Cordycepin 5 triphosphate 3 α 32p

Manufactured by PerkinElmer

Sourced in United States

Cordycepin 5′-triphosphate 3′-[α-32P] is a labeled nucleotide analog used in various biochemical and molecular biology applications. It serves as a radioactive tracer for studying nucleic acid synthesis, modification, and interactions.

Automatically generated - may contain errors

Lab products found in correlation

Micro bio spin 6 chromatography column, by Bio-Rad (7 mentions) Terminal deoxynucleotidyl transferase, by Thermo Fisher Scientific (6 mentions) Radionucleotides γ 32p atp, by PerkinElmer (5 mentions) T4 polynucleotide kinase, by Thermo Fisher Scientific (4 mentions) Deoxynucleoside 5 triphosphates dntps, by Thermo Fisher Scientific (3 mentions) γ 32p atp, by PerkinElmer (3 mentions) Deoxynucleotide 5 triphosphates dntps, by Thermo Fisher Scientific (2 mentions) Dna oligonucleotides, by Eurofins (1 mentions) T4 polynucleotide kinase pnk, by Thermo Fisher Scientific (1 mentions) Oligonucleotide, by Integrated DNA Technologies (1 mentions) Micro bio spin 6 column, by Bio-Rad (1 mentions) Quikchange 2 xl site directed mutagenesis kit, by Agilent Technologies (1 mentions) Uracil dna glycosylase, by New England Biolabs (1 mentions) Trypsin edta, by Thermo Fisher Scientific (1 mentions) Escherichia coli uracil dna glycosylase, by New England Biolabs (1 mentions) Dna oligonucleotide, by Integrated DNA Technologies (1 mentions) S1 nuclease, by Promega (1 mentions)

Close spelling variants of this product

[α-32P]-3′-deoxyadenosine 5′-triphosphate (cordycepin 5′-triphosphate) [α-32P]cordycepin 5′-triphosphate

8 protocols using cordycepin 5 triphosphate 3 α 32p

Synthesis and Characterization of 8-oxoG Oligonucleotides

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DNA oligonucleotides containing an 8-oxoG were synthesized by Eurofins MWG Operon (Huntsville, AL, USA). All other oligonucleotides were from Integrated DNA Technologies (IDT, Coralville, IA, USA). Deoxynucleoside 5′-triphosphates (dNTPs) and terminal deoxynucleotidyl transferase were from Fermentas (Glen Burnie, MD, USA). T4 polynucleotide kinase was from USB Corp. (Cleveland, OH, USA). All standard chemical reagents were from Sigma-Aldrich (St. Louis, MO, USA) and Thermo Fisher Scientific (Pittsburgh, PA, USA). The radionucleotides [γ-³²P] ATP (6000 mCi/mmol) and Cordycepin 5′-triphosphate 3′-[α-³²P] (5000 mCi/mmol) were purchased from PerkinElmer Inc. (Boston, MA, USA). Micro Bio-Spin 6 chromatography columns were from Bio-Rad (Hercules, CA, USA). The Mus81/Eme1 expression vector pET21d-Mus81/HIS-Eme1 was a generous gift from Dr Stephen West at Clare Hall Laboratories, London Research Institute, Cancer Research UK, Hertfordshire, UK. Purified OGG1, AP endonuclease 1 (APE1), pol β and DNA ligase I (LIG I) were generous gifts from Dr Samuel Wilson at the National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, or were expressed and purified according to the procedures described previously (30 (link)).

Xu M., Lai Y., Torner J., Zhang Y., Zhang Z, & Liu Y. (2014). Base excision repair of oxidative DNA damage coupled with removal of a CAG repeat hairpin attenuates trinucleotide repeat expansion. Nucleic Acids Research, 42(6), 3675-3691.

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DNA Oligonucleotide Synthesis and Protein Purification

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The DNA oligonucleotides were synthesized by Integrated DNA Technologies (IDT, Coralville, IA, USA). Deoxynucleotide 5′-triphosphates (dNTPs) were from Fermentas (Glen Burnie, MD, USA). T4 polynucleotide kinase and terminal deoxynucleotidyltransferase were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Radionucleotides [γ-³²P] ATP (6000 mCi/mmol) and Cordycepin 5′-triphosphate 3′-[α-³²P] (5000 mCi/mmol) were purchased from PerkinElmer Inc. (Boston, MA, USA). Micro Bio-Spin 6 chromatography columns were purchased from Bio-Rad Laboratories (Hercules, CA, USA). All standard chemical reagents were purchased from Sigma-Aldrich (St. Louis, MO, USA) and Thermo Fisher Scientific (Waltham, MA, USA). PCNA was purchased from Enzymax (Lexington, KY, USA). Pol β was a generous gift from Dr. Samuel H. Wilson at the National Institute of Environmental Health Sciences/National Institutes of Health. APE1, FEN1, and LIG I were expressed in Escherichia coli and purified as described below.

