trna sepharose column Search Results


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  • 99
    Thermo Fisher dynabeads protein g
    Dynabeads Protein G, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 18160 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore genelute mammalian total rna miniprep kit
    Genelute Mammalian Total Rna Miniprep Kit, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 4036 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen rneasy mini kit
    Rneasy Mini Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 343576 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen rneasy kit
    Rneasy Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 112221 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher t4 dna ligase
    Detection of tRNAs by microarray analysis. ( A ) Array scheme. Total cellular or viral RNA were deacylated, and directly labeled with a Cy3 or Cy5 containing oligonucleotide using <t>T4</t> DNA ligase. The labeling samples with the opposite fluorophores were combined
    T4 Dna Ligase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 25057 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher dynabeads protein a
    Ritonavir does not affect BACE1 protein stability in primary neurons. A: Primary rat neurons were pulse labeled for 30 minutes with 35 S-methionine/cysteine-containing Dulbecco's modified Eagle's medium and chased with neurobasal media plus B27. Radiolabeled BACE1 was immunoprecipitated with <t>Dynabeads</t> <t>Protein</t> A and 2 μg anti-BACE1 12 hours after labeling to confirm enrichment. B: Neurons were pulse labeled, as in A , and chased with neurobasal media with or without 10 μmol/L ritonavir for 24 hours. BACE1 was immunoprecipitated, as in A Representative autoradiogram shown. C: The levels of 35 S-methionine/cysteine-labeled BACE1 were quantified and the percentage changes, relative to 0 hour time point, are plotted. No significant differences in BACE1 half-life were observed between control and ritonavir-treated neurons ( P > 0.05, linear regression analysis). All values represent means ± SEM ( C ). n = 3 ( B and C ). M, molecular weight; mAb, monoclonal antibody; ms, mouse; rb, rabbit; WC, whole cell.
    Dynabeads Protein A, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 6501 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher protein g agarose
    Active involvement of the A–I base pair in coordinating pre-tRNA cleavage. a , Pre-tRNA cleavage assay comparing recombinant, inactive TSEN tetramer (TSEN2 H377A and TSEN34 H255A double mutant) to the TSEN/CLP1 complex. Cleavage products are visualized by denaturing Urea-PAGE with subsequent Toluidine blue staining. RNA size markers are indicated on the left of the gel. b , Pull-down assay with fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN captured on <t>protein</t> G agarose functionalized with an α-His-antibody. Protein size markers are indicated on the left of each immunoblot, protein and RNA identities on the right. Input and co-precipitated, labeled pre-tRNAs were visualized by in-gel fluorescence, TSEN subunits and the immunoglobulin G (IgG) heavy chain by immunoblotting. The IgG heavy chain served as loading control. c, Thermodynamic binding parameters of fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. d , Thermodynamic binding parameters of fluorescently labeled tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. e , Schematic depiction of a pre-tRNA molecule showing ribonucleotides belonging to the mature domain (grey spheres), the intronic region (white spheres), the anticodon (black spheres), and the A-I base pair (yellow spheres). Proposed 5’ and 3’ splice sites (ss) are indicated. f , Impact of A-I base pair mutations in S.c. pre-tRNA Phe GAA on endonucleolytic activity of tetrameric TSEN revealed by a pre-tRNA cleavage assay. C 32 :G 54 – canonical A-I base pair, C 32 :C 54 – disrupted A-I base pair, G 32 :C 54 – inverted A-I base pair. All experiments are representatives of three independent assays. Unprocessed gels for a , b and f are shown in Source Data 3.
    Protein G Agarose, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 3244 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen rneasy plant mini kit
    Active involvement of the A–I base pair in coordinating pre-tRNA cleavage. a , Pre-tRNA cleavage assay comparing recombinant, inactive TSEN tetramer (TSEN2 H377A and TSEN34 H255A double mutant) to the TSEN/CLP1 complex. Cleavage products are visualized by denaturing Urea-PAGE with subsequent Toluidine blue staining. RNA size markers are indicated on the left of the gel. b , Pull-down assay with fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN captured on <t>protein</t> G agarose functionalized with an α-His-antibody. Protein size markers are indicated on the left of each immunoblot, protein and RNA identities on the right. Input and co-precipitated, labeled pre-tRNAs were visualized by in-gel fluorescence, TSEN subunits and the immunoglobulin G (IgG) heavy chain by immunoblotting. The IgG heavy chain served as loading control. c, Thermodynamic binding parameters of fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. d , Thermodynamic binding parameters of fluorescently labeled tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. e , Schematic depiction of a pre-tRNA molecule showing ribonucleotides belonging to the mature domain (grey spheres), the intronic region (white spheres), the anticodon (black spheres), and the A-I base pair (yellow spheres). Proposed 5’ and 3’ splice sites (ss) are indicated. f , Impact of A-I base pair mutations in S.c. pre-tRNA Phe GAA on endonucleolytic activity of tetrameric TSEN revealed by a pre-tRNA cleavage assay. C 32 :G 54 – canonical A-I base pair, C 32 :C 54 – disrupted A-I base pair, G 32 :C 54 – inverted A-I base pair. All experiments are representatives of three independent assays. Unprocessed gels for a , b and f are shown in Source Data 3.
    Rneasy Plant Mini Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 39071 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen rneasy midi kit
