon sequences are represented by rectangles, introns by thin lines, the thick horizontal lines at the beginning of the transcripts correspond to sequences generated by plasmid pBluescriptKSII + . The 5′ss, 3′ss and ESS2 are indicated. In transcripts C3 and L3, the junction between the two HIV-1 RNA regions within the intron is indicated by a vertical broken line. ( B ) Examples of primer extension analyses of enzymatically digested and chemically modified L3 transcript. Lanes marked by V, S and CMCT correspond to <t>V1</t> RNase digestion, S1 nuclease digestion and CMCT modification, respectively. Conditions for digestion and modification are given in Materials and Methods. Lanes marked by c correspond to control experiments with the untreated RNA transcript, lanes UGCA to the sequencing ladders. Numbering of nucleotides in the HIV-1/BRU RNA is on the right of the autoradiogram, as well as the positions of the 3′ss (A3, A4c, A4a, A4b and A5). Positions of the various stem–loop structures identified on the basis of this analysis (Fig. 1C) and of ESS2 are shown on the left. The primers used for extension with reverse transcriptase are indicated below each autoradiogram. ( C ) The results of enzymatic probing are schematically represented on the proposed secondary structure model. Cleavages by enzymes are shown by arrows surmounted with circles for S1 nuclease and squares for V1 RNase. Three red circles or squares indicate a strong cleavage, two orange circles or squares a medium cleavage, one green circle or square a low cleavage. The free energy of the proposed stem–loop structures at 37°C, in 1 M NaCl were calculated with the MFold software. Positions of nucleotides in the HIV-1/BRU RNA are given. Stem–loop structures are designated as SLS1–5. The various 3′ss are indicated by blue arrows. The ESS2 inhibitory element is squared. Results of CMCT modification of SLS1 and SLS2 are shown in the inset. Red circles indicate a strong, orange a medium and green a low level of modification. Squared nucleotides were not modified.
    Mu Rnase V1, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mu rnase v1/product/Roche
    Average 85 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    mu rnase v1 - by Bioz Stars, 2020-07
    85/100 stars
      Buy from Supplier

    Image Search Results


    Secondary structure analysis of the HIV-1/BRU RNA region from positions 5303 to 5559. ( A ) Schematic representation of the HIV-1 genome and of the RNAs used for secondary structure analysis. In the HIV-1 genome, the 5′ss (D) and 3′ss (A) are shown; boxes, open reading frames. In the four RNA transcripts (L3 to A3C), numbering of HIV-1/BRU RNA sequences is according to Ratner et al. (25), exon sequences are represented by rectangles, introns by thin lines, the thick horizontal lines at the beginning of the transcripts correspond to sequences generated by plasmid pBluescriptKSII + . The 5′ss, 3′ss and ESS2 are indicated. In transcripts C3 and L3, the junction between the two HIV-1 RNA regions within the intron is indicated by a vertical broken line. ( B ) Examples of primer extension analyses of enzymatically digested and chemically modified L3 transcript. Lanes marked by V, S and CMCT correspond to V1 RNase digestion, S1 nuclease digestion and CMCT modification, respectively. Conditions for digestion and modification are given in Materials and Methods. Lanes marked by c correspond to control experiments with the untreated RNA transcript, lanes UGCA to the sequencing ladders. Numbering of nucleotides in the HIV-1/BRU RNA is on the right of the autoradiogram, as well as the positions of the 3′ss (A3, A4c, A4a, A4b and A5). Positions of the various stem–loop structures identified on the basis of this analysis (Fig. 1C) and of ESS2 are shown on the left. The primers used for extension with reverse transcriptase are indicated below each autoradiogram. ( C ) The results of enzymatic probing are schematically represented on the proposed secondary structure model. Cleavages by enzymes are shown by arrows surmounted with circles for S1 nuclease and squares for V1 RNase. Three red circles or squares indicate a strong cleavage, two orange circles or squares a medium cleavage, one green circle or square a low cleavage. The free energy of the proposed stem–loop structures at 37°C, in 1 M NaCl were calculated with the MFold software. Positions of nucleotides in the HIV-1/BRU RNA are given. Stem–loop structures are designated as SLS1–5. The various 3′ss are indicated by blue arrows. The ESS2 inhibitory element is squared. Results of CMCT modification of SLS1 and SLS2 are shown in the inset. Red circles indicate a strong, orange a medium and green a low level of modification. Squared nucleotides were not modified.

