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  • 99
    Thermo Fisher rnase out recombinant rnase inhibitor
    Rnase Out Recombinant Rnase Inhibitor, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 25 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Millipore rnase ribonuclease inhibitor
    Rnase Ribonuclease Inhibitor, supplied by Millipore, used in various techniques. Bioz Stars score: 94/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    Millipore rnase inhibitor
    m 6 A alters RNA structure to recruit <t>HNRNPG.</t> ( A ) Sequence logo of the most enriched motif within HNRNPG PAR-CLIP peaks. ( B ) Left: secondary structure of the MALAT1 hairpin, showing the A-2,515-to-G/C/U mutations that were introduced at the m 6 A site. Right: quantification of relative HNRNPG pull-down with the original (2,515-A) and mutated (2,515-G/C/U) MALAT1 hairpins, normalized to pulled-down HIST1H1C. Data shown as mean; error bar = standard deviation; n = 3 biological replicates. ( C ) Left: structural probing of the unmethylated and methylated MALAT1 hairpins. The orange lines indicate regions with marked differences between the unmethylated and methylated hairpins. The location of the m 6 A residue is indicated by a red dot. Ctrl, no nuclease added; V1; <t>RNase</t> V1 digestion; S1, S1 nuclease digestion; T1, RNase T1 digestion; G-L, G-ladder; AH, alkaline hydrolysis. Right: secondary structure of the unmethylated and methylated MALAT1 hairpins, marked at their S1 nuclease (red lines) and V1 nuclease (green lines) cleavage sites. ( D ) Model showing that m 6 A disrupts RNA structure, exposes a motif that includes the m 6 A site, and recruits an RNA binding protein.
    Rnase Inhibitor, supplied by Millipore, used in various techniques. Bioz Stars score: 97/100, based on 1112 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Thermo Fisher ribonuclease inhibitor
    MBNL1 recognizes a <t>RNA</t> hairpin upstream of the Tnnt3 fetal exon. ( A ) Cleavage pattern (left) of the 5′-end labeled Tnnt3 151-nt transcript (a 5′ truncated form of the 200 nt T5.45 RNA) encompassing the fetal (F) exon 3′ splice site (110-nt of intron 8, 41-nt of F exon) obtained with use of three structure probes. Lanes are: Ci, incubation control or no probe added; Pb, lead ions (0.25, 0.5 mM); S1, S1 nuclease (1, 2 U/µl and 1 mM ZnCl 2 was present in each reaction); T1, <t>RNase</t> T1 (0.5, 1 U/µl); F, formamide (statistical ladder); T, guanine-specific ladder. The sequences forming the 18-nt stem-loop structure are also indicated. Also illustrated (right) is the proposed secondary structure model of the 151-nt transcript. The cleavage sites are indicated for each probe used and the figure inset shows the probe designations and cleavage intensity classification. The F exon sequence is marked in upper case and intron 8 in lower case. The positions of the G, A and U substitutions in the 18-nt stem-loop are also indicated. ( B ) Photocrosslinking analysis indicates reduced MBNL1, but not CUGBP1, binding to the Tnnt3 Δ10, gg and au mutants in contrast to wild-type RNA. Photocrosslinking analysis was performed as described in Figure 1 using the same lysates (protein loading controls shown in Figure 1 B) except only MBNL1 FL (MBNL1) protein was used. ( C ) Tnnt3 F exon skipping is impaired in the Δ10 and au mutants compared to wild type while F exon inclusion is eliminated in the gg double mutant. C2C12 cells were co-transfected with either a wild type, Δ10, gg or au point mutant splicing reporter plasmid and a protein expression plasmid for either CUGBP1mycHis or MBNL1mycHis (full-length protein only). 32 P-labeled splicing products, which included (+F) or excluded (−F) the Tnnt3 F exon (black box), were detected by RT-PCR, using primers positioned in Tnnt3 exons 8 and 9 (open boxes with arrows), followed by gel electrophoresis.