    Active involvement of the A–I base pair in coordinating pre-tRNA cleavage. a , Pre-tRNA cleavage assay comparing recombinant, inactive TSEN tetramer (TSEN2 H377A and TSEN34 H255A double mutant) to the TSEN/CLP1 complex. Cleavage products are visualized by denaturing Urea-PAGE with subsequent Toluidine blue staining. RNA size markers are indicated on the left of the gel. b , Pull-down assay with fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN captured on <t>protein</t> G agarose functionalized with an α-His-antibody. Protein size markers are indicated on the left of each immunoblot, protein and RNA identities on the right. Input and co-precipitated, labeled pre-tRNAs were visualized by in-gel fluorescence, TSEN subunits and the immunoglobulin G (IgG) heavy chain by immunoblotting. The IgG heavy chain served as loading control. c, Thermodynamic binding parameters of fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. d , Thermodynamic binding parameters of fluorescently labeled tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. e , Schematic depiction of a pre-tRNA molecule showing ribonucleotides belonging to the mature domain (grey spheres), the intronic region (white spheres), the anticodon (black spheres), and the A-I base pair (yellow spheres). Proposed 5’ and 3’ splice sites (ss) are indicated. f , Impact of A-I base pair mutations in S.c. pre-tRNA Phe GAA on endonucleolytic activity of tetrameric TSEN revealed by a pre-tRNA cleavage assay. C 32 :G 54 – canonical A-I base pair, C 32 :C 54 – disrupted A-I base pair, G 32 :C 54 – inverted A-I base pair. All experiments are representatives of three independent assays. Unprocessed gels for a , b and f are shown in Source Data 3.
    Rneasy Midi Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 7875 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen qiaquick gel extraction kit
    Active involvement of the A–I base pair in coordinating pre-tRNA cleavage. a , Pre-tRNA cleavage assay comparing recombinant, inactive TSEN tetramer (TSEN2 H377A and TSEN34 H255A double mutant) to the TSEN/CLP1 complex. Cleavage products are visualized by denaturing Urea-PAGE with subsequent Toluidine blue staining. RNA size markers are indicated on the left of the gel. b , Pull-down assay with fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN captured on <t>protein</t> G agarose functionalized with an α-His-antibody. Protein size markers are indicated on the left of each immunoblot, protein and RNA identities on the right. Input and co-precipitated, labeled pre-tRNAs were visualized by in-gel fluorescence, TSEN subunits and the immunoglobulin G (IgG) heavy chain by immunoblotting. The IgG heavy chain served as loading control. c, Thermodynamic binding parameters of fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. d , Thermodynamic binding parameters of fluorescently labeled tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. e , Schematic depiction of a pre-tRNA molecule showing ribonucleotides belonging to the mature domain (grey spheres), the intronic region (white spheres), the anticodon (black spheres), and the A-I base pair (yellow spheres). Proposed 5’ and 3’ splice sites (ss) are indicated. f , Impact of A-I base pair mutations in S.c. pre-tRNA Phe GAA on endonucleolytic activity of tetrameric TSEN revealed by a pre-tRNA cleavage assay. C 32 :G 54 – canonical A-I base pair, C 32 :C 54 – disrupted A-I base pair, G 32 :C 54 – inverted A-I base pair. All experiments are representatives of three independent assays. Unprocessed gels for a , b and f are shown in Source Data 3.
    Qiaquick Gel Extraction Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 113321 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher qubit fluorometer
    Active involvement of the A–I base pair in coordinating pre-tRNA cleavage. a , Pre-tRNA cleavage assay comparing recombinant, inactive TSEN tetramer (TSEN2 H377A and TSEN34 H255A double mutant) to the TSEN/CLP1 complex. Cleavage products are visualized by denaturing Urea-PAGE with subsequent Toluidine blue staining. RNA size markers are indicated on the left of the gel. b , Pull-down assay with fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN captured on <t>protein</t> G agarose functionalized with an α-His-antibody. Protein size markers are indicated on the left of each immunoblot, protein and RNA identities on the right. Input and co-precipitated, labeled pre-tRNAs were visualized by in-gel fluorescence, TSEN subunits and the immunoglobulin G (IgG) heavy chain by immunoblotting. The IgG heavy chain served as loading control. c, Thermodynamic binding parameters of fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. d , Thermodynamic binding parameters of fluorescently labeled tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. e , Schematic depiction of a pre-tRNA molecule showing ribonucleotides belonging to the mature domain (grey spheres), the intronic region (white spheres), the anticodon (black spheres), and the A-I base pair (yellow spheres). Proposed 5’ and 3’ splice sites (ss) are indicated. f , Impact of A-I base pair mutations in S.c. pre-tRNA Phe GAA on endonucleolytic activity of tetrameric TSEN revealed by a pre-tRNA cleavage assay. C 32 :G 54 – canonical A-I base pair, C 32 :C 54 – disrupted A-I base pair, G 32 :C 54 – inverted A-I base pair. All experiments are representatives of three independent assays. Unprocessed gels for a , b and f are shown in Source Data 3.
    Qubit Fluorometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 26970 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    GE Healthcare nylon membrane
    Active involvement of the A–I base pair in coordinating pre-tRNA cleavage. a , Pre-tRNA cleavage assay comparing recombinant, inactive TSEN tetramer (TSEN2 H377A and TSEN34 H255A double mutant) to the TSEN/CLP1 complex. Cleavage products are visualized by denaturing Urea-PAGE with subsequent Toluidine blue staining. RNA size markers are indicated on the left of the gel. b , Pull-down assay with fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN captured on <t>protein</t> G agarose functionalized with an α-His-antibody. Protein size markers are indicated on the left of each immunoblot, protein and RNA identities on the right. Input and co-precipitated, labeled pre-tRNAs were visualized by in-gel fluorescence, TSEN subunits and the immunoglobulin G (IgG) heavy chain by immunoblotting. The IgG heavy chain served as loading control. c, Thermodynamic binding parameters of fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. d , Thermodynamic binding parameters of fluorescently labeled tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. e , Schematic depiction of a pre-tRNA molecule showing ribonucleotides belonging to the mature domain (grey spheres), the intronic region (white spheres), the anticodon (black spheres), and the A-I base pair (yellow spheres). Proposed 5’ and 3’ splice sites (ss) are indicated. f , Impact of A-I base pair mutations in S.c. pre-tRNA Phe GAA on endonucleolytic activity of tetrameric TSEN revealed by a pre-tRNA cleavage assay. C 32 :G 54 – canonical A-I base pair, C 32 :C 54 – disrupted A-I base pair, G 32 :C 54 – inverted A-I base pair. All experiments are representatives of three independent assays. Unprocessed gels for a , b and f are shown in Source Data 3.
