low molecular weight rna marker  (Thermo Fisher)


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    Structured Review

    Thermo Fisher low molecular weight rna marker
    Low Molecular Weight Rna Marker, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/low molecular weight rna marker/product/Thermo Fisher
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    low molecular weight rna marker - by Bioz Stars, 2020-04
    94/100 stars

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    In Vitro:

    Article Title: A regulatory RNA is involved in RNA duplex formation and biofilm regulation in Sulfolobus acidocaldarius
    Article Snippet: Paragraph title: In vitro transcription and RNAs substrate preparation ... Low Molecular Weight RNA Marker, 10–100 nt (Affymetrix, cat# 76410) was 5′- radiolabeled in a 20 μl reaction volume as following: 10 μl of the RNA, 2 μl 10× T4 Polynucleotide Kinase (PNK) buffer (New England Biolabs (NEB)), 25 U T4 PNK (NEB) and 2.0 μl of [γ 32 P]-ATP (800 Ci/mmol, 10 μCi/μl) at 37°C for 30 min.

    Labeling:

    Article Title: A regulatory RNA is involved in RNA duplex formation and biofilm regulation in Sulfolobus acidocaldarius
    Article Snippet: An RrrR duplex (dsRrrR) was produced by hybridizing the [α 32 P]-ATP labeled RrrR ssRNA sense transcript with the non-labeled RrrR ssRNA antisense transcript. .. Low Molecular Weight RNA Marker, 10–100 nt (Affymetrix, cat# 76410) was 5′- radiolabeled in a 20 μl reaction volume as following: 10 μl of the RNA, 2 μl 10× T4 Polynucleotide Kinase (PNK) buffer (New England Biolabs (NEB)), 25 U T4 PNK (NEB) and 2.0 μl of [γ 32 P]-ATP (800 Ci/mmol, 10 μCi/μl) at 37°C for 30 min.

    Produced:

    Article Title: A regulatory RNA is involved in RNA duplex formation and biofilm regulation in Sulfolobus acidocaldarius
    Article Snippet: An RrrR duplex (dsRrrR) was produced by hybridizing the [α 32 P]-ATP labeled RrrR ssRNA sense transcript with the non-labeled RrrR ssRNA antisense transcript. .. Low Molecular Weight RNA Marker, 10–100 nt (Affymetrix, cat# 76410) was 5′- radiolabeled in a 20 μl reaction volume as following: 10 μl of the RNA, 2 μl 10× T4 Polynucleotide Kinase (PNK) buffer (New England Biolabs (NEB)), 25 U T4 PNK (NEB) and 2.0 μl of [γ 32 P]-ATP (800 Ci/mmol, 10 μCi/μl) at 37°C for 30 min.

    Incubation:

    Article Title: A regulatory RNA is involved in RNA duplex formation and biofilm regulation in Sulfolobus acidocaldarius
    Article Snippet: Both RNA molecules were mixed in DEPC water in a 1:10 ratio (sense:antisense), incubated at 95°C during 5 min and subsequently cooled down to room temperature. .. Low Molecular Weight RNA Marker, 10–100 nt (Affymetrix, cat# 76410) was 5′- radiolabeled in a 20 μl reaction volume as following: 10 μl of the RNA, 2 μl 10× T4 Polynucleotide Kinase (PNK) buffer (New England Biolabs (NEB)), 25 U T4 PNK (NEB) and 2.0 μl of [γ 32 P]-ATP (800 Ci/mmol, 10 μCi/μl) at 37°C for 30 min.

    Polyacrylamide Gel Electrophoresis:

    Article Title: A regulatory RNA is involved in RNA duplex formation and biofilm regulation in Sulfolobus acidocaldarius
    Article Snippet: RNA in vitro transcripts were separated by denaturing PAGE (8 M urea; 1× TBE; 10% polyacrylamide), and full-length bands were cut out using sterile scalpels after brief autoradiographic exposure. .. Low Molecular Weight RNA Marker, 10–100 nt (Affymetrix, cat# 76410) was 5′- radiolabeled in a 20 μl reaction volume as following: 10 μl of the RNA, 2 μl 10× T4 Polynucleotide Kinase (PNK) buffer (New England Biolabs (NEB)), 25 U T4 PNK (NEB) and 2.0 μl of [γ 32 P]-ATP (800 Ci/mmol, 10 μCi/μl) at 37°C for 30 min.