    Journal: Nucleic Acids Research

    Article Title: Conserved stem-loop structures in the HIV-1 RNA region containing the A3 3? splice site and its cis-regulatory element: possible involvement in RNA splicing

    doi:

    Figure Lengend Snippet: Secondary structure analysis of the HIV-1/BRU RNA region from positions 5303 to 5559. ( A ) Schematic representation of the HIV-1 genome and of the RNAs used for secondary structure analysis. In the HIV-1 genome, the 5′ss (D) and 3′ss (A) are shown; boxes, open reading frames. In the four RNA transcripts (L3 to A3C), numbering of HIV-1/BRU RNA sequences is according to Ratner et al. (25), exon sequences are represented by rectangles, introns by thin lines, the thick horizontal lines at the beginning of the transcripts correspond to sequences generated by plasmid pBluescriptKSII + . The 5′ss, 3′ss and ESS2 are indicated. In transcripts C3 and L3, the junction between the two HIV-1 RNA regions within the intron is indicated by a vertical broken line. ( B ) Examples of primer extension analyses of enzymatically digested and chemically modified L3 transcript. Lanes marked by V, S and CMCT correspond to V1 RNase digestion, S1 nuclease digestion and CMCT modification, respectively. Conditions for digestion and modification are given in Materials and Methods. Lanes marked by c correspond to control experiments with the untreated RNA transcript, lanes UGCA to the sequencing ladders. Numbering of nucleotides in the HIV-1/BRU RNA is on the right of the autoradiogram, as well as the positions of the 3′ss (A3, A4c, A4a, A4b and A5). Positions of the various stem–loop structures identified on the basis of this analysis (Fig. 1C) and of ESS2 are shown on the left. The primers used for extension with reverse transcriptase are indicated below each autoradiogram. ( C ) The results of enzymatic probing are schematically represented on the proposed secondary structure model. Cleavages by enzymes are shown by arrows surmounted with circles for S1 nuclease and squares for V1 RNase. Three red circles or squares indicate a strong cleavage, two orange circles or squares a medium cleavage, one green circle or square a low cleavage. The free energy of the proposed stem–loop structures at 37°C, in 1 M NaCl were calculated with the MFold software. Positions of nucleotides in the HIV-1/BRU RNA are given. Stem–loop structures are designated as SLS1–5. The various 3′ss are indicated by blue arrows. The ESS2 inhibitory element is squared. Results of CMCT modification of SLS1 and SLS2 are shown in the inset. Red circles indicate a strong, orange a medium and green a low level of modification. Squared nucleotides were not modified.

    Article Snippet: Enzymatic digestions with V1 RNase and S1 nuclease were carried out, as previously described , using 1 µl of in vitro synthesized RNA in the presence of 1.25 µg of a commercial yeast tRNA mixture (Roche Diagnostics) for V1 RNase digestion and 2.5 µg of yeast tRNA for S1 nuclease digestion.

    Techniques: Generated, Plasmid Preparation, Modification, Sequencing, Software

    Conservation of SLS2 and SLS1 in the groups M and O of HIV-1 strains and in the SIVcpz strains. Nucleotide sequences in this figure are from the HIV sequence database (http://hiv-web.lanl.gov/, Los Alamos National Laboratory, Los Alamos, NM). They were identified by alignment of the HIV-1/BRU RNA sequence with sequences from HIV-1 RNAs of other strains and the SIVcpz strains using the ClustalW program (43). ( A ) SLS2s are drawn for various strains of the group M of HIV-1 strains, for the ANT70C strain of group O and for the SIVcpzGAB strain. The name of the strains, the clade and the group are indicated below each structure. The free energy of each SLS2, at 37°C, in 1 M NaCl, as calculated by the MFold program is indicated. Sequence variations as compared to BRU are indicated by red nucleotides. Base pairs within green rectangles are conserved by semi-compensatory mutations. ( B ) Schematic representation of the transcript used for the experimental study of the HIV-1/MAL RNA region containing site A3. The same symbols were used as in Figure 1A. ( C ) Probing of the secondary structure of the L3-MAL RNA with V1 RNase (lane V) and S1 nuclease (lane S). Primer 1458 was used for reverse transcriptase analysis of cleaved and intact RNA (lane c) and for generating the sequencing ladders (lanes UGCA). Numbering of the HIV-1/MAL RNA sequence on the right of the autoradiogram is according to the Los Alamos HIV sequence database. Beside the autoradiogram, a schematic representation of the cleavages observed is given on the MAL SLS2 model (squares for V1 cleavages; dots for S1 cleavages; red, orange and green for strong, medium and low cleavages, respectively). Helix and loop positions are indicated on the left of the autoradiogram. ( D ) Based on the experimentally identified SLS1 of the BRU RNA, ‘SLS1-like’ structures were drawn for the HIV-1/ANT70C, SIVcpzGAB and SIVcpzANT strains. Base pairs in red and green rectangles are conserved by compensatory and semi-compensatory mutations, respectively. The upper part of SLS1, that is not conserved in the SIVcpzANT RNA, is represented by a discontinuous line.