    Nylon Membrane, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 99/100, based on 17892 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher dynabeads oligo
    Active involvement of the A–I base pair in coordinating pre-tRNA cleavage. a , Pre-tRNA cleavage assay comparing recombinant, inactive TSEN tetramer (TSEN2 H377A and TSEN34 H255A double mutant) to the TSEN/CLP1 complex. Cleavage products are visualized by denaturing Urea-PAGE with subsequent Toluidine blue staining. RNA size markers are indicated on the left of the gel. b , Pull-down assay with fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN captured on <t>protein</t> G agarose functionalized with an α-His-antibody. Protein size markers are indicated on the left of each immunoblot, protein and RNA identities on the right. Input and co-precipitated, labeled pre-tRNAs were visualized by in-gel fluorescence, TSEN subunits and the immunoglobulin G (IgG) heavy chain by immunoblotting. The IgG heavy chain served as loading control. c, Thermodynamic binding parameters of fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. d , Thermodynamic binding parameters of fluorescently labeled tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. e , Schematic depiction of a pre-tRNA molecule showing ribonucleotides belonging to the mature domain (grey spheres), the intronic region (white spheres), the anticodon (black spheres), and the A-I base pair (yellow spheres). Proposed 5’ and 3’ splice sites (ss) are indicated. f , Impact of A-I base pair mutations in S.c. pre-tRNA Phe GAA on endonucleolytic activity of tetrameric TSEN revealed by a pre-tRNA cleavage assay. C 32 :G 54 – canonical A-I base pair, C 32 :C 54 – disrupted A-I base pair, G 32 :C 54 – inverted A-I base pair. All experiments are representatives of three independent assays. Unprocessed gels for a , b and f are shown in Source Data 3.
    Dynabeads Oligo, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2196 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher superscript iii first strand synthesis system
    Rad52-mediated S-region DSB repair favours intra-S region DNA recombination. ( a ) Each S region consists of highly repetitive motifs, which can facilitate the formation of microhomologies, in particular within the S region core. As the characteristically repetitive sequences are virtually unique to S regions, DSB ends in the same S region are better suited substrates for Rad52-mediated complementary DNA single-strand annealing than those in two different S regions, such as Sμ and Sγ1. Repetitive sequence elements in human and mouse Sμ and Sγ1 that can potentially form microhomologies were identified by Pustell Matrix dot plot using MacVector software and are depicted by small dots. Thick lines indicate the core regions of Sμ and Sγ1. ( b ) Schematic representation of the detection of intra-S region recombination (deletion) in Sμ region by PCR amplification. DNA-amplified sequences of Sμ region that underwent intra-S region DNA recombination are shorter than those of Sμ in the germline configuration. ( c ) Rad52 +/+ and Rad52 −/− B cells were stimulated with LPS plus IL-4 for 96 h. Sμ region DNA was amplified by nested PCR. PCR amplification products were then cloned into the TOPO cloning vector. Sμ region sequences from individual clones amplified by PCR and resolved through a 0.8% agarose gel. PCR amplification products smaller than that amplified from the germline Sμ region DNAs (indicated by arrows) are from Sμ region DNAs that underwent intra-S region recombination, thereby deleting variable lengths of DNA: 14 of 30 Sμ region DNAs in Rad52 +/+ B cells and 4 out of 30 Sμ region DNAs in Rad52 −/− B cells underwent intra-S region recombination. Data are from <t>three</t> pairs of Rad52 +/+ and Rad52 −/− C57BL/6 mice.
    Superscript Iii First Strand Synthesis System, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 53495 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher t4 polynucleotide kinase
    Rad52-mediated S-region DSB repair favours intra-S region DNA recombination. ( a ) Each S region consists of highly repetitive motifs, which can facilitate the formation of microhomologies, in particular within the S region core. As the characteristically repetitive sequences are virtually unique to S regions, DSB ends in the same S region are better suited substrates for Rad52-mediated complementary DNA single-strand annealing than those in two different S regions, such as Sμ and Sγ1. Repetitive sequence elements in human and mouse Sμ and Sγ1 that can potentially form microhomologies were identified by Pustell Matrix dot plot using MacVector software and are depicted by small dots. Thick lines indicate the core regions of Sμ and Sγ1. ( b ) Schematic representation of the detection of intra-S region recombination (deletion) in Sμ region by PCR amplification. DNA-amplified sequences of Sμ region that underwent intra-S region DNA recombination are shorter than those of Sμ in the germline configuration. ( c ) Rad52 +/+ and Rad52 −/− B cells were stimulated with LPS plus IL-4 for 96 h. Sμ region DNA was amplified by nested PCR. PCR amplification products were then cloned into the TOPO cloning vector. Sμ region sequences from individual clones amplified by PCR and resolved through a 0.8% agarose gel. PCR amplification products smaller than that amplified from the germline Sμ region DNAs (indicated by arrows) are from Sμ region DNAs that underwent intra-S region recombination, thereby deleting variable lengths of DNA: 14 of 30 Sμ region DNAs in Rad52 +/+ B cells and 4 out of 30 Sμ region DNAs in Rad52 −/− B cells underwent intra-S region recombination. Data are from <t>three</t> pairs of Rad52 +/+ and Rad52 −/− C57BL/6 mice.
    T4 Polynucleotide Kinase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 9937 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher human cot 1 dna