Beaver J.M., Lai Y., Rolle S.J, & Liu Y. (2016). Proliferating cell nuclear antigen prevents trinucleotide repeat expansions by promoting repeat deletion and hairpin removal. DNA repair, 48, 17-29.

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Enzymatic Processing of DNA Substrates

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Oligonucleotides were synthesized by Integrated DNA Technologies Inc. (Coralville, IA). The radionucleotides [γ-³²P] ATP (6000Ci/mmol) and cordycepin 5′-triphosphate 3′-[α-³²P] (5000Ci/mmol) were purchased from PerkinElmer Inc. (Boston, MA). Micro Bio-Spin 6 chromatography columns were from Bio-Rad (Hercules, CA). T4 polynucleotide kinase (PNK) and terminal deoxynucleotidyl transferase (TdT) were from Fermentas (Glen Burnie, MD). Adenosine 5′-triphosphate (ATP) (100 mM) was from USB (Cleveland, Ohio). Purified thymine DNA glycosylase (TDG) was from Enzymax, LLC (Lexington, Kentucky). Purified APE1, pol β, flap endonuclease 1 (FEN1) and DNA ligase I (LIG I) were generous gifts from Dr. Samuel H. Wilson at the Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science/National Institutes of Health (NIEHS), Research Triangle Park, NC. All other reagents were from Thermo Fisher Scientific (Pittsburgh, PA) and Sigma-Aldrich (St. Louis, MO).

Lai Y., Jiang Z., Zhou J., Osemota E, & Liu Y. (2016). AP endonuclease 1 prevents the extension of a T/G mismatch by DNA polymerase β to prevent mutations in CpGs during base excision repair. DNA repair, 43, 89-97.

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Synthesis and Purification of Modified DNA Oligonucleotides

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DNA oligonucleotides containing a 5′R-cdA or 5′S-cdA were synthesized and purified by HPLC as described previously (45 ). The structures of 5′R-cdA and 5′S-cdA were illustrated in Figure 1. All other oligonucleotides were synthesized by Integrated DNA Technologies (IDT, Coralville, IA, USA). Deoxynucleoside 5′-triphosphates (dNTPs) were purchased from Fermentas (Glen Burnie, MD, USA). Radionucleotides, [γ-³²P] ATP (6000 mCi/mmol) and cordycepin 5′-triphosphate 3′-[α-³²P] (5000 mCi/mmol) were purchased from Perkin Elmer Inc. (Boston, MA, USA). Micro Bio-Spin 6 chromatography columns were from Bio-Rad (Hercules, CA, USA). All other standard chemical reagents were from Sigma-Aldrich (St. Louis, MO, USA) and Thermo Fisher Scientific (Pittsburgh, PA, USA). Purified pol β, flap endonuclease 1 (FEN1) and DNA ligase I (LIG I) were generous gifts from Dr. Samuel H. Wilson at the National Institute of Environmental Health Sciences (NIEHS)/National Institutes of Health, Research Triangle Park, North Carolina.

Jiang Z., Xu M., Lai Y., Laverde E.E., Terzidis M.A., Masi A., Chatgilialoglu C, & Liu Y. (2015). Bypass of a 5′,8-cyclopurine-2′-deoxynucleoside by DNA polymerase β during DNA replication and base excision repair leads to nucleotide misinsertions and DNA strand breaks. DNA repair, 33, 24-34.

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Synthesis and Radiolabeling of DNA Oligonucleotides

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DNA oligonucleotide substrates were synthesized by Integrated DNA Technologies (Coralville, IA, USA). The radionucleotides [γ-³²P] ATP (6000 mCi/mmol) and Cordycepin 5’-triphosphate 3’-[α-³²P] (5000 mCi/mmol) were purchased from PerkinElmer Inc. (Boston, MA). T4 polynucleotide kinase, terminal deoxynucleotidyl transferase and deoxynucleoside 5’-triphosphates (dNTPs) were purchased from Thermo Fisher Scientific (Waltham, MA). Micro Bio-Spin 6 Columns were purchased from Bio-Rad Laboratories (Hercules, CA). Pierce Avidin Agarose resin was from Thermo Fisher Scientific (Waltham, MA). QuikChange II XL Site-Directed Mutagenesis kit was purchased from Agilent Technologies (Santa Clara, CA). All other standard chemical reagents were from Thermo Fisher Scientific (Waltham, MA) and Sigma-Aldrich (St. Louis, MO). Purified enzymes including APE1, pol β, FEN1 and LIG I were made according to the procedures described previously [71 (link), 72 (link)].

Ren Y., Lai Y., Laverde E.E., Lei R., Rein H.L, & Liu Y. (2017). Modulation of trinucleotide repeat instability by DNA polymerase β polymorphic variant R137Q. PLoS ONE, 12(5), e0177299.