    Journal: Nucleic Acids Research

    Article Title: Conserved stem-loop structures in the HIV-1 RNA region containing the A3 3? splice site and its cis-regulatory element: possible involvement in RNA splicing

    doi:

    Figure Lengend Snippet: Conservation of SLS2 and SLS1 in the groups M and O of HIV-1 strains and in the SIVcpz strains. Nucleotide sequences in this figure are from the HIV sequence database (http://hiv-web.lanl.gov/, Los Alamos National Laboratory, Los Alamos, NM). They were identified by alignment of the HIV-1/BRU RNA sequence with sequences from HIV-1 RNAs of other strains and the SIVcpz strains using the ClustalW program (43). ( A ) SLS2s are drawn for various strains of the group M of HIV-1 strains, for the ANT70C strain of group O and for the SIVcpzGAB strain. The name of the strains, the clade and the group are indicated below each structure. The free energy of each SLS2, at 37°C, in 1 M NaCl, as calculated by the MFold program is indicated. Sequence variations as compared to BRU are indicated by red nucleotides. Base pairs within green rectangles are conserved by semi-compensatory mutations. ( B ) Schematic representation of the transcript used for the experimental study of the HIV-1/MAL RNA region containing site A3. The same symbols were used as in Figure 1A. ( C ) Probing of the secondary structure of the L3-MAL RNA with V1 RNase (lane V) and S1 nuclease (lane S). Primer 1458 was used for reverse transcriptase analysis of cleaved and intact RNA (lane c) and for generating the sequencing ladders (lanes UGCA). Numbering of the HIV-1/MAL RNA sequence on the right of the autoradiogram is according to the Los Alamos HIV sequence database. Beside the autoradiogram, a schematic representation of the cleavages observed is given on the MAL SLS2 model (squares for V1 cleavages; dots for S1 cleavages; red, orange and green for strong, medium and low cleavages, respectively). Helix and loop positions are indicated on the left of the autoradiogram. ( D ) Based on the experimentally identified SLS1 of the BRU RNA, ‘SLS1-like’ structures were drawn for the HIV-1/ANT70C, SIVcpzGAB and SIVcpzANT strains. Base pairs in red and green rectangles are conserved by compensatory and semi-compensatory mutations, respectively. The upper part of SLS1, that is not conserved in the SIVcpzANT RNA, is represented by a discontinuous line.

    Article Snippet: Enzymatic digestions with V1 RNase and S1 nuclease were carried out, as previously described , using 1 µl of in vitro synthesized RNA in the presence of 1.25 µg of a commercial yeast tRNA mixture (Roche Diagnostics) for V1 RNase digestion and 2.5 µg of yeast tRNA for S1 nuclease digestion.

    Techniques: Sequencing

     The HIV-1/BRU SLS3  is formed in a nuclear extract and two structural motifs A and B  are protected by association with nuclear components. ( A )  The S3 transcript used for the experimental analysis is shown. ( B ) Examples of primer extension analyses of the  S3 transcript cleaved by V1, T1 or T2 nucleases (lanes marked by  V, T1, T2, respectively) or modified by kethoxal or DMS (lanes marked  by K or D, respectively) are presented. Enzymatic and chemical reactions  were either performed in the splicing buffer D (B) or in a nuclear  extract (NE). As a control, a primer extension was made with the  intact RNA transcript incubated in the absence of reagent, either  in buffer D or in the nuclear extract (lanes marked by c). Lanes  UGCA correspond to the sequencing ladders. Numbering of the nucleotides  in the HIV-1/BRU RNA is indicated on the right. Positions  of the loops and helices 3 and of ESS2 are shown on the left. ( C ) Schematic representation of results of chemical  and enzymatic probing of S3, in the splicing buffer D (C1) or in  the nuclear extract (C2). In Panel C1, the circled nucleotides were  modified by DMS or kethoxal. Cleavages by RNases are shown by arrows,  surmounted with a circle for T2 RNase, a star for T1 RNase and a  square for V1 RNase. Green, orange and red symbols indicate low,  medium and strong modifications or cleavages, respectively. In C2,  protection against the action of chemical reagents and nucleases  are shown in blue, the intensity of the blue color reflects the  level of protection. Increased sensitivity to chemical reagents  and nucleases is indicated in yellow (low increase) or orange (medium  increase). In both C1 and C2, the oligonucleotide primer 954 used  for the reverse transcriptase analysis is indicated. The 3G residues  at the 5′-end of the S3 transcript were  generated by the T7 RNA polymerase promoter. The portion of the  S3 RNA that was analyzed is delimited by the two broken arrows in  C1. Due to pause of reverse transcriptase at some of the V1 cleavage  sites in the region from positions 5397 to 5438 in the nuclear extract, no  estimation of their variation of intensity as compared to naked  RNA is given for this part of SLS3. In C3, the HIV-1/BRU  functional sequences contained in SLS3 are indicated, namely: the  tat  start codon and  vpr  stop codon  (squared in green), the putative SC35 binding site (red letters),  the branched sites (circled in blue) and PPT (in blue rectangles)  of the A4c 3′ss and the branched sites  for A4a and b 3′ss (circled in orange).  The limits of the RNA fragments used by Caputi  et al.  (11)  and Del Gatto-Konczak  et al . (32) for hnRNP A/B  crosslinking experiments are indicated by black and red arrows,  respectively.