    Rad52-mediated S-region DSB repair favours intra-S region DNA recombination. ( a ) Each S region consists of highly repetitive motifs, which can facilitate the formation of microhomologies, in particular within the S region core. As the characteristically repetitive sequences are virtually unique to S regions, DSB ends in the same S region are better suited substrates for Rad52-mediated complementary DNA single-strand annealing than those in two different S regions, such as Sμ and Sγ1. Repetitive sequence elements in human and mouse Sμ and Sγ1 that can potentially form microhomologies were identified by Pustell Matrix dot plot using MacVector software and are depicted by small dots. Thick lines indicate the core regions of Sμ and Sγ1. ( b ) Schematic representation of the detection of intra-S region recombination (deletion) in Sμ region by PCR amplification. DNA-amplified sequences of Sμ region that underwent intra-S region DNA recombination are shorter than those of Sμ in the germline configuration. ( c ) Rad52 +/+ and Rad52 −/− B cells were stimulated with LPS plus IL-4 for 96 h. Sμ region DNA was amplified by nested PCR. PCR amplification products were then cloned into the TOPO cloning vector. Sμ region sequences from individual clones amplified by PCR and resolved through a 0.8% agarose gel. PCR amplification products smaller than that amplified from the germline Sμ region DNAs (indicated by arrows) are from Sμ region DNAs that underwent intra-S region recombination, thereby deleting variable lengths of DNA: 14 of 30 Sμ region DNAs in Rad52 +/+ B cells and 4 out of 30 Sμ region DNAs in Rad52 −/− B cells underwent intra-S region recombination. Data are from <t>three</t> pairs of Rad52 +/+ and Rad52 −/− C57BL/6 mice.
    Human Cot 1 Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2644 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen mirneasy mini kit
    Rad52-mediated S-region DSB repair favours intra-S region DNA recombination. ( a ) Each S region consists of highly repetitive motifs, which can facilitate the formation of microhomologies, in particular within the S region core. As the characteristically repetitive sequences are virtually unique to S regions, DSB ends in the same S region are better suited substrates for Rad52-mediated complementary DNA single-strand annealing than those in two different S regions, such as Sμ and Sγ1. Repetitive sequence elements in human and mouse Sμ and Sγ1 that can potentially form microhomologies were identified by Pustell Matrix dot plot using MacVector software and are depicted by small dots. Thick lines indicate the core regions of Sμ and Sγ1. ( b ) Schematic representation of the detection of intra-S region recombination (deletion) in Sμ region by PCR amplification. DNA-amplified sequences of Sμ region that underwent intra-S region DNA recombination are shorter than those of Sμ in the germline configuration. ( c ) Rad52 +/+ and Rad52 −/− B cells were stimulated with LPS plus IL-4 for 96 h. Sμ region DNA was amplified by nested PCR. PCR amplification products were then cloned into the TOPO cloning vector. Sμ region sequences from individual clones amplified by PCR and resolved through a 0.8% agarose gel. PCR amplification products smaller than that amplified from the germline Sμ region DNAs (indicated by arrows) are from Sμ region DNAs that underwent intra-S region recombination, thereby deleting variable lengths of DNA: 14 of 30 Sμ region DNAs in Rad52 +/+ B cells and 4 out of 30 Sμ region DNAs in Rad52 −/− B cells underwent intra-S region recombination. Data are from <t>three</t> pairs of Rad52 +/+ and Rad52 −/− C57BL/6 mice.
    Mirneasy Mini Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 33903 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen oligotex mrna kit
    Rad52-mediated S-region DSB repair favours intra-S region DNA recombination. ( a ) Each S region consists of highly repetitive motifs, which can facilitate the formation of microhomologies, in particular within the S region core. As the characteristically repetitive sequences are virtually unique to S regions, DSB ends in the same S region are better suited substrates for Rad52-mediated complementary DNA single-strand annealing than those in two different S regions, such as Sμ and Sγ1. Repetitive sequence elements in human and mouse Sμ and Sγ1 that can potentially form microhomologies were identified by Pustell Matrix dot plot using MacVector software and are depicted by small dots. Thick lines indicate the core regions of Sμ and Sγ1. ( b ) Schematic representation of the detection of intra-S region recombination (deletion) in Sμ region by PCR amplification. DNA-amplified sequences of Sμ region that underwent intra-S region DNA recombination are shorter than those of Sμ in the germline configuration. ( c ) Rad52 +/+ and Rad52 −/− B cells were stimulated with LPS plus IL-4 for 96 h. Sμ region DNA was amplified by nested PCR. PCR amplification products were then cloned into the TOPO cloning vector. Sμ region sequences from individual clones amplified by PCR and resolved through a 0.8% agarose gel. PCR amplification products smaller than that amplified from the germline Sμ region DNAs (indicated by arrows) are from Sμ region DNAs that underwent intra-S region recombination, thereby deleting variable lengths of DNA: 14 of 30 Sμ region DNAs in Rad52 +/+ B cells and 4 out of 30 Sμ region DNAs in Rad52 −/− B cells underwent intra-S region recombination. Data are from <t>three</t> pairs of Rad52 +/+ and Rad52 −/− C57BL/6 mice.
