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  • 94
    Thermo Fisher ec68852box tbe urea gels
    Ec68852box Tbe Urea Gels, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bio-Rad tbe urea ready gel
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    Thermo Fisher tbe urea gel
    Ribosome protected fragments (RPFs) were enriched between 28-34nt (marked with an asterisk). S2 cells were treated with 100 nM of rapamycin (RAPA), Torin, or DMSO. Cell lysate was treated with MNase and passed through Sephacryl S-400 columns to purify monosomes. <t>RNA</t> was purified from the flowthrough of the columns. 5’-end of RNA was labelled by γ-[32P] ATP, resolved on a 15% <t>TBE-ureagel</t> and visualized.
    Tbe Urea Gel, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 1481 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Bio-Rad tbe urea gels
    Ribosome protected fragments (RPFs) were enriched between 28-34nt (marked with an asterisk). S2 cells were treated with 100 nM of rapamycin (RAPA), Torin, or DMSO. Cell lysate was treated with MNase and passed through Sephacryl S-400 columns to purify monosomes. <t>RNA</t> was purified from the flowthrough of the columns. 5’-end of RNA was labelled by γ-[32P] ATP, resolved on a 15% <t>TBE-ureagel</t> and visualized.
    Tbe Urea Gels, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 96/100, based on 133 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Bio-Rad tbe urea precast gel
    Ribosome protected fragments (RPFs) were enriched between 28-34nt (marked with an asterisk). S2 cells were treated with 100 nM of rapamycin (RAPA), Torin, or DMSO. Cell lysate was treated with MNase and passed through Sephacryl S-400 columns to purify monosomes. <t>RNA</t> was purified from the flowthrough of the columns. 5’-end of RNA was labelled by γ-[32P] ATP, resolved on a 15% <t>TBE-ureagel</t> and visualized.
    Tbe Urea Precast Gel, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 94/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bio-Rad criteriontm tbe urea precast gels
    Ribosome protected fragments (RPFs) were enriched between 28-34nt (marked with an asterisk). S2 cells were treated with 100 nM of rapamycin (RAPA), Torin, or DMSO. Cell lysate was treated with MNase and passed through Sephacryl S-400 columns to purify monosomes. <t>RNA</t> was purified from the flowthrough of the columns. 5’-end of RNA was labelled by γ-[32P] ATP, resolved on a 15% <t>TBE-ureagel</t> and visualized.
    Criteriontm Tbe Urea Precast Gels, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 94/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Thermo Fisher tbe urea acrylamide gel
    Ribosome protected fragments (RPFs) were enriched between 28-34nt (marked with an asterisk). S2 cells were treated with 100 nM of rapamycin (RAPA), Torin, or DMSO. Cell lysate was treated with MNase and passed through Sephacryl S-400 columns to purify monosomes. <t>RNA</t> was purified from the flowthrough of the columns. 5’-end of RNA was labelled by γ-[32P] ATP, resolved on a 15% <t>TBE-ureagel</t> and visualized.
    Tbe Urea Acrylamide Gel, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 89/100, based on 113 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher tbe urea polyacrylamide gels
    Ribosome protected fragments (RPFs) were enriched between 28-34nt (marked with an asterisk). S2 cells were treated with 100 nM of rapamycin (RAPA), Torin, or DMSO. Cell lysate was treated with MNase and passed through Sephacryl S-400 columns to purify monosomes. <t>RNA</t> was purified from the flowthrough of the columns. 5’-end of RNA was labelled by γ-[32P] ATP, resolved on a 15% <t>TBE-ureagel</t> and visualized.
    Tbe Urea Polyacrylamide Gels, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 89/100, based on 77 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bio-Rad tbe urea
    Ribosome protected fragments (RPFs) were enriched between 28-34nt (marked with an asterisk). S2 cells were treated with 100 nM of rapamycin (RAPA), Torin, or DMSO. Cell lysate was treated with MNase and passed through Sephacryl S-400 columns to purify monosomes. <t>RNA</t> was purified from the flowthrough of the columns. 5’-end of RNA was labelled by γ-[32P] ATP, resolved on a 15% <t>TBE-ureagel</t> and visualized.
    Tbe Urea, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 88/100, based on 157 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher acrylamide tbe urea gels
    Ribosome protected fragments (RPFs) were enriched between 28-34nt (marked with an asterisk). S2 cells were treated with 100 nM of rapamycin (RAPA), Torin, or DMSO. Cell lysate was treated with MNase and passed through Sephacryl S-400 columns to purify monosomes. <t>RNA</t> was purified from the flowthrough of the columns. 5’-end of RNA was labelled by γ-[32P] ATP, resolved on a 15% <t>TBE-ureagel</t> and visualized.
    Acrylamide Tbe Urea Gels, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher precast tbe urea gel
    Ribosome protected fragments (RPFs) were enriched between 28-34nt (marked with an asterisk). S2 cells were treated with 100 nM of rapamycin (RAPA), Torin, or DMSO. Cell lysate was treated with MNase and passed through Sephacryl S-400 columns to purify monosomes. <t>RNA</t> was purified from the flowthrough of the columns. 5’-end of RNA was labelled by γ-[32P] ATP, resolved on a 15% <t>TBE-ureagel</t> and visualized.
    Precast Tbe Urea Gel, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Ribosome protected fragments (RPFs) were enriched between 28-34nt (marked with an asterisk). S2 cells were treated with 100 nM of rapamycin (RAPA), Torin, or DMSO. Cell lysate was treated with MNase and passed through Sephacryl S-400 columns to purify monosomes. RNA was purified from the flowthrough of the columns. 5’-end of RNA was labelled by γ-[32P] ATP, resolved on a 15% TBE-ureagel and visualized.

