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2 Deoxy Atp, supplied by Valiant Co Ltd, used in various techniques. Bioz Stars score: 96/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "Ubiquitylation of nucleic acids by DELTEX ubiquitin E3 ligase DTX3L"

Article Title: Ubiquitylation of nucleic acids by DELTEX ubiquitin E3 ligase DTX3L

Journal: EMBO Reports

doi: 10.1038/s44319-024-00235-1

Reagents and tools table
Figure Legend Snippet: Reagents and tools table

Techniques Used: Protease Inhibitor, TNKS1 Histone Ribosylation Assay, Recombinant, Sequencing

Related Articles

Labeling:

Article Title: High-fat diet, microbiome-gut-brain axis signaling, and anxiety-like behavior in male rats
Article Snippet: To detect slc6a4 mRNA, a synthetic 50-base antisense oligonucleotide (5′-ACT GCA GAG TAC CCA TTG GAT ATT TGG CTA GGC TCT GCC CTG TCC GCT GT-3′, Integrated DNA Technologies) based on the published sequence of the rat serotonin transporter cDNA clone [ ] of slc6a4 mRNA ( Rattus norvegicus solute carrier family 6 (neurotransmitter transporter, serotonin), member 4, mRNA; GenBank® Accession no., NM_013034.3) was used as previously described [ , ]. .. The oligonucleotides were labeled at the 3’end with [ 35 S]-deoxyadenosine-5′-triphosphate (Cat. No. 5,620,001, MP Biomedicals, Santa Ana, CA, USA) using terminal deoxynucleotidyl transferase (20 U/μL, Cat. No. EP0161, Fermentas, Glen Burnie, MD, USA) for 1 h at 37 °C, cleaned using a QIAquick® nucleotide removal kit (Cat. No. 28,304, Qiagen, Valencia, CA, USA), and used in an in situ hybridization histochemistry assay as described previously [ , ]. ..

Article Title: Effects of chronic caffeine exposure during adolescence and subsequent acute caffeine challenge during adulthood on rat brain serotonergic systems
Article Snippet: To detect slc6a4 mRNA, a synthetic 50-base antisense oligonucleotide (5′-ACT GCA GAG TAC CCA TTG GAT ATT TGG CTA GGC TCT GCC CTG TCC GCT GT-3′, Integrated DNA Technologies), complementary to bases 207–256 of rat slc6a4 mRNA (previously reported as bases 77–126; ( Fujita et al. 1993 ; Hansen and Mikkelsen 1998 ) based on the published sequence of the rat serotonin transporter cDNA clone ( Blakely et al. 1991 ) of slc6a4 mRNA (Rattus norvegicus solute carrier family 6 (neurotransmitter transporter, serotonin), member 4, mRNA; GenBank® Accession no., {"type":"entrez-nucleotide","attrs":{"text":"NM_013034.3","term_id":"158631205","term_text":"NM_013034.3"}} NM_013034.3 ) was used as previously described ( Donner et al. 2018 ; Gardner et al. 2009 ). .. The oligonucleotides were labeled at the 3’ end with [ 35 S]-deoxyadenosine-5′-triphosphate (Cat. No. 5620001, MP Biomedicals, Santa Ana, CA, USA) using terminal deoxynucleotidyl transferase (20 U/μL, Cat. No. EP0161, Fermentas, Glen Burnie, MD, USA) for 1 h at 37 °C, cleaned using a QIAquick® nucleotide removal kit (Cat. No. 28304, Qiagen, Valencia, CA, USA), and used in an in situ hybridization histochemistry assay as described previously ( Donner et al. 2018 ; Gardner et al. 2009 ). .. Air-dried slides were apposed to a BioMax® MR autoradiography film (Cat. No. 871 5187, Carestream Health, Rochester, NY, USA) 17 ( htr1a ) or 11 ( slc6a4 ) days, respectively.