    Ribonuclease Inhibitor, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 1430 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Promega rnase ribonuclease inhibitor
    MBNL1 recognizes a <t>RNA</t> hairpin upstream of the Tnnt3 fetal exon. ( A ) Cleavage pattern (left) of the 5′-end labeled Tnnt3 151-nt transcript (a 5′ truncated form of the 200 nt T5.45 RNA) encompassing the fetal (F) exon 3′ splice site (110-nt of intron 8, 41-nt of F exon) obtained with use of three structure probes. Lanes are: Ci, incubation control or no probe added; Pb, lead ions (0.25, 0.5 mM); S1, S1 nuclease (1, 2 U/µl and 1 mM ZnCl 2 was present in each reaction); T1, <t>RNase</t> T1 (0.5, 1 U/µl); F, formamide (statistical ladder); T, guanine-specific ladder. The sequences forming the 18-nt stem-loop structure are also indicated. Also illustrated (right) is the proposed secondary structure model of the 151-nt transcript. The cleavage sites are indicated for each probe used and the figure inset shows the probe designations and cleavage intensity classification. The F exon sequence is marked in upper case and intron 8 in lower case. The positions of the G, A and U substitutions in the 18-nt stem-loop are also indicated. ( B ) Photocrosslinking analysis indicates reduced MBNL1, but not CUGBP1, binding to the Tnnt3 Δ10, gg and au mutants in contrast to wild-type RNA. Photocrosslinking analysis was performed as described in Figure 1 using the same lysates (protein loading controls shown in Figure 1 B) except only MBNL1 FL (MBNL1) protein was used. ( C ) Tnnt3 F exon skipping is impaired in the Δ10 and au mutants compared to wild type while F exon inclusion is eliminated in the gg double mutant. C2C12 cells were co-transfected with either a wild type, Δ10, gg or au point mutant splicing reporter plasmid and a protein expression plasmid for either CUGBP1mycHis or MBNL1mycHis (full-length protein only). 32 P-labeled splicing products, which included (+F) or excluded (−F) the Tnnt3 F exon (black box), were detected by RT-PCR, using primers positioned in Tnnt3 exons 8 and 9 (open boxes with arrows), followed by gel electrophoresis.
    Rnase Ribonuclease Inhibitor, supplied by Promega, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Roche ribonuclease rnase inhibitor
    MBNL1 recognizes a <t>RNA</t> hairpin upstream of the Tnnt3 fetal exon. ( A ) Cleavage pattern (left) of the 5′-end labeled Tnnt3 151-nt transcript (a 5′ truncated form of the 200 nt T5.45 RNA) encompassing the fetal (F) exon 3′ splice site (110-nt of intron 8, 41-nt of F exon) obtained with use of three structure probes. Lanes are: Ci, incubation control or no probe added; Pb, lead ions (0.25, 0.5 mM); S1, S1 nuclease (1, 2 U/µl and 1 mM ZnCl 2 was present in each reaction); T1, <t>RNase</t> T1 (0.5, 1 U/µl); F, formamide (statistical ladder); T, guanine-specific ladder. The sequences forming the 18-nt stem-loop structure are also indicated. Also illustrated (right) is the proposed secondary structure model of the 151-nt transcript. The cleavage sites are indicated for each probe used and the figure inset shows the probe designations and cleavage intensity classification. The F exon sequence is marked in upper case and intron 8 in lower case. The positions of the G, A and U substitutions in the 18-nt stem-loop are also indicated. ( B ) Photocrosslinking analysis indicates reduced MBNL1, but not CUGBP1, binding to the Tnnt3 Δ10, gg and au mutants in contrast to wild-type RNA. Photocrosslinking analysis was performed as described in Figure 1 using the same lysates (protein loading controls shown in Figure 1 B) except only MBNL1 FL (MBNL1) protein was used. ( C ) Tnnt3 F exon skipping is impaired in the Δ10 and au mutants compared to wild type while F exon inclusion is eliminated in the gg double mutant. C2C12 cells were co-transfected with either a wild type, Δ10, gg or au point mutant splicing reporter plasmid and a protein expression plasmid for either CUGBP1mycHis or MBNL1mycHis (full-length protein only). 32 P-labeled splicing products, which included (+F) or excluded (−F) the Tnnt3 F exon (black box), were detected by RT-PCR, using primers positioned in Tnnt3 exons 8 and 9 (open boxes with arrows), followed by gel electrophoresis.