    Journal: bioRxiv

    Article Title: TRIBE editing reveals specific mRNA targets of eIF4E-BP in Drosophila and in mammals

    doi: 10.1101/2020.02.24.962852

    Figure Lengend Snippet: Ribosome protected fragments (RPFs) were enriched between 28-34nt (marked with an asterisk). S2 cells were treated with 100 nM of rapamycin (RAPA), Torin, or DMSO. Cell lysate was treated with MNase and passed through Sephacryl S-400 columns to purify monosomes. RNA was purified from the flowthrough of the columns. 5’-end of RNA was labelled by γ-[32P] ATP, resolved on a 15% TBE-ureagel and visualized.

    Article Snippet: 5’end of RNA was phosphorylated and labelled by γ-[32P] ATP using T4 Polynucleotide Kinase (New England Biolabs) at 37°C for 45 min. 3’adaptor-ligated RNA was resolved on a 15% TBE-urea gel (Invitrogen) and the RNA in the size of 54–75 nt for input and 48-54 nt for RPF was purified.

    Techniques: Purification

    Stability and live-cell detection of fluorescent tricRNAs. ( A ) HEK293T cells were transfected with pTRIC-Y:Broccoli-U6, treated with actinomycin D (ActD) and harvested after the indicated times. Total RNA was run on a 10% TBE-urea gel, renatured, stained with DFHBI-1T for Broccoli ( right panel) and then SYBR Gold for total RNA ( left panel). ( B ) Quantification of linear and circular Broccoli RNA bands shown in F ; (a.u.) arbitrary units. ( C ) Broccoli RNA detection by flow cytometry. HEK293T cells were transfected with either a mock or circular Broccoli-expressing plasmid (pTRIC-Y:Broc-U6). mCherry was also expressed from a separate plasmid as a transfection efficiency control ( y -axis). In addition, Broccoli-tricRNA expressing cells were also treated with actinomycin D for 2 h before sorting. All cells were stained with DFHBI-1T and analyzed by flow cytometry in green and red channels. ( D ) Localization of circular Broccoli in living cells. Light microscopy of the same cells as described in C , stained with DFHBI-1T (Broccoli) and Hoechst. Scale bar, 20 µm.

    Journal: RNA

    Article Title: Metazoan tRNA introns generate stable circular RNAs in vivo

    doi: 10.1261/rna.052944.115

    Figure Lengend Snippet: Stability and live-cell detection of fluorescent tricRNAs. ( A ) HEK293T cells were transfected with pTRIC-Y:Broccoli-U6, treated with actinomycin D (ActD) and harvested after the indicated times. Total RNA was run on a 10% TBE-urea gel, renatured, stained with DFHBI-1T for Broccoli ( right panel) and then SYBR Gold for total RNA ( left panel). ( B ) Quantification of linear and circular Broccoli RNA bands shown in F ; (a.u.) arbitrary units. ( C ) Broccoli RNA detection by flow cytometry. HEK293T cells were transfected with either a mock or circular Broccoli-expressing plasmid (pTRIC-Y:Broc-U6). mCherry was also expressed from a separate plasmid as a transfection efficiency control ( y -axis). In addition, Broccoli-tricRNA expressing cells were also treated with actinomycin D for 2 h before sorting. All cells were stained with DFHBI-1T and analyzed by flow cytometry in green and red channels. ( D ) Localization of circular Broccoli in living cells. Light microscopy of the same cells as described in C , stained with DFHBI-1T (Broccoli) and Hoechst. Scale bar, 20 µm.