Article Title: High-fat diet, microbiome-gut-brain axis signaling, and anxiety-like behavior in male rats.
Article Snippet: To detect slc6a4 mRNA, a synthetic 50-base antisense oligonucleotide (5′-ACT GCA GAG TAC CCA TTG GAT ATT TGG CTA GGC TCT GCC CTG TCC GCT GT-3′, Integrated DNA Technologies) based on the published sequence of the rat serotonin transporter cDNA clone [38] of slc6a4 mRNA (Rattus norvegicus solute carrier family 6 (neurotransmitter transporter, serotonin), member 4, mRNA; GenBank® Accession no., NM_013034.3) was used as previously described [13, 15]. .. The oligonucleotides were labeled at the 3’end with [35S]-deoxyadenosine-5′-triphosphate (Cat. No. 5,620,001, MP Biomedicals, Santa Ana, CA, USA) using terminal deoxynucleotidyl transferase (20 U/μL, Cat. No. EP0161, Fermentas, Glen Burnie, MD, USA) for 1 h at 37 °C, cleaned using a QIAquick® nucleotide removal kit (Cat. No. 28,304, Qiagen, Valencia, CA, USA), and used in an in situ hybridization histochemistry assay as described previously [15, 37]. ..

In Situ Hybridization:

Article Title: High-fat diet, microbiome-gut-brain axis signaling, and anxiety-like behavior in male rats
Article Snippet: To detect slc6a4 mRNA, a synthetic 50-base antisense oligonucleotide (5′-ACT GCA GAG TAC CCA TTG GAT ATT TGG CTA GGC TCT GCC CTG TCC GCT GT-3′, Integrated DNA Technologies) based on the published sequence of the rat serotonin transporter cDNA clone [ ] of slc6a4 mRNA ( Rattus norvegicus solute carrier family 6 (neurotransmitter transporter, serotonin), member 4, mRNA; GenBank® Accession no., NM_013034.3) was used as previously described [ , ]. .. The oligonucleotides were labeled at the 3’end with [ 35 S]-deoxyadenosine-5′-triphosphate (Cat. No. 5,620,001, MP Biomedicals, Santa Ana, CA, USA) using terminal deoxynucleotidyl transferase (20 U/μL, Cat. No. EP0161, Fermentas, Glen Burnie, MD, USA) for 1 h at 37 °C, cleaned using a QIAquick® nucleotide removal kit (Cat. No. 28,304, Qiagen, Valencia, CA, USA), and used in an in situ hybridization histochemistry assay as described previously [ , ]. ..

Article Title: Effects of chronic caffeine exposure during adolescence and subsequent acute caffeine challenge during adulthood on rat brain serotonergic systems
Article Snippet: To detect slc6a4 mRNA, a synthetic 50-base antisense oligonucleotide (5′-ACT GCA GAG TAC CCA TTG GAT ATT TGG CTA GGC TCT GCC CTG TCC GCT GT-3′, Integrated DNA Technologies), complementary to bases 207–256 of rat slc6a4 mRNA (previously reported as bases 77–126; ( Fujita et al. 1993 ; Hansen and Mikkelsen 1998 ) based on the published sequence of the rat serotonin transporter cDNA clone ( Blakely et al. 1991 ) of slc6a4 mRNA (Rattus norvegicus solute carrier family 6 (neurotransmitter transporter, serotonin), member 4, mRNA; GenBank® Accession no., {"type":"entrez-nucleotide","attrs":{"text":"NM_013034.3","term_id":"158631205","term_text":"NM_013034.3"}} NM_013034.3 ) was used as previously described ( Donner et al. 2018 ; Gardner et al. 2009 ). .. The oligonucleotides were labeled at the 3’ end with [ 35 S]-deoxyadenosine-5′-triphosphate (Cat. No. 5620001, MP Biomedicals, Santa Ana, CA, USA) using terminal deoxynucleotidyl transferase (20 U/μL, Cat. No. EP0161, Fermentas, Glen Burnie, MD, USA) for 1 h at 37 °C, cleaned using a QIAquick® nucleotide removal kit (Cat. No. 28304, Qiagen, Valencia, CA, USA), and used in an in situ hybridization histochemistry assay as described previously ( Donner et al. 2018 ; Gardner et al. 2009 ). .. Air-dried slides were apposed to a BioMax® MR autoradiography film (Cat. No. 871 5187, Carestream Health, Rochester, NY, USA) 17 ( htr1a ) or 11 ( slc6a4 ) days, respectively.