    Oligotex Mrna Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 1725 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Rad52-mediated S-region DSB repair favours intra-S region DNA recombination. ( a ) Each S region consists of highly repetitive motifs, which can facilitate the formation of microhomologies, in particular within the S region core. As the characteristically repetitive sequences are virtually unique to S regions, DSB ends in the same S region are better suited substrates for Rad52-mediated complementary DNA single-strand annealing than those in two different S regions, such as Sμ and Sγ1. Repetitive sequence elements in human and mouse Sμ and Sγ1 that can potentially form microhomologies were identified by Pustell Matrix dot plot using MacVector software and are depicted by small dots. Thick lines indicate the core regions of Sμ and Sγ1. ( b ) Schematic representation of the detection of intra-S region recombination (deletion) in Sμ region by PCR amplification. DNA-amplified sequences of Sμ region that underwent intra-S region DNA recombination are shorter than those of Sμ in the germline configuration. ( c ) Rad52 +/+ and Rad52 −/− B cells were stimulated with LPS plus IL-4 for 96 h. Sμ region DNA was amplified by nested PCR. PCR amplification products were then cloned into the TOPO cloning vector. Sμ region sequences from individual clones amplified by PCR and resolved through a 0.8% agarose gel. PCR amplification products smaller than that amplified from the germline Sμ region DNAs (indicated by arrows) are from Sμ region DNAs that underwent intra-S region recombination, thereby deleting variable lengths of DNA: 14 of 30 Sμ region DNAs in Rad52 +/+ B cells and 4 out of 30 Sμ region DNAs in Rad52 −/− B cells underwent intra-S region recombination. Data are from <t>three</t> pairs of Rad52 +/+ and Rad52 −/− C57BL/6 mice.
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    Rad52-mediated S-region DSB repair favours intra-S region DNA recombination. ( a ) Each S region consists of highly repetitive motifs, which can facilitate the formation of microhomologies, in particular within the S region core. As the characteristically repetitive sequences are virtually unique to S regions, DSB ends in the same S region are better suited substrates for Rad52-mediated complementary DNA single-strand annealing than those in two different S regions, such as Sμ and Sγ1. Repetitive sequence elements in human and mouse Sμ and Sγ1 that can potentially form microhomologies were identified by Pustell Matrix dot plot using MacVector software and are depicted by small dots. Thick lines indicate the core regions of Sμ and Sγ1. ( b ) Schematic representation of the detection of intra-S region recombination (deletion) in Sμ region by PCR amplification. DNA-amplified sequences of Sμ region that underwent intra-S region DNA recombination are shorter than those of Sμ in the germline configuration. ( c ) Rad52 +/+ and Rad52 −/− B cells were stimulated with LPS plus IL-4 for 96 h. Sμ region DNA was amplified by nested PCR. PCR amplification products were then cloned into the TOPO cloning vector. Sμ region sequences from individual clones amplified by PCR and resolved through a 0.8% agarose gel. PCR amplification products smaller than that amplified from the germline Sμ region DNAs (indicated by arrows) are from Sμ region DNAs that underwent intra-S region recombination, thereby deleting variable lengths of DNA: 14 of 30 Sμ region DNAs in Rad52 +/+ B cells and 4 out of 30 Sμ region DNAs in Rad52 −/− B cells underwent intra-S region recombination. Data are from <t>three</t> pairs of Rad52 +/+ and Rad52 −/− C57BL/6 mice.
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    Rad52-mediated S-region DSB repair favours intra-S region DNA recombination. ( a ) Each S region consists of highly repetitive motifs, which can facilitate the formation of microhomologies, in particular within the S region core. As the characteristically repetitive sequences are virtually unique to S regions, DSB ends in the same S region are better suited substrates for Rad52-mediated complementary DNA single-strand annealing than those in two different S regions, such as Sμ and Sγ1. Repetitive sequence elements in human and mouse Sμ and Sγ1 that can potentially form microhomologies were identified by Pustell Matrix dot plot using MacVector software and are depicted by small dots. Thick lines indicate the core regions of Sμ and Sγ1. ( b ) Schematic representation of the detection of intra-S region recombination (deletion) in Sμ region by PCR amplification. DNA-amplified sequences of Sμ region that underwent intra-S region DNA recombination are shorter than those of Sμ in the germline configuration. ( c ) Rad52 +/+ and Rad52 −/− B cells were stimulated with LPS plus IL-4 for 96 h. Sμ region DNA was amplified by nested PCR. PCR amplification products were then cloned into the TOPO cloning vector. Sμ region sequences from individual clones amplified by PCR and resolved through a 0.8% agarose gel. PCR amplification products smaller than that amplified from the germline Sμ region DNAs (indicated by arrows) are from Sμ region DNAs that underwent intra-S region recombination, thereby deleting variable lengths of DNA: 14 of 30 Sμ region DNAs in Rad52 +/+ B cells and 4 out of 30 Sμ region DNAs in Rad52 −/− B cells underwent intra-S region recombination. Data are from <t>three</t> pairs of Rad52 +/+ and Rad52 −/− C57BL/6 mice.
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    Rad52-mediated S-region DSB repair favours intra-S region DNA recombination. ( a ) Each S region consists of highly repetitive motifs, which can facilitate the formation of microhomologies, in particular within the S region core. As the characteristically repetitive sequences are virtually unique to S regions, DSB ends in the same S region are better suited substrates for Rad52-mediated complementary DNA single-strand annealing than those in two different S regions, such as Sμ and Sγ1. Repetitive sequence elements in human and mouse Sμ and Sγ1 that can potentially form microhomologies were identified by Pustell Matrix dot plot using MacVector software and are depicted by small dots. Thick lines indicate the core regions of Sμ and Sγ1. ( b ) Schematic representation of the detection of intra-S region recombination (deletion) in Sμ region by PCR amplification. DNA-amplified sequences of Sμ region that underwent intra-S region DNA recombination are shorter than those of Sμ in the germline configuration. ( c ) Rad52 +/+ and Rad52 −/− B cells were stimulated with LPS plus IL-4 for 96 h. Sμ region DNA was amplified by nested PCR. PCR amplification products were then cloned into the TOPO cloning vector. Sμ region sequences from individual clones amplified by PCR and resolved through a 0.8% agarose gel. PCR amplification products smaller than that amplified from the germline Sμ region DNAs (indicated by arrows) are from Sμ region DNAs that underwent intra-S region recombination, thereby deleting variable lengths of DNA: 14 of 30 Sμ region DNAs in Rad52 +/+ B cells and 4 out of 30 Sμ region DNAs in Rad52 −/− B cells underwent intra-S region recombination. Data are from <t>three</t> pairs of Rad52 +/+ and Rad52 −/− C57BL/6 mice.
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    Image Search Results