    Journal: Nucleic Acids Research

    Article Title: Conserved stem-loop structures in the HIV-1 RNA region containing the A3 3? splice site and its cis-regulatory element: possible involvement in RNA splicing

    doi:

    Figure Lengend Snippet: The HIV-1/BRU SLS3 is formed in a nuclear extract and two structural motifs A and B are protected by association with nuclear components. ( A ) The S3 transcript used for the experimental analysis is shown. ( B ) Examples of primer extension analyses of the S3 transcript cleaved by V1, T1 or T2 nucleases (lanes marked by V, T1, T2, respectively) or modified by kethoxal or DMS (lanes marked by K or D, respectively) are presented. Enzymatic and chemical reactions were either performed in the splicing buffer D (B) or in a nuclear extract (NE). As a control, a primer extension was made with the intact RNA transcript incubated in the absence of reagent, either in buffer D or in the nuclear extract (lanes marked by c). Lanes UGCA correspond to the sequencing ladders. Numbering of the nucleotides in the HIV-1/BRU RNA is indicated on the right. Positions of the loops and helices 3 and of ESS2 are shown on the left. ( C ) Schematic representation of results of chemical and enzymatic probing of S3, in the splicing buffer D (C1) or in the nuclear extract (C2). In Panel C1, the circled nucleotides were modified by DMS or kethoxal. Cleavages by RNases are shown by arrows, surmounted with a circle for T2 RNase, a star for T1 RNase and a square for V1 RNase. Green, orange and red symbols indicate low, medium and strong modifications or cleavages, respectively. In C2, protection against the action of chemical reagents and nucleases are shown in blue, the intensity of the blue color reflects the level of protection. Increased sensitivity to chemical reagents and nucleases is indicated in yellow (low increase) or orange (medium increase). In both C1 and C2, the oligonucleotide primer 954 used for the reverse transcriptase analysis is indicated. The 3G residues at the 5′-end of the S3 transcript were generated by the T7 RNA polymerase promoter. The portion of the S3 RNA that was analyzed is delimited by the two broken arrows in C1. Due to pause of reverse transcriptase at some of the V1 cleavage sites in the region from positions 5397 to 5438 in the nuclear extract, no estimation of their variation of intensity as compared to naked RNA is given for this part of SLS3. In C3, the HIV-1/BRU functional sequences contained in SLS3 are indicated, namely: the tat start codon and vpr stop codon (squared in green), the putative SC35 binding site (red letters), the branched sites (circled in blue) and PPT (in blue rectangles) of the A4c 3′ss and the branched sites for A4a and b 3′ss (circled in orange). The limits of the RNA fragments used by Caputi et al. (11) and Del Gatto-Konczak et al . (32) for hnRNP A/B crosslinking experiments are indicated by black and red arrows, respectively.

    Article Snippet: Enzymatic digestions with V1 RNase and S1 nuclease were carried out, as previously described , using 1 µl of in vitro synthesized RNA in the presence of 1.25 µg of a commercial yeast tRNA mixture (Roche Diagnostics) for V1 RNase digestion and 2.5 µg of yeast tRNA for S1 nuclease digestion.

    Techniques: Modification, Incubation, Sequencing, Generated, Functional Assay, Binding Assay