Article Title: High-fat diet, microbiome-gut-brain axis signaling, and anxiety-like behavior in male rats.
Article Snippet: To detect slc6a4 mRNA, a synthetic 50-base antisense oligonucleotide (5′-ACT GCA GAG TAC CCA TTG GAT ATT TGG CTA GGC TCT GCC CTG TCC GCT GT-3′, Integrated DNA Technologies) based on the published sequence of the rat serotonin transporter cDNA clone [38] of slc6a4 mRNA (Rattus norvegicus solute carrier family 6 (neurotransmitter transporter, serotonin), member 4, mRNA; GenBank® Accession no., NM_013034.3) was used as previously described [13, 15]. .. The oligonucleotides were labeled at the 3’end with [35S]-deoxyadenosine-5′-triphosphate (Cat. No. 5,620,001, MP Biomedicals, Santa Ana, CA, USA) using terminal deoxynucleotidyl transferase (20 U/μL, Cat. No. EP0161, Fermentas, Glen Burnie, MD, USA) for 1 h at 37 °C, cleaned using a QIAquick® nucleotide removal kit (Cat. No. 28,304, Qiagen, Valencia, CA, USA), and used in an in situ hybridization histochemistry assay as described previously [15, 37]. ..

Incubation:

Article Title: Ubiquitylation of nucleic acids by DELTEX ubiquitin E3 ligase DTX3L
Article Snippet: The multiply charged envelope was deconvoluted using the charge deconvolution tool in Agilent OpenLab CDS ChemStation software to obtain the average [M] value. .. 12 mM of ADP-ribose (Sigma A0752) or AMP (Santa Cruz Biotechnology sc-214504A) or TMP (Sigma T7004) or GMP (Abcam ab146534) or CMP (Sigma C1006) or 2′-deoxy-ATP (MP Biomedicals 0210054925) or 3′-deoxy-ATP (Santa Cruz Biotechnology sc-396713) were incubated with 5 μM DTX3L-RD, 0.5 μM UBE1, 2.5 μM UBCH5A, and 20 μM Ub in 50 mM HEPES (pH 7.5), 50 mM NaCl, 5 mM MgCl 2 , 0.5 mM DTT, and 2 mM ATP. ..

Article Title: Ubiquitylation of nucleic acids by DELTEX ubiquitin E3 ligase DTX3L.
Article Snippet: The multiply charged envelope was deconvoluted using the charge deconvolution tool in Agilent OpenLab CDS ChemStation software to obtain the average [M] value. .. HPLC-MS monitoring of the enzymatic reactions 12 mM of ADP-ribose (Sigma A0752) or AMP (Santa Cruz Biotechnology sc-214504A) or TMP (Sigma T7004) or GMP (Abcam ab146534) or CMP (Sigma C1006) or 2′-deoxy-ATP (MP Biomedicals 0210054925) or 3′-deoxy-ATP (Santa Cruz Biotechnology sc-396713) were incubated with 5 μM DTX3L-RD, 0.5 μM UBE1, 2.5 μM UBCH5A, and 20 μM Ub in 50 mM HEPES (pH 7.5), 50 mM NaCl, 5 mM MgCl2, 0.5 mM DTT, and 2 mM ATP. ..

High Performance Liquid Chromatography:

Article Title: Ubiquitylation of nucleic acids by DELTEX ubiquitin E3 ligase DTX3L.
Article Snippet: The multiply charged envelope was deconvoluted using the charge deconvolution tool in Agilent OpenLab CDS ChemStation software to obtain the average [M] value. .. HPLC-MS monitoring of the enzymatic reactions 12 mM of ADP-ribose (Sigma A0752) or AMP (Santa Cruz Biotechnology sc-214504A) or TMP (Sigma T7004) or GMP (Abcam ab146534) or CMP (Sigma C1006) or 2′-deoxy-ATP (MP Biomedicals 0210054925) or 3′-deoxy-ATP (Santa Cruz Biotechnology sc-396713) were incubated with 5 μM DTX3L-RD, 0.5 μM UBE1, 2.5 μM UBCH5A, and 20 μM Ub in 50 mM HEPES (pH 7.5), 50 mM NaCl, 5 mM MgCl2, 0.5 mM DTT, and 2 mM ATP. ..



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Reagents and tools table

Journal: EMBO Reports

Article Title: Ubiquitylation of nucleic acids by DELTEX ubiquitin E3 ligase DTX3L

doi: 10.1038/s44319-024-00235-1

Figure Lengend Snippet: Reagents and tools table

Article Snippet: 2′-deoxy ATP , MP Biomedicals , 0210054925.

Techniques: Protease Inhibitor, TNKS1 Histone Ribosylation Assay, Recombinant, Sequencing