    Article Snippet: RNA samples were electrophoresed through 6% or 10% TBE-urea gels (Life Technologies).

    Techniques: Transfection, Staining, RNA Detection, Flow Cytometry, Cytometry, Expressing, Plasmid Preparation, Light Microscopy

    In vivo expression of stable, heterologous tricRNAs in human cells. ( A ) tricRNA vectors used for circular RNA expression, showing the tricRNA scaffold. The gray arrows represent the A and B boxes of the intragenic tRNA promoters. External 5S and U6 promoter constructs were also generated. ( B ) pTRIC31905 (tRNA:Tyr GUA ) and pTRIC31143 (tRNA:Leu CAA ) native intron vectors were transfected into HeLa cells for 24 h and their expression was measured by qRT-PCR. β-actin mRNA was used as normalization standard. U1 snRNA was used as a negative control (Control). tric31905-c and tric31143-c are convergent primer pairs, whereas tric31905-d and tric31143-d are divergent primer pairs used to measure expression of tric31905 and tric31143, respectively. Standard deviations were calculated from three biological replicates. ( C ) Secondary structures of RNAs expressed from pTRIC-Y and pTRIC-L scaffolds, highlighting the TSEN cleavage sites (arrows), anticodons (blue) and NotI–SacII restriction sites (gray). ( D ) Vectors for two circular Spinach2 constructs, pTRIC-Y:Sp2 (blue) and pTRIC-L:Sp2 (red), were transfected into HeLa cells and expression was determined using qRT-PCR. A control pTRIC31905 native intron vector was also used (black). The three experiments were analyzed using convergent (Spinach2-c) and divergent (Spinach2-d) primer pairs. β-actin mRNA was used as normalization standard and U1 snRNA was used as a negative PCR control (Control). Standard deviations were calculated from three biological replicates. ( E ) In-gel detection of Broccoli-tagged RNAs expressed from three different pTRIC-Y constructs bearing tRNA, U6 sRNA, or 5S rRNA promoters. HEK293T cells were transfected and total RNA was run on a 6% TBE-urea gel. The gel was washed to remove the urea, renatured in buffer, and stained with DFHBI-1T to reveal Broccoli ( right panel), then stained with SYBR Gold to reveal total RNA ( left panel). (RnR) RNase R treatment prior to gel electrophoresis. In vitro transcribed pre-tRNA-Broccoli (5 ng) was used as a positive control (first lane). In the experimental lanes, the upper bands (bracket) correspond to the precursor tRNAs; the lower band (arrow) corresponds to the mature circular Broccoli tricRNA. ( F ) Capping of the pre-tRNA improves production of circular RNAs. Two different U6 snRNA promoter constructs were tested, one that includes the first 4 nt of human U6 snRNA (U6) and a construct that includes the first 27 nt (U6*). HEK293T cells were transfected for the indicated times prior to harvesting total RNA. Electrophoresis, gel-detection, and band labels as described in E .