    Marker:

    Article Title: A regulatory RNA is involved in RNA duplex formation and biofilm regulation in Sulfolobus acidocaldarius
    Article Snippet: .. Low Molecular Weight RNA Marker, 10–100 nt (Affymetrix, cat# 76410) was 5′- radiolabeled in a 20 μl reaction volume as following: 10 μl of the RNA, 2 μl 10× T4 Polynucleotide Kinase (PNK) buffer (New England Biolabs (NEB)), 25 U T4 PNK (NEB) and 2.0 μl of [γ 32 P]-ATP (800 Ci/mmol, 10 μCi/μl) at 37°C for 30 min. .. Northern blot analyses Semi-dry electrophoretic transfer was used to transfer RNA that was separated on denaturing polyacrylamide gels onto a positively charged nylon membrane (Roti® -Nylon plus, pore size 0.45 μm).

    Molecular Weight:

    Article Title: A regulatory RNA is involved in RNA duplex formation and biofilm regulation in Sulfolobus acidocaldarius
    Article Snippet: .. Low Molecular Weight RNA Marker, 10–100 nt (Affymetrix, cat# 76410) was 5′- radiolabeled in a 20 μl reaction volume as following: 10 μl of the RNA, 2 μl 10× T4 Polynucleotide Kinase (PNK) buffer (New England Biolabs (NEB)), 25 U T4 PNK (NEB) and 2.0 μl of [γ 32 P]-ATP (800 Ci/mmol, 10 μCi/μl) at 37°C for 30 min. .. Northern blot analyses Semi-dry electrophoretic transfer was used to transfer RNA that was separated on denaturing polyacrylamide gels onto a positively charged nylon membrane (Roti® -Nylon plus, pore size 0.45 μm).

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    Thermo Fisher riboruler low range rna ladder
    Incubation of in vitro transcripts of CRISPR1, 2 and 3 with Cas6-1. ( A ) A total of 2.3 μM of CRISPR1 transcript is cleaved by 6.2 μM Cas6-1 by incubation for 1 h. ( B ) A total of 2 μM of CRISPR2 transcript is cleaved by 6.2 μM Cas6-1 by incubation for 1 h. ( C ) A total of 3.2 μM of CRISPR3 transcript is not cleaved by 6.5 μM Cas6-1 by incubation for 2 h. ( D ) The cleavage of 6.6 μM of the shorter CRISPR1* in vitro transcript by 5.8 μM Cas6-1 monitored over a time of 2 h 20 min. Since no finally mature crRNA ( 17 ) was detected, the in vivo presence of an unknown ribonuclease is suggested. All reactions were performed at 37°C in a reaction volume of 5 μl. <t>RNA</t> was separated by 8 M urea 10% PAGE and bands were visualized by ethidium bromide staining. Diamonds represent repeats and rectangles spacer sequences. Transcripts were not gel purified, explaining the appearance of fragments smaller than the full length transcripts of CRISPR1 and 2 in absence of Cas6-1. Eb1, elution buffer 1 used as negative control. Molecular markers: MN, Low Range ssRNA Ladder (NEB); MF, <t>RiboRuler</t> Low Range RNA Ladder (Thermo Fisher Scientific).
    Riboruler Low Range Rna Ladder, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/riboruler low range rna ladder/product/Thermo Fisher
    Average 99 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    riboruler low range rna ladder - by Bioz Stars, 2020-04
    99/100 stars
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    Incubation of in vitro transcripts of CRISPR1, 2 and 3 with Cas6-1. ( A ) A total of 2.3 μM of CRISPR1 transcript is cleaved by 6.2 μM Cas6-1 by incubation for 1 h. ( B ) A total of 2 μM of CRISPR2 transcript is cleaved by 6.2 μM Cas6-1 by incubation for 1 h. ( C ) A total of 3.2 μM of CRISPR3 transcript is not cleaved by 6.5 μM Cas6-1 by incubation for 2 h. ( D ) The cleavage of 6.6 μM of the shorter CRISPR1* in vitro transcript by 5.8 μM Cas6-1 monitored over a time of 2 h 20 min. Since no finally mature crRNA ( 17 ) was detected, the in vivo presence of an unknown ribonuclease is suggested. All reactions were performed at 37°C in a reaction volume of 5 μl. RNA was separated by 8 M urea 10% PAGE and bands were visualized by ethidium bromide staining. Diamonds represent repeats and rectangles spacer sequences. Transcripts were not gel purified, explaining the appearance of fragments smaller than the full length transcripts of CRISPR1 and 2 in absence of Cas6-1. Eb1, elution buffer 1 used as negative control. Molecular markers: MN, Low Range ssRNA Ladder (NEB); MF, RiboRuler Low Range RNA Ladder (Thermo Fisher Scientific).