    Ribonuclease Rnase Inhibitor, supplied by Roche, used in various techniques. Bioz Stars score: 88/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore rnase
    MBNL1 recognizes a <t>RNA</t> hairpin upstream of the Tnnt3 fetal exon. ( A ) Cleavage pattern (left) of the 5′-end labeled Tnnt3 151-nt transcript (a 5′ truncated form of the 200 nt T5.45 RNA) encompassing the fetal (F) exon 3′ splice site (110-nt of intron 8, 41-nt of F exon) obtained with use of three structure probes. Lanes are: Ci, incubation control or no probe added; Pb, lead ions (0.25, 0.5 mM); S1, S1 nuclease (1, 2 U/µl and 1 mM ZnCl 2 was present in each reaction); T1, <t>RNase</t> T1 (0.5, 1 U/µl); F, formamide (statistical ladder); T, guanine-specific ladder. The sequences forming the 18-nt stem-loop structure are also indicated. Also illustrated (right) is the proposed secondary structure model of the 151-nt transcript. The cleavage sites are indicated for each probe used and the figure inset shows the probe designations and cleavage intensity classification. The F exon sequence is marked in upper case and intron 8 in lower case. The positions of the G, A and U substitutions in the 18-nt stem-loop are also indicated. ( B ) Photocrosslinking analysis indicates reduced MBNL1, but not CUGBP1, binding to the Tnnt3 Δ10, gg and au mutants in contrast to wild-type RNA. Photocrosslinking analysis was performed as described in Figure 1 using the same lysates (protein loading controls shown in Figure 1 B) except only MBNL1 FL (MBNL1) protein was used. ( C ) Tnnt3 F exon skipping is impaired in the Δ10 and au mutants compared to wild type while F exon inclusion is eliminated in the gg double mutant. C2C12 cells were co-transfected with either a wild type, Δ10, gg or au point mutant splicing reporter plasmid and a protein expression plasmid for either CUGBP1mycHis or MBNL1mycHis (full-length protein only). 32 P-labeled splicing products, which included (+F) or excluded (−F) the Tnnt3 F exon (black box), were detected by RT-PCR, using primers positioned in Tnnt3 exons 8 and 9 (open boxes with arrows), followed by gel electrophoresis.
    Rnase, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 13936 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher rnaseout recombinant ribounclease inhibitor
    MBNL1 recognizes a <t>RNA</t> hairpin upstream of the Tnnt3 fetal exon. ( A ) Cleavage pattern (left) of the 5′-end labeled Tnnt3 151-nt transcript (a 5′ truncated form of the 200 nt T5.45 RNA) encompassing the fetal (F) exon 3′ splice site (110-nt of intron 8, 41-nt of F exon) obtained with use of three structure probes. Lanes are: Ci, incubation control or no probe added; Pb, lead ions (0.25, 0.5 mM); S1, S1 nuclease (1, 2 U/µl and 1 mM ZnCl 2 was present in each reaction); T1, <t>RNase</t> T1 (0.5, 1 U/µl); F, formamide (statistical ladder); T, guanine-specific ladder. The sequences forming the 18-nt stem-loop structure are also indicated. Also illustrated (right) is the proposed secondary structure model of the 151-nt transcript. The cleavage sites are indicated for each probe used and the figure inset shows the probe designations and cleavage intensity classification. The F exon sequence is marked in upper case and intron 8 in lower case. The positions of the G, A and U substitutions in the 18-nt stem-loop are also indicated. ( B ) Photocrosslinking analysis indicates reduced MBNL1, but not CUGBP1, binding to the Tnnt3 Δ10, gg and au mutants in contrast to wild-type RNA. Photocrosslinking analysis was performed as described in Figure 1 using the same lysates (protein loading controls shown in Figure 1 B) except only MBNL1 FL (MBNL1) protein was used. ( C ) Tnnt3 F exon skipping is impaired in the Δ10 and au mutants compared to wild type while F exon inclusion is eliminated in the gg double mutant. C2C12 cells were co-transfected with either a wild type, Δ10, gg or au point mutant splicing reporter plasmid and a protein expression plasmid for either CUGBP1mycHis or MBNL1mycHis (full-length protein only). 32 P-labeled splicing products, which included (+F) or excluded (−F) the Tnnt3 F exon (black box), were detected by RT-PCR, using primers positioned in Tnnt3 exons 8 and 9 (open boxes with arrows), followed by gel electrophoresis.