    Detection of tRNAs by microarray analysis. ( A ) Array scheme. Total cellular or viral RNA were deacylated, and directly labeled with a Cy3 or Cy5 containing oligonucleotide using T4 DNA ligase. The labeling samples with the opposite fluorophores were combined

    Journal: RNA

    Article Title: Profiling non-lysyl tRNAs in HIV-1

    doi: 10.1261/rna.1928110

    Figure Lengend Snippet: Detection of tRNAs by microarray analysis. ( A ) Array scheme. Total cellular or viral RNA were deacylated, and directly labeled with a Cy3 or Cy5 containing oligonucleotide using T4 DNA ligase. The labeling samples with the opposite fluorophores were combined

    Article Snippet: The ligation reaction was carried out overnight (∼16 h) at 16°C with 0.13 μg/μL total RNA in 1X T4 DNA ligase buffer, 0.5 U/μL T4 DNA ligase (USB Corporation, 70042X), 15% DMSO, and 4.5 μM labeling oligonucleotide.

    Techniques: Microarray, Labeling

    Ritonavir does not affect BACE1 protein stability in primary neurons. A: Primary rat neurons were pulse labeled for 30 minutes with 35 S-methionine/cysteine-containing Dulbecco's modified Eagle's medium and chased with neurobasal media plus B27. Radiolabeled BACE1 was immunoprecipitated with Dynabeads Protein A and 2 μg anti-BACE1 12 hours after labeling to confirm enrichment. B: Neurons were pulse labeled, as in A , and chased with neurobasal media with or without 10 μmol/L ritonavir for 24 hours. BACE1 was immunoprecipitated, as in A Representative autoradiogram shown. C: The levels of 35 S-methionine/cysteine-labeled BACE1 were quantified and the percentage changes, relative to 0 hour time point, are plotted. No significant differences in BACE1 half-life were observed between control and ritonavir-treated neurons ( P > 0.05, linear regression analysis). All values represent means ± SEM ( C ). n = 3 ( B and C ). M, molecular weight; mAb, monoclonal antibody; ms, mouse; rb, rabbit; WC, whole cell.