    Journal: Nucleic Acids Research

    Article Title: Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs

    doi: 10.1093/nar/gkw786

    Figure Lengend Snippet: Incubation of in vitro transcripts of CRISPR1, 2 and 3 with Cas6-1. ( A ) A total of 2.3 μM of CRISPR1 transcript is cleaved by 6.2 μM Cas6-1 by incubation for 1 h. ( B ) A total of 2 μM of CRISPR2 transcript is cleaved by 6.2 μM Cas6-1 by incubation for 1 h. ( C ) A total of 3.2 μM of CRISPR3 transcript is not cleaved by 6.5 μM Cas6-1 by incubation for 2 h. ( D ) The cleavage of 6.6 μM of the shorter CRISPR1* in vitro transcript by 5.8 μM Cas6-1 monitored over a time of 2 h 20 min. Since no finally mature crRNA ( 17 ) was detected, the in vivo presence of an unknown ribonuclease is suggested. All reactions were performed at 37°C in a reaction volume of 5 μl. RNA was separated by 8 M urea 10% PAGE and bands were visualized by ethidium bromide staining. Diamonds represent repeats and rectangles spacer sequences. Transcripts were not gel purified, explaining the appearance of fragments smaller than the full length transcripts of CRISPR1 and 2 in absence of Cas6-1. Eb1, elution buffer 1 used as negative control. Molecular markers: MN, Low Range ssRNA Ladder (NEB); MF, RiboRuler Low Range RNA Ladder (Thermo Fisher Scientific).

    Article Snippet: Before loading onto denaturing 8 M urea 10% PAA gels, reactions were incubated at 95°C for 5 min. As size markers served the Low Range ssRNA Ladder from NEB (MN ), the RiboRuler Low Range RNA Ladder from Thermo Fisher Scientific (MF ) and the Low Molecular Weight Marker from Affymetrix (MA ).

    Techniques: Incubation, In Vitro, In Vivo, Polyacrylamide Gel Electrophoresis, Staining, Purification, Negative Control

    Purification and in vitro cleavage assay of Synechocystis WT Cas6-1 and mutated Cas6-1 proteins. (A) Coomassie-stained 15% SDS-PAGE of heterologously overexpressed and purified Cas6-1 protein variants. The expected molecular weight of Cas6-1_6xHis is ∼ 30 kDa. 66.67 pmol recombinant enzyme was loaded on each lane and PageRuler™ Prestained Protein Ladder (Thermo Fisher Scientific) served for protein size estimation. (B, C) In in vitro cleavage assays both the (B) CRISPR1 RNA oligo repeat sequence and the (C) pre-acrRNA cassette is processed with variable efficiency by the purified Cas6-1 protein variants shown in (A). After incubation at 30°C the RNA fragments were electrophoretically size separated on a 15% PAA sequencing gel and visualized with SYBR® Gold Nucleic Acid Gel Stain. The processing results in a pattern of RNA fragments of distinct lengths. Cleavage assays were conducted with a three-fold excess (B) or a 1:1 ratio (C) of protein to RNA-substrate in cleavage buffer and incubated at 30°C for the indicated time. Expected RNA fragments and their corresponding sizes are illustrated by cartoons. Another Cas6-1 WT protein sample, which was overexpressed and purified independently, is indicated by an asterisk. Negative controls were complemented with 1 μL of H 2 O or 1 μL eluate of a mock control. Two additional nucleotides resulting from in vitro transcription were added to the 215 nt long acrRNA yielding a 217 nt long pre-acrRNA. For RNA size estimation a CRISPR1 repeat oligo ladder (C1L), RiboRuler low range RNA ladder (Thermo Fisher Scientific), low range ssRNA ladder or microRNA marker (both from New England Biolabs) were used.