    Rnaseout Recombinant Ribounclease Inhibitor, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 53 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher rnase
    MBNL1 recognizes a <t>RNA</t> hairpin upstream of the Tnnt3 fetal exon. ( A ) Cleavage pattern (left) of the 5′-end labeled Tnnt3 151-nt transcript (a 5′ truncated form of the 200 nt T5.45 RNA) encompassing the fetal (F) exon 3′ splice site (110-nt of intron 8, 41-nt of F exon) obtained with use of three structure probes. Lanes are: Ci, incubation control or no probe added; Pb, lead ions (0.25, 0.5 mM); S1, S1 nuclease (1, 2 U/µl and 1 mM ZnCl 2 was present in each reaction); T1, <t>RNase</t> T1 (0.5, 1 U/µl); F, formamide (statistical ladder); T, guanine-specific ladder. The sequences forming the 18-nt stem-loop structure are also indicated. Also illustrated (right) is the proposed secondary structure model of the 151-nt transcript. The cleavage sites are indicated for each probe used and the figure inset shows the probe designations and cleavage intensity classification. The F exon sequence is marked in upper case and intron 8 in lower case. The positions of the G, A and U substitutions in the 18-nt stem-loop are also indicated. ( B ) Photocrosslinking analysis indicates reduced MBNL1, but not CUGBP1, binding to the Tnnt3 Δ10, gg and au mutants in contrast to wild-type RNA. Photocrosslinking analysis was performed as described in Figure 1 using the same lysates (protein loading controls shown in Figure 1 B) except only MBNL1 FL (MBNL1) protein was used. ( C ) Tnnt3 F exon skipping is impaired in the Δ10 and au mutants compared to wild type while F exon inclusion is eliminated in the gg double mutant. C2C12 cells were co-transfected with either a wild type, Δ10, gg or au point mutant splicing reporter plasmid and a protein expression plasmid for either CUGBP1mycHis or MBNL1mycHis (full-length protein only). 32 P-labeled splicing products, which included (+F) or excluded (−F) the Tnnt3 F exon (black box), were detected by RT-PCR, using primers positioned in Tnnt3 exons 8 and 9 (open boxes with arrows), followed by gel electrophoresis.
    Rnase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 9347 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    TaKaRa ribonuclease inhibitor
    MBNL1 recognizes a <t>RNA</t> hairpin upstream of the Tnnt3 fetal exon. ( A ) Cleavage pattern (left) of the 5′-end labeled Tnnt3 151-nt transcript (a 5′ truncated form of the 200 nt T5.45 RNA) encompassing the fetal (F) exon 3′ splice site (110-nt of intron 8, 41-nt of F exon) obtained with use of three structure probes. Lanes are: Ci, incubation control or no probe added; Pb, lead ions (0.25, 0.5 mM); S1, S1 nuclease (1, 2 U/µl and 1 mM ZnCl 2 was present in each reaction); T1, <t>RNase</t> T1 (0.5, 1 U/µl); F, formamide (statistical ladder); T, guanine-specific ladder. The sequences forming the 18-nt stem-loop structure are also indicated. Also illustrated (right) is the proposed secondary structure model of the 151-nt transcript. The cleavage sites are indicated for each probe used and the figure inset shows the probe designations and cleavage intensity classification. The F exon sequence is marked in upper case and intron 8 in lower case. The positions of the G, A and U substitutions in the 18-nt stem-loop are also indicated. ( B ) Photocrosslinking analysis indicates reduced MBNL1, but not CUGBP1, binding to the Tnnt3 Δ10, gg and au mutants in contrast to wild-type RNA. Photocrosslinking analysis was performed as described in Figure 1 using the same lysates (protein loading controls shown in Figure 1 B) except only MBNL1 FL (MBNL1) protein was used. ( C ) Tnnt3 F exon skipping is impaired in the Δ10 and au mutants compared to wild type while F exon inclusion is eliminated in the gg double mutant. C2C12 cells were co-transfected with either a wild type, Δ10, gg or au point mutant splicing reporter plasmid and a protein expression plasmid for either CUGBP1mycHis or MBNL1mycHis (full-length protein only). 32 P-labeled splicing products, which included (+F) or excluded (−F) the Tnnt3 F exon (black box), were detected by RT-PCR, using primers positioned in Tnnt3 exons 8 and 9 (open boxes with arrows), followed by gel electrophoresis.