    Journal: The American Journal of Pathology

    Article Title: HIV Protease Inhibitors Alter Amyloid Precursor Protein Processing via β-Site Amyloid Precursor Protein Cleaving Enzyme-1 Translational Up-Regulation

    doi: 10.1016/j.ajpath.2016.09.006

    Figure Lengend Snippet: Ritonavir does not affect BACE1 protein stability in primary neurons. A: Primary rat neurons were pulse labeled for 30 minutes with 35 S-methionine/cysteine-containing Dulbecco's modified Eagle's medium and chased with neurobasal media plus B27. Radiolabeled BACE1 was immunoprecipitated with Dynabeads Protein A and 2 μg anti-BACE1 12 hours after labeling to confirm enrichment. B: Neurons were pulse labeled, as in A , and chased with neurobasal media with or without 10 μmol/L ritonavir for 24 hours. BACE1 was immunoprecipitated, as in A Representative autoradiogram shown. C: The levels of 35 S-methionine/cysteine-labeled BACE1 were quantified and the percentage changes, relative to 0 hour time point, are plotted. No significant differences in BACE1 half-life were observed between control and ritonavir-treated neurons ( P > 0.05, linear regression analysis). All values represent means ± SEM ( C ). n = 3 ( B and C ). M, molecular weight; mAb, monoclonal antibody; ms, mouse; rb, rabbit; WC, whole cell.

    Article Snippet: Lysates were immunoprecipitated with Dynabeads Protein A (Thermo Fisher Scientific) and 2 μg anti-BACE1 (Cell Signaling Technology), run on a 4% to 12% Bis-Tris gradient gel for separation, and transferred onto polyvinylidene difluoride membranes for approximately 7 hours.

    Techniques: Labeling, Modification, Immunoprecipitation, Molecular Weight, Mass Spectrometry

    Active involvement of the A–I base pair in coordinating pre-tRNA cleavage. a , Pre-tRNA cleavage assay comparing recombinant, inactive TSEN tetramer (TSEN2 H377A and TSEN34 H255A double mutant) to the TSEN/CLP1 complex. Cleavage products are visualized by denaturing Urea-PAGE with subsequent Toluidine blue staining. RNA size markers are indicated on the left of the gel. b , Pull-down assay with fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN captured on protein G agarose functionalized with an α-His-antibody. Protein size markers are indicated on the left of each immunoblot, protein and RNA identities on the right. Input and co-precipitated, labeled pre-tRNAs were visualized by in-gel fluorescence, TSEN subunits and the immunoglobulin G (IgG) heavy chain by immunoblotting. The IgG heavy chain served as loading control. c, Thermodynamic binding parameters of fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. d , Thermodynamic binding parameters of fluorescently labeled tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. e , Schematic depiction of a pre-tRNA molecule showing ribonucleotides belonging to the mature domain (grey spheres), the intronic region (white spheres), the anticodon (black spheres), and the A-I base pair (yellow spheres). Proposed 5’ and 3’ splice sites (ss) are indicated. f , Impact of A-I base pair mutations in S.c. pre-tRNA Phe GAA on endonucleolytic activity of tetrameric TSEN revealed by a pre-tRNA cleavage assay. C 32 :G 54 – canonical A-I base pair, C 32 :C 54 – disrupted A-I base pair, G 32 :C 54 – inverted A-I base pair. All experiments are representatives of three independent assays. Unprocessed gels for a , b and f are shown in Source Data 3.

    Journal: bioRxiv

    Article Title: Assembly defects of the human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia

    doi: 10.1101/2020.08.03.234229

    Figure Lengend Snippet: Active involvement of the A–I base pair in coordinating pre-tRNA cleavage. a , Pre-tRNA cleavage assay comparing recombinant, inactive TSEN tetramer (TSEN2 H377A and TSEN34 H255A double mutant) to the TSEN/CLP1 complex. Cleavage products are visualized by denaturing Urea-PAGE with subsequent Toluidine blue staining. RNA size markers are indicated on the left of the gel. b , Pull-down assay with fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN captured on protein G agarose functionalized with an α-His-antibody. Protein size markers are indicated on the left of each immunoblot, protein and RNA identities on the right. Input and co-precipitated, labeled pre-tRNAs were visualized by in-gel fluorescence, TSEN subunits and the immunoglobulin G (IgG) heavy chain by immunoblotting. The IgG heavy chain served as loading control. c, Thermodynamic binding parameters of fluorescently labeled S.c. pre-tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. d , Thermodynamic binding parameters of fluorescently labeled tRNA Phe GAA and inactive, tetrameric TSEN revealed by fluorescence anisotropy. e , Schematic depiction of a pre-tRNA molecule showing ribonucleotides belonging to the mature domain (grey spheres), the intronic region (white spheres), the anticodon (black spheres), and the A-I base pair (yellow spheres). Proposed 5’ and 3’ splice sites (ss) are indicated. f , Impact of A-I base pair mutations in S.c. pre-tRNA Phe GAA on endonucleolytic activity of tetrameric TSEN revealed by a pre-tRNA cleavage assay. C 32 :G 54 – canonical A-I base pair, C 32 :C 54 – disrupted A-I base pair, G 32 :C 54 – inverted A-I base pair. All experiments are representatives of three independent assays. Unprocessed gels for a , b and f are shown in Source Data 3.