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Synthesis and Purification of Oligonucleotides

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Oligonucleotides containing the DOB lesion were synthesized as previously described [31 (link)]. All other DNA oligonucleotides were synthesized by Integrated DNA Technologies (IDT, Coralville, IA, USA). T4 polynucleotide kinase and terminal deoxynucleotidyltransferase were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Radionucleotides [γ-³²P] ATP (6000 mCi/mmol) and Cordycepin 5’-triphosphate 3’-[α-³²P] (5000 mCi/mmol) were purchased from Perkin Elmer Inc. (Boston, MA, USA). Deoxynucleotide 5’-triphosphates (dNTPs) were from Fermentas (Glen Burnie, MD, USA). Micro Bio-Spin 6 chromatography columns were purchased from Bio-Rad Laboratories (Hercules, CA, USA). All other chemical reagents were purchased from Thermo Fisher Scientific (Waltham, MA, USA) and Sigma-Aldrich (St. Louis, MO, USA). Uracil-DNA glycosylase (UDG) was from New England Biolabs (Ipswich, MA). Recombinant human pol β was expressed in Escherichia coli and purified as described previously [13 (link)]. Pol β K72A mutant protein was a generous gift from Dr. Samuel H. Wilson at the National Institute of Environmental Health Sciences/National Institutes of Health.

Beaver J.M., Lai Y., Rolle S.J., Weng L., Greenberg M.M, & Liu Y. (2018). An oxidized abasic lesion inhibits base excision repair leading to DNA strand breaks in a trinucleotide repeat tract. PLoS ONE, 13(2), e0192148.

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Oligonucleotide Synthesis and Preparation

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DNA oligonucleotides were synthesized by Integrated DNA Technologies (IDT, Coralville, IA, USA). Deoxynucleotide 5′-triphosphates (dNTPs) were obtained from Sigma-Aldrich (St. Louis, MO, USA). T4 polynucleotide kinase and terminal deoxynucleotidyl transferase were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Radionucleotides [γ-³²P] ATP (3000 Ci/mmol) and Cordycepin 5′-triphosphate 3′-[α-³²P] (5000 Ci/mmol) were purchased from Perkin Elmer Inc. (Boston, MA, USA). Micro Bio-Spin 6 chromatography columns were acquired from Bio-Rad Laboratories (Hercules, CA, USA). Dulbecco's modified Eagle's medium (DMEM), fetal bovine serum (FBS), l(+)-glutamine, and 0.25% trypsin-EDTA were purchased from Thermo Fisher Scientific (Waltham, MA, USA). All standard chemical reagents were purchased from Sigma-Aldrich (St. Louis, MO, USA) and Thermo Fisher Scientific (Waltham, MA, USA). Escherichia coli uracil-DNA glycosylase (UDG) was purchased from New England BioLabs Inc. (Ipswich, MA, USA). Purified recombinant pol β dRP lyase mutant (K72A and H34G) and pol β 8 kD domain proteins were generous gifts from Dr Samuel H. Wilson at the National Institute of Environmental Health Sciences/National Institutes of Health. Purified recombinant human APE1, wild-type (WT) pol β, FEN1 and DNA ligase I (LIG I) were expressed and purified as described previously (14 (link),18 (link),32 (link)).

Lai Y., Weizmann Y, & Liu Y. (2018). The deoxyribose phosphate lyase of DNA polymerase β suppresses a processive DNA synthesis to prevent trinucleotide repeat instability. Nucleic Acids Research, 46(17), 8940-8952.

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Synthesis and Purification of Radiolabeled Oligonucleotides

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DNA oligonucleotides containing a 5′S-cdA or 5′R-cdA were synthesized and purified by High-performance liquid chromatography (HPLC) according to the procedures described previously (63 ). All other oligonucleotides were purchased from Integrated DNA Technologies (IDT Inc., Coralville, IA, USA). The radionuclides [γ-³²P] ATP (6000 mCi/mmol) and Cordycepin 5′-triphosphate 3′-[α-³²P] (5000 mCi/mmol) were purchased from PerkinElmer Inc. (Boston, MA, USA). Micro Bio-Spin 6 chromatography columns were from Bio-Rad (Hercules, CA, USA). Deoxynucleoside 5′-triphosphates (dNTPs) were from Fermentas (Glen Burnie, MD, USA). S1 Nuclease was from Promega (Madison, WI, USA). All other standard chemical reagents were purchased from Sigma-Aldrich (St. Louis, MO, USA) and Thermo Fisher Scientific (Pittsburgh, PA, USA). Purified pol β, FEN1 and DNA ligase I (LIG I) were generous gifts from Dr Samuel H. Wilson at the National Institute of Environmental Health Sciences (NIEHS)/National Institutes of Health, Research Triangle Park, NC.

Xu M., Lai Y., Jiang Z., Terzidis M.A., Masi A., Chatgilialoglu C, & Liu Y. (2014). A 5′, 8-cyclo-2′-deoxypurine lesion induces trinucleotide repeat deletion via a unique lesion bypass by DNA polymerase β. Nucleic Acids Research, 42(22), 13749-13763.

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