    Journal: RNA Biology

    Article Title: Biochemical analysis of the Cas6-1 RNA endonuclease associated with the subtype I-D CRISPR-Cas system in Synechocystis sp. PCC 6803

    doi: 10.1080/15476286.2018.1447742

    Figure Lengend Snippet: Purification and in vitro cleavage assay of Synechocystis WT Cas6-1 and mutated Cas6-1 proteins. (A) Coomassie-stained 15% SDS-PAGE of heterologously overexpressed and purified Cas6-1 protein variants. The expected molecular weight of Cas6-1_6xHis is ∼ 30 kDa. 66.67 pmol recombinant enzyme was loaded on each lane and PageRuler™ Prestained Protein Ladder (Thermo Fisher Scientific) served for protein size estimation. (B, C) In in vitro cleavage assays both the (B) CRISPR1 RNA oligo repeat sequence and the (C) pre-acrRNA cassette is processed with variable efficiency by the purified Cas6-1 protein variants shown in (A). After incubation at 30°C the RNA fragments were electrophoretically size separated on a 15% PAA sequencing gel and visualized with SYBR® Gold Nucleic Acid Gel Stain. The processing results in a pattern of RNA fragments of distinct lengths. Cleavage assays were conducted with a three-fold excess (B) or a 1:1 ratio (C) of protein to RNA-substrate in cleavage buffer and incubated at 30°C for the indicated time. Expected RNA fragments and their corresponding sizes are illustrated by cartoons. Another Cas6-1 WT protein sample, which was overexpressed and purified independently, is indicated by an asterisk. Negative controls were complemented with 1 μL of H 2 O or 1 μL eluate of a mock control. Two additional nucleotides resulting from in vitro transcription were added to the 215 nt long acrRNA yielding a 217 nt long pre-acrRNA. For RNA size estimation a CRISPR1 repeat oligo ladder (C1L), RiboRuler low range RNA ladder (Thermo Fisher Scientific), low range ssRNA ladder or microRNA marker (both from New England Biolabs) were used.

    Article Snippet: The low range ssRNA ladder (ssRNA marker) (New England Biolabs), the RiboRuler low range RNA ladder (Thermo Fisher Scientific) and the microRNA marker (New England Biolabs) served as RNA ladders for size estimation.

    Techniques: Purification, In Vitro, Cleavage Assay, Staining, SDS Page, Molecular Weight, Recombinant, Sequencing, Incubation, Marker

    In vivo cleavage assay of Cas6-1 protein variants and pre-acrRNA. Northern Blot analysis using a radioactively labeled transcript probe spanning the entire pre-acrRNA cassette. The RiboRuler low range RNA ladder was used as a size marker. Cas6-1 expression was controlled by the copper inducible petE , ], whereas acrRNA was zinc inducible by the ziaA ]. The smallest detectable processing intermediate of 73 nt in size is marked by asterisks. WT Cas6-1 and the R67A protein variant show comparable cleavage performance indicating that R67A is not involved in the active site or RNA binding of the enzyme. In contrast, the remaining mutated proteins show distinct acrRNA accumulation and lack acrRNA derived cleavage intermediates.

    Journal: RNA Biology

    Article Title: Biochemical analysis of the Cas6-1 RNA endonuclease associated with the subtype I-D CRISPR-Cas system in Synechocystis sp. PCC 6803

    doi: 10.1080/15476286.2018.1447742

    Figure Lengend Snippet: In vivo cleavage assay of Cas6-1 protein variants and pre-acrRNA. Northern Blot analysis using a radioactively labeled transcript probe spanning the entire pre-acrRNA cassette. The RiboRuler low range RNA ladder was used as a size marker. Cas6-1 expression was controlled by the copper inducible petE , ], whereas acrRNA was zinc inducible by the ziaA ]. The smallest detectable processing intermediate of 73 nt in size is marked by asterisks. WT Cas6-1 and the R67A protein variant show comparable cleavage performance indicating that R67A is not involved in the active site or RNA binding of the enzyme. In contrast, the remaining mutated proteins show distinct acrRNA accumulation and lack acrRNA derived cleavage intermediates.

    Article Snippet: The low range ssRNA ladder (ssRNA marker) (New England Biolabs), the RiboRuler low range RNA ladder (Thermo Fisher Scientific) and the microRNA marker (New England Biolabs) served as RNA ladders for size estimation.

    Techniques: In Vivo, Cleavage Assay, Northern Blot, Labeling, Marker, Expressing, Variant Assay, RNA Binding Assay, Derivative Assay