    Ribonuclease Inhibitor, supplied by TaKaRa, used in various techniques. Bioz Stars score: 93/100, based on 726 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Roche ribonuclease inhibitor
    MBNL1 recognizes a <t>RNA</t> hairpin upstream of the Tnnt3 fetal exon. ( A ) Cleavage pattern (left) of the 5′-end labeled Tnnt3 151-nt transcript (a 5′ truncated form of the 200 nt T5.45 RNA) encompassing the fetal (F) exon 3′ splice site (110-nt of intron 8, 41-nt of F exon) obtained with use of three structure probes. Lanes are: Ci, incubation control or no probe added; Pb, lead ions (0.25, 0.5 mM); S1, S1 nuclease (1, 2 U/µl and 1 mM ZnCl 2 was present in each reaction); T1, <t>RNase</t> T1 (0.5, 1 U/µl); F, formamide (statistical ladder); T, guanine-specific ladder. The sequences forming the 18-nt stem-loop structure are also indicated. Also illustrated (right) is the proposed secondary structure model of the 151-nt transcript. The cleavage sites are indicated for each probe used and the figure inset shows the probe designations and cleavage intensity classification. The F exon sequence is marked in upper case and intron 8 in lower case. The positions of the G, A and U substitutions in the 18-nt stem-loop are also indicated. ( B ) Photocrosslinking analysis indicates reduced MBNL1, but not CUGBP1, binding to the Tnnt3 Δ10, gg and au mutants in contrast to wild-type RNA. Photocrosslinking analysis was performed as described in Figure 1 using the same lysates (protein loading controls shown in Figure 1 B) except only MBNL1 FL (MBNL1) protein was used. ( C ) Tnnt3 F exon skipping is impaired in the Δ10 and au mutants compared to wild type while F exon inclusion is eliminated in the gg double mutant. C2C12 cells were co-transfected with either a wild type, Δ10, gg or au point mutant splicing reporter plasmid and a protein expression plasmid for either CUGBP1mycHis or MBNL1mycHis (full-length protein only). 32 P-labeled splicing products, which included (+F) or excluded (−F) the Tnnt3 F exon (black box), were detected by RT-PCR, using primers positioned in Tnnt3 exons 8 and 9 (open boxes with arrows), followed by gel electrophoresis.
    Ribonuclease Inhibitor, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 53 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    FUJIFILM ribonuclease inhibitor
    MBNL1 recognizes a <t>RNA</t> hairpin upstream of the Tnnt3 fetal exon. ( A ) Cleavage pattern (left) of the 5′-end labeled Tnnt3 151-nt transcript (a 5′ truncated form of the 200 nt T5.45 RNA) encompassing the fetal (F) exon 3′ splice site (110-nt of intron 8, 41-nt of F exon) obtained with use of three structure probes. Lanes are: Ci, incubation control or no probe added; Pb, lead ions (0.25, 0.5 mM); S1, S1 nuclease (1, 2 U/µl and 1 mM ZnCl 2 was present in each reaction); T1, <t>RNase</t> T1 (0.5, 1 U/µl); F, formamide (statistical ladder); T, guanine-specific ladder. The sequences forming the 18-nt stem-loop structure are also indicated. Also illustrated (right) is the proposed secondary structure model of the 151-nt transcript. The cleavage sites are indicated for each probe used and the figure inset shows the probe designations and cleavage intensity classification. The F exon sequence is marked in upper case and intron 8 in lower case. The positions of the G, A and U substitutions in the 18-nt stem-loop are also indicated. ( B ) Photocrosslinking analysis indicates reduced MBNL1, but not CUGBP1, binding to the Tnnt3 Δ10, gg and au mutants in contrast to wild-type RNA. Photocrosslinking analysis was performed as described in Figure 1 using the same lysates (protein loading controls shown in Figure 1 B) except only MBNL1 FL (MBNL1) protein was used. ( C ) Tnnt3 F exon skipping is impaired in the Δ10 and au mutants compared to wild type while F exon inclusion is eliminated in the gg double mutant. C2C12 cells were co-transfected with either a wild type, Δ10, gg or au point mutant splicing reporter plasmid and a protein expression plasmid for either CUGBP1mycHis or MBNL1mycHis (full-length protein only). 32 P-labeled splicing products, which included (+F) or excluded (−F) the Tnnt3 F exon (black box), were detected by RT-PCR, using primers positioned in Tnnt3 exons 8 and 9 (open boxes with arrows), followed by gel electrophoresis.