    Journal: RNA

    Article Title: Metazoan tRNA introns generate stable circular RNAs in vivo

    doi: 10.1261/rna.052944.115

    Figure Lengend Snippet: In vivo expression of stable, heterologous tricRNAs in human cells. ( A ) tricRNA vectors used for circular RNA expression, showing the tricRNA scaffold. The gray arrows represent the A and B boxes of the intragenic tRNA promoters. External 5S and U6 promoter constructs were also generated. ( B ) pTRIC31905 (tRNA:Tyr GUA ) and pTRIC31143 (tRNA:Leu CAA ) native intron vectors were transfected into HeLa cells for 24 h and their expression was measured by qRT-PCR. β-actin mRNA was used as normalization standard. U1 snRNA was used as a negative control (Control). tric31905-c and tric31143-c are convergent primer pairs, whereas tric31905-d and tric31143-d are divergent primer pairs used to measure expression of tric31905 and tric31143, respectively. Standard deviations were calculated from three biological replicates. ( C ) Secondary structures of RNAs expressed from pTRIC-Y and pTRIC-L scaffolds, highlighting the TSEN cleavage sites (arrows), anticodons (blue) and NotI–SacII restriction sites (gray). ( D ) Vectors for two circular Spinach2 constructs, pTRIC-Y:Sp2 (blue) and pTRIC-L:Sp2 (red), were transfected into HeLa cells and expression was determined using qRT-PCR. A control pTRIC31905 native intron vector was also used (black). The three experiments were analyzed using convergent (Spinach2-c) and divergent (Spinach2-d) primer pairs. β-actin mRNA was used as normalization standard and U1 snRNA was used as a negative PCR control (Control). Standard deviations were calculated from three biological replicates. ( E ) In-gel detection of Broccoli-tagged RNAs expressed from three different pTRIC-Y constructs bearing tRNA, U6 sRNA, or 5S rRNA promoters. HEK293T cells were transfected and total RNA was run on a 6% TBE-urea gel. The gel was washed to remove the urea, renatured in buffer, and stained with DFHBI-1T to reveal Broccoli ( right panel), then stained with SYBR Gold to reveal total RNA ( left panel). (RnR) RNase R treatment prior to gel electrophoresis. In vitro transcribed pre-tRNA-Broccoli (5 ng) was used as a positive control (first lane). In the experimental lanes, the upper bands (bracket) correspond to the precursor tRNAs; the lower band (arrow) corresponds to the mature circular Broccoli tricRNA. ( F ) Capping of the pre-tRNA improves production of circular RNAs. Two different U6 snRNA promoter constructs were tested, one that includes the first 4 nt of human U6 snRNA (U6) and a construct that includes the first 27 nt (U6*). HEK293T cells were transfected for the indicated times prior to harvesting total RNA. Electrophoresis, gel-detection, and band labels as described in E .

    Article Snippet: RNA samples were electrophoresed through 6% or 10% TBE-urea gels (Life Technologies).

    Techniques: In Vivo, Expressing, RNA Expression, Construct, Generated, Cellular Antioxidant Activity Assay, Transfection, Quantitative RT-PCR, Negative Control, Plasmid Preparation, Polymerase Chain Reaction, Staining, Nucleic Acid Electrophoresis, In Vitro, Positive Control, Electrophoresis

    Detection of endogenous tricRNAs in Drosophila melanogaster . ( A ) RNA-seq reads spanning the circular junction of the intron of tRNA:Y1:28C-RA (tRNA:Tyr:GUA, CR31905). rRNA-depleted pharate adult RNA-seq data were mapped using Bowtie2 (for end-to-end and partially mapped reads) and a modified version of Vicinal (for circular junction-spanning reads). The structure of the pre-tRNA gene is shown under the tracks, with the thinner line representing the intron and the thicker lines representing the exons. The junction-spanning reads (counts ≥100) are shown beneath the gene structure. ( B ) Distribution of tRNA intron sizes among select eukaryotic genomes. The box plots show the first, second, and third quartiles; the whiskers represent a 1.5 interquartile range. Box thickness is proportional to the square root of the number of tRNA introns in each genome. Outliers are drawn as dots; the Drosophila CR31905 intron is marked by a blue box. The number of introns for each species is as follows: Saccharomyces cerevisiae 59, D. melanogaster 16, Anopheles gambiae 29, Aedes aegypti 32, Apis mellifera 11, Mus musculus 24, Rattus norvegicus 10, Caenorhabditis elegans 32, Tribolium castaneum 21, Homo sapiens 39. The plot was drawn using the boxplot R package. ( C ) Conservation of predicted secondary structure for tric31905 among Drosophilids. Sequences of the orthologous CR31905 tRNA intron from various species of Drosophila are shown. Note the compensatory base changes that maintain base-pairing within the predicted structure. ( D ) RT-PCR detection of tric31905 from total larval RNA. Cartoon shows schematic of an intronic tRNA gene with convergent (Con) and divergent (Div) primer pairs. Four pairs of primers (two Div and two Con) were tested. The ladders of PCR products correspond to amplification of concatemers of the cDNA via rolling circle reverse transcription. Experimental results agree well with the expected lengths (in base pairs) of the PCR products. Lane 1 : 82 + 113 n ; lane 2 : 75 + 113 n ; lane 3 : 100 + 113 n ; lane 4 : 78 + 113 n ; n = 0, 1, 2, … etc. ( E ) Abnormal migration of the 113-nt circular RNA tric31905. Total larval RNA samples were electrophoresed through 10% or 6% TBE-urea gels and tric31905 was detected by Northern blotting using a radiolabeled circular RNA junction oligomer. ( F ) Total larval RNA samples were treated with or without RNase R and run on a 10% TBE-urea gel. RNA was imaged using SYBR Gold ( left panel), whereas tric31905 ( right upper panel), U1 and U4 snRNAs ( right lower panel) were detected by Northern blotting.