    Article Snippet: tRNA pull-down assays 25 μl of the monoclonal α-His antibody (Catalog-ID H1029, Sigma-Aldrich) were mixed with 100 μl buffer comprising 50 mM HEPES-NaOH, pH 7.4, 400 mM NaCl (HS buffer) and coupled to 25 μl of Protein G Agarose (Thermo Fischer Scientific) for 30 min at 4 °C under agitation.

    Techniques: Cleavage Assay, Recombinant, Mutagenesis, Polyacrylamide Gel Electrophoresis, Staining, Pull Down Assay, Labeling, Fluorescence, Binding Assay, Activity Assay

    Rad52-mediated S-region DSB repair favours intra-S region DNA recombination. ( a ) Each S region consists of highly repetitive motifs, which can facilitate the formation of microhomologies, in particular within the S region core. As the characteristically repetitive sequences are virtually unique to S regions, DSB ends in the same S region are better suited substrates for Rad52-mediated complementary DNA single-strand annealing than those in two different S regions, such as Sμ and Sγ1. Repetitive sequence elements in human and mouse Sμ and Sγ1 that can potentially form microhomologies were identified by Pustell Matrix dot plot using MacVector software and are depicted by small dots. Thick lines indicate the core regions of Sμ and Sγ1. ( b ) Schematic representation of the detection of intra-S region recombination (deletion) in Sμ region by PCR amplification. DNA-amplified sequences of Sμ region that underwent intra-S region DNA recombination are shorter than those of Sμ in the germline configuration. ( c ) Rad52 +/+ and Rad52 −/− B cells were stimulated with LPS plus IL-4 for 96 h. Sμ region DNA was amplified by nested PCR. PCR amplification products were then cloned into the TOPO cloning vector. Sμ region sequences from individual clones amplified by PCR and resolved through a 0.8% agarose gel. PCR amplification products smaller than that amplified from the germline Sμ region DNAs (indicated by arrows) are from Sμ region DNAs that underwent intra-S region recombination, thereby deleting variable lengths of DNA: 14 of 30 Sμ region DNAs in Rad52 +/+ B cells and 4 out of 30 Sμ region DNAs in Rad52 −/− B cells underwent intra-S region recombination. Data are from three pairs of Rad52 +/+ and Rad52 −/− C57BL/6 mice.

    Journal: Nature Communications

    Article Title: Rad52 competes with Ku70/Ku86 for binding to S-region DSB ends to modulate antibody class-switch DNA recombination

    doi: 10.1038/ncomms14244

    Figure Lengend Snippet: Rad52-mediated S-region DSB repair favours intra-S region DNA recombination. ( a ) Each S region consists of highly repetitive motifs, which can facilitate the formation of microhomologies, in particular within the S region core. As the characteristically repetitive sequences are virtually unique to S regions, DSB ends in the same S region are better suited substrates for Rad52-mediated complementary DNA single-strand annealing than those in two different S regions, such as Sμ and Sγ1. Repetitive sequence elements in human and mouse Sμ and Sγ1 that can potentially form microhomologies were identified by Pustell Matrix dot plot using MacVector software and are depicted by small dots. Thick lines indicate the core regions of Sμ and Sγ1. ( b ) Schematic representation of the detection of intra-S region recombination (deletion) in Sμ region by PCR amplification. DNA-amplified sequences of Sμ region that underwent intra-S region DNA recombination are shorter than those of Sμ in the germline configuration. ( c ) Rad52 +/+ and Rad52 −/− B cells were stimulated with LPS plus IL-4 for 96 h. Sμ region DNA was amplified by nested PCR. PCR amplification products were then cloned into the TOPO cloning vector. Sμ region sequences from individual clones amplified by PCR and resolved through a 0.8% agarose gel. PCR amplification products smaller than that amplified from the germline Sμ region DNAs (indicated by arrows) are from Sμ region DNAs that underwent intra-S region recombination, thereby deleting variable lengths of DNA: 14 of 30 Sμ region DNAs in Rad52 +/+ B cells and 4 out of 30 Sμ region DNAs in Rad52 −/− B cells underwent intra-S region recombination. Data are from three pairs of Rad52 +/+ and Rad52 −/− C57BL/6 mice.

    Article Snippet: Residual DNA was removed using genomic DNA eliminator columns (Qiagen). cDNA was synthesized from 1 to 2 μg total RNA with the SuperScript III First-Strand Synthesis System (Invitrogen) using oligo-dT primer.

    Techniques: Sequencing, Software, Polymerase Chain Reaction, Amplification, Nested PCR, Clone Assay, Plasmid Preparation, Agarose Gel Electrophoresis, Mouse Assay