    Ribonuclease Inhibitor, supplied by FUJIFILM, used in various techniques. Bioz Stars score: 92/100, based on 45 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Toyobo ribonuclease inhibitor
    MBNL1 recognizes a <t>RNA</t> hairpin upstream of the Tnnt3 fetal exon. ( A ) Cleavage pattern (left) of the 5′-end labeled Tnnt3 151-nt transcript (a 5′ truncated form of the 200 nt T5.45 RNA) encompassing the fetal (F) exon 3′ splice site (110-nt of intron 8, 41-nt of F exon) obtained with use of three structure probes. Lanes are: Ci, incubation control or no probe added; Pb, lead ions (0.25, 0.5 mM); S1, S1 nuclease (1, 2 U/µl and 1 mM ZnCl 2 was present in each reaction); T1, <t>RNase</t> T1 (0.5, 1 U/µl); F, formamide (statistical ladder); T, guanine-specific ladder. The sequences forming the 18-nt stem-loop structure are also indicated. Also illustrated (right) is the proposed secondary structure model of the 151-nt transcript. The cleavage sites are indicated for each probe used and the figure inset shows the probe designations and cleavage intensity classification. The F exon sequence is marked in upper case and intron 8 in lower case. The positions of the G, A and U substitutions in the 18-nt stem-loop are also indicated. ( B ) Photocrosslinking analysis indicates reduced MBNL1, but not CUGBP1, binding to the Tnnt3 Δ10, gg and au mutants in contrast to wild-type RNA. Photocrosslinking analysis was performed as described in Figure 1 using the same lysates (protein loading controls shown in Figure 1 B) except only MBNL1 FL (MBNL1) protein was used. ( C ) Tnnt3 F exon skipping is impaired in the Δ10 and au mutants compared to wild type while F exon inclusion is eliminated in the gg double mutant. C2C12 cells were co-transfected with either a wild type, Δ10, gg or au point mutant splicing reporter plasmid and a protein expression plasmid for either CUGBP1mycHis or MBNL1mycHis (full-length protein only). 32 P-labeled splicing products, which included (+F) or excluded (−F) the Tnnt3 F exon (black box), were detected by RT-PCR, using primers positioned in Tnnt3 exons 8 and 9 (open boxes with arrows), followed by gel electrophoresis.
    Ribonuclease Inhibitor, supplied by Toyobo, used in various techniques. Bioz Stars score: 92/100, based on 240 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    moloX GmbH ribonuclease inhibitor
    MBNL1 recognizes a <t>RNA</t> hairpin upstream of the Tnnt3 fetal exon. ( A ) Cleavage pattern (left) of the 5′-end labeled Tnnt3 151-nt transcript (a 5′ truncated form of the 200 nt T5.45 RNA) encompassing the fetal (F) exon 3′ splice site (110-nt of intron 8, 41-nt of F exon) obtained with use of three structure probes. Lanes are: Ci, incubation control or no probe added; Pb, lead ions (0.25, 0.5 mM); S1, S1 nuclease (1, 2 U/µl and 1 mM ZnCl 2 was present in each reaction); T1, <t>RNase</t> T1 (0.5, 1 U/µl); F, formamide (statistical ladder); T, guanine-specific ladder. The sequences forming the 18-nt stem-loop structure are also indicated. Also illustrated (right) is the proposed secondary structure model of the 151-nt transcript. The cleavage sites are indicated for each probe used and the figure inset shows the probe designations and cleavage intensity classification. The F exon sequence is marked in upper case and intron 8 in lower case. The positions of the G, A and U substitutions in the 18-nt stem-loop are also indicated. ( B ) Photocrosslinking analysis indicates reduced MBNL1, but not CUGBP1, binding to the Tnnt3 Δ10, gg and au mutants in contrast to wild-type RNA. Photocrosslinking analysis was performed as described in Figure 1 using the same lysates (protein loading controls shown in Figure 1 B) except only MBNL1 FL (MBNL1) protein was used. ( C ) Tnnt3 F exon skipping is impaired in the Δ10 and au mutants compared to wild type while F exon inclusion is eliminated in the gg double mutant. C2C12 cells were co-transfected with either a wild type, Δ10, gg or au point mutant splicing reporter plasmid and a protein expression plasmid for either CUGBP1mycHis or MBNL1mycHis (full-length protein only). 32 P-labeled splicing products, which included (+F) or excluded (−F) the Tnnt3 F exon (black box), were detected by RT-PCR, using primers positioned in Tnnt3 exons 8 and 9 (open boxes with arrows), followed by gel electrophoresis.