    Journal: RNA

    Article Title: Metazoan tRNA introns generate stable circular RNAs in vivo

    doi: 10.1261/rna.052944.115

    Figure Lengend Snippet: Detection of endogenous tricRNAs in Drosophila melanogaster . ( A ) RNA-seq reads spanning the circular junction of the intron of tRNA:Y1:28C-RA (tRNA:Tyr:GUA, CR31905). rRNA-depleted pharate adult RNA-seq data were mapped using Bowtie2 (for end-to-end and partially mapped reads) and a modified version of Vicinal (for circular junction-spanning reads). The structure of the pre-tRNA gene is shown under the tracks, with the thinner line representing the intron and the thicker lines representing the exons. The junction-spanning reads (counts ≥100) are shown beneath the gene structure. ( B ) Distribution of tRNA intron sizes among select eukaryotic genomes. The box plots show the first, second, and third quartiles; the whiskers represent a 1.5 interquartile range. Box thickness is proportional to the square root of the number of tRNA introns in each genome. Outliers are drawn as dots; the Drosophila CR31905 intron is marked by a blue box. The number of introns for each species is as follows: Saccharomyces cerevisiae 59, D. melanogaster 16, Anopheles gambiae 29, Aedes aegypti 32, Apis mellifera 11, Mus musculus 24, Rattus norvegicus 10, Caenorhabditis elegans 32, Tribolium castaneum 21, Homo sapiens 39. The plot was drawn using the boxplot R package. ( C ) Conservation of predicted secondary structure for tric31905 among Drosophilids. Sequences of the orthologous CR31905 tRNA intron from various species of Drosophila are shown. Note the compensatory base changes that maintain base-pairing within the predicted structure. ( D ) RT-PCR detection of tric31905 from total larval RNA. Cartoon shows schematic of an intronic tRNA gene with convergent (Con) and divergent (Div) primer pairs. Four pairs of primers (two Div and two Con) were tested. The ladders of PCR products correspond to amplification of concatemers of the cDNA via rolling circle reverse transcription. Experimental results agree well with the expected lengths (in base pairs) of the PCR products. Lane 1 : 82 + 113 n ; lane 2 : 75 + 113 n ; lane 3 : 100 + 113 n ; lane 4 : 78 + 113 n ; n = 0, 1, 2, … etc. ( E ) Abnormal migration of the 113-nt circular RNA tric31905. Total larval RNA samples were electrophoresed through 10% or 6% TBE-urea gels and tric31905 was detected by Northern blotting using a radiolabeled circular RNA junction oligomer. ( F ) Total larval RNA samples were treated with or without RNase R and run on a 10% TBE-urea gel. RNA was imaged using SYBR Gold ( left panel), whereas tric31905 ( right upper panel), U1 and U4 snRNAs ( right lower panel) were detected by Northern blotting.

    Article Snippet: RNA samples were electrophoresed through 6% or 10% TBE-urea gels (Life Technologies).

    Techniques: RNA Sequencing Assay, Modification, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Amplification, Migration, Northern Blot

    RNA degradosomes mediate tRNA decay in vitro. ( A ) Coomasie-stained gel image of Flag-RNase E immunoprecipitated fraction. Indicated bands were identified through peptide mass spectrometry. ( B ) In vitro tRNA-Tyr decay assay. Time course of tRNA-Tyr resolved in 10% TBE-UREA gel stained with SYBR Gold at the indicated time. Upper and Lower show reactions with degradosomes from the WT and from the PNPase catalytic mutant, respectively. ( C ) Decay curves of tRNA-Tyr from WT and Δ thiI mutant strains based on data shown in B .

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: The RNA degradosome promotes tRNA quality control through clearance of hypomodified tRNA

    doi: 10.1073/pnas.1814130116

    Figure Lengend Snippet: RNA degradosomes mediate tRNA decay in vitro. ( A ) Coomasie-stained gel image of Flag-RNase E immunoprecipitated fraction. Indicated bands were identified through peptide mass spectrometry. ( B ) In vitro tRNA-Tyr decay assay. Time course of tRNA-Tyr resolved in 10% TBE-UREA gel stained with SYBR Gold at the indicated time. Upper and Lower show reactions with degradosomes from the WT and from the PNPase catalytic mutant, respectively. ( C ) Decay curves of tRNA-Tyr from WT and Δ thiI mutant strains based on data shown in B .

    Article Snippet: In total, 0.1–1 μg RNA was electrophoresed on 10% Novex TBE-UREA gels (Thermofisher) and stained with SYBR Gold (Life Technologies).

    Techniques: In Vitro, Staining, Immunoprecipitation, Mass Spectrometry, Mutagenesis