    Ribonuclease Inhibitor, supplied by moloX GmbH, used in various techniques. Bioz Stars score: 92/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    m 6 A alters RNA structure to recruit HNRNPG. ( A ) Sequence logo of the most enriched motif within HNRNPG PAR-CLIP peaks. ( B ) Left: secondary structure of the MALAT1 hairpin, showing the A-2,515-to-G/C/U mutations that were introduced at the m 6 A site. Right: quantification of relative HNRNPG pull-down with the original (2,515-A) and mutated (2,515-G/C/U) MALAT1 hairpins, normalized to pulled-down HIST1H1C. Data shown as mean; error bar = standard deviation; n = 3 biological replicates. ( C ) Left: structural probing of the unmethylated and methylated MALAT1 hairpins. The orange lines indicate regions with marked differences between the unmethylated and methylated hairpins. The location of the m 6 A residue is indicated by a red dot. Ctrl, no nuclease added; V1; RNase V1 digestion; S1, S1 nuclease digestion; T1, RNase T1 digestion; G-L, G-ladder; AH, alkaline hydrolysis. Right: secondary structure of the unmethylated and methylated MALAT1 hairpins, marked at their S1 nuclease (red lines) and V1 nuclease (green lines) cleavage sites. ( D ) Model showing that m 6 A disrupts RNA structure, exposes a motif that includes the m 6 A site, and recruits an RNA binding protein.

    Journal: Nucleic Acids Research

    Article Title: N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein

    doi: 10.1093/nar/gkx141

    Figure Lengend Snippet: m 6 A alters RNA structure to recruit HNRNPG. ( A ) Sequence logo of the most enriched motif within HNRNPG PAR-CLIP peaks. ( B ) Left: secondary structure of the MALAT1 hairpin, showing the A-2,515-to-G/C/U mutations that were introduced at the m 6 A site. Right: quantification of relative HNRNPG pull-down with the original (2,515-A) and mutated (2,515-G/C/U) MALAT1 hairpins, normalized to pulled-down HIST1H1C. Data shown as mean; error bar = standard deviation; n = 3 biological replicates. ( C ) Left: structural probing of the unmethylated and methylated MALAT1 hairpins. The orange lines indicate regions with marked differences between the unmethylated and methylated hairpins. The location of the m 6 A residue is indicated by a red dot. Ctrl, no nuclease added; V1; RNase V1 digestion; S1, S1 nuclease digestion; T1, RNase T1 digestion; G-L, G-ladder; AH, alkaline hydrolysis. Right: secondary structure of the unmethylated and methylated MALAT1 hairpins, marked at their S1 nuclease (red lines) and V1 nuclease (green lines) cleavage sites. ( D ) Model showing that m 6 A disrupts RNA structure, exposes a motif that includes the m 6 A site, and recruits an RNA binding protein.

    Article Snippet: The HNRNPG PAR-CLIP RNA sample was incubated with m6 A-specific antibody (202003, SYSY), RNase inhibitor (80 units, Sigma-Aldrich), human placental RNase inhibitor (NEB) in 200 μl 1× IP buffer (50 mM Tris-Cl (pH 7.4), 750 mM NaCl and 0.5% (vol/vol) Igepal CA-630) at 4°C for 2 h under gentle shaking conditions.

    Techniques: Sequencing, Cross-linking Immunoprecipitation, Standard Deviation, Methylation, RNA Binding Assay

    MBNL1 recognizes a RNA hairpin upstream of the Tnnt3 fetal exon. ( A ) Cleavage pattern (left) of the 5′-end labeled Tnnt3 151-nt transcript (a 5′ truncated form of the 200 nt T5.45 RNA) encompassing the fetal (F) exon 3′ splice site (110-nt of intron 8, 41-nt of F exon) obtained with use of three structure probes. Lanes are: Ci, incubation control or no probe added; Pb, lead ions (0.25, 0.5 mM); S1, S1 nuclease (1, 2 U/µl and 1 mM ZnCl 2 was present in each reaction); T1, RNase T1 (0.5, 1 U/µl); F, formamide (statistical ladder); T, guanine-specific ladder. The sequences forming the 18-nt stem-loop structure are also indicated. Also illustrated (right) is the proposed secondary structure model of the 151-nt transcript. The cleavage sites are indicated for each probe used and the figure inset shows the probe designations and cleavage intensity classification. The F exon sequence is marked in upper case and intron 8 in lower case. The positions of the G, A and U substitutions in the 18-nt stem-loop are also indicated. ( B ) Photocrosslinking analysis indicates reduced MBNL1, but not CUGBP1, binding to the Tnnt3 Δ10, gg and au mutants in contrast to wild-type RNA. Photocrosslinking analysis was performed as described in Figure 1 using the same lysates (protein loading controls shown in Figure 1 B) except only MBNL1 FL (MBNL1) protein was used. ( C ) Tnnt3 F exon skipping is impaired in the Δ10 and au mutants compared to wild type while F exon inclusion is eliminated in the gg double mutant. C2C12 cells were co-transfected with either a wild type, Δ10, gg or au point mutant splicing reporter plasmid and a protein expression plasmid for either CUGBP1mycHis or MBNL1mycHis (full-length protein only). 32 P-labeled splicing products, which included (+F) or excluded (−F) the Tnnt3 F exon (black box), were detected by RT-PCR, using primers positioned in Tnnt3 exons 8 and 9 (open boxes with arrows), followed by gel electrophoresis.

    Journal: Nucleic Acids Research

    Article Title: Muscleblind-like 1 interacts with RNA hairpins in splicing target and pathogenic RNAs

    doi: 10.1093/nar/gkm601

    Figure Lengend Snippet: MBNL1 recognizes a RNA hairpin upstream of the Tnnt3 fetal exon. ( A ) Cleavage pattern (left) of the 5′-end labeled Tnnt3 151-nt transcript (a 5′ truncated form of the 200 nt T5.45 RNA) encompassing the fetal (F) exon 3′ splice site (110-nt of intron 8, 41-nt of F exon) obtained with use of three structure probes. Lanes are: Ci, incubation control or no probe added; Pb, lead ions (0.25, 0.5 mM); S1, S1 nuclease (1, 2 U/µl and 1 mM ZnCl 2 was present in each reaction); T1, RNase T1 (0.5, 1 U/µl); F, formamide (statistical ladder); T, guanine-specific ladder. The sequences forming the 18-nt stem-loop structure are also indicated. Also illustrated (right) is the proposed secondary structure model of the 151-nt transcript. The cleavage sites are indicated for each probe used and the figure inset shows the probe designations and cleavage intensity classification. The F exon sequence is marked in upper case and intron 8 in lower case. The positions of the G, A and U substitutions in the 18-nt stem-loop are also indicated. ( B ) Photocrosslinking analysis indicates reduced MBNL1, but not CUGBP1, binding to the Tnnt3 Δ10, gg and au mutants in contrast to wild-type RNA. Photocrosslinking analysis was performed as described in Figure 1 using the same lysates (protein loading controls shown in Figure 1 B) except only MBNL1 FL (MBNL1) protein was used. ( C ) Tnnt3 F exon skipping is impaired in the Δ10 and au mutants compared to wild type while F exon inclusion is eliminated in the gg double mutant. C2C12 cells were co-transfected with either a wild type, Δ10, gg or au point mutant splicing reporter plasmid and a protein expression plasmid for either CUGBP1mycHis or MBNL1mycHis (full-length protein only). 32 P-labeled splicing products, which included (+F) or excluded (−F) the Tnnt3 F exon (black box), were detected by RT-PCR, using primers positioned in Tnnt3 exons 8 and 9 (open boxes with arrows), followed by gel electrophoresis.

    Article Snippet: Chemical and enzymatic analysis of RNA structures Transcription reactions were carried out in a 50 µl volume which contained 2 μg of each DNA template, 1 mM rNTPs, 3.3 mM guanosine, 60 U of ribonuclease inhibitor RNase Out (Invitrogen), 200 U of T7 RNA polymerase (Ambion, Austin, TX, USA), 10 mM DTT, 40 mM Tris-HCl (pH 7.9), 6 mM MgCl2 , 2 mM spermidine, 10 mM NaCl.

    Techniques: Labeling, Incubation, Sequencing, Binding Assay, Mutagenesis, Transfection, Plasmid Preparation, Expressing, Reverse Transcription Polymerase Chain Reaction, Nucleic Acid Electrophoresis