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6 protocols using inosine triphosphate

1

Poly(U) Polymerase Assay for RNA Tailing

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To test for tailing 32P-labeled A24 as a substrate using residues (ATP, CTP, GTP, UTP, or ITP) a reaction containing labeled A24 RNA, 0.5 mM NTP, 50 mM NaCl, 10 mM MgCl2, 10 mM Tris-Cl pH 7.9, 1 mM DTT, 500 µg/mL Bovine Serum Albumin (BSA), and 0.6 units of NEB poly(U) polymerase in a final volume of 5 µL was incubated at 37°C for 30 min. The standard reaction for adding homopolymers to the 3′ends of model mRNAs and yeast RNA preparations using Cid1 poly(U) polymerase is as follows: RNA (various amounts) in 0.1 mM EDTA in volumes up to 2.95 µL is denatured at 95°C for 2 min then placed on ice for 2 min. The RNA is added to a reaction containing 4mM NTP (ATP, CTP, GTP, UTP, or ITP) 50 mM NaCl, 13.5 mM MgCl2, 10 mM Tris-Cl pH 7.9, 1 mM DTT, 500 µg/mL BSA, and 0.6 units of NEB poly(U) polymerase in a final volume of 7.5 µL and incubated at 37°C for 1 h. To test for incorporation of modified U residues, 200 fmol MYL6(A+) RNA was incubated with 1 mM concentration of modified UTP analog or a combination of 0.5 mM modified UTP analog and 0.5 mM UTP following the standard poly(U) polymerase reaction. Inosine triphosphate was purchased from Sigma. Modified UTP analogs were purchased from TriLink, Inc.
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2

Vascular Reactivity Regulation Mechanisms

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NaCl, KCl, MgCl2, KH2PO4,CaCl2, NaHCO3, glucose, NaHS, l‐cysteine, phenylephrine, ACh, 5‐HT, l‐NIO (N5‐(1‐Iminoethyl)‐L‐ornithine dihydrochloride), Tris‐HCl, sodium deoxycholate, sodium dodecyl sulfate, EDTA, Igepal, protease inhibitor cocktail, BSA, Tween 20, β‐actin, methanol, ammonium acetate, acetic acid, creatine phosphokinase, creatine phosphate DEA‐NO, zinc acetate and, inosine triphosphate and stock solution of cGMP, cAMP and cIMP were supplied by Sigma‐Aldrich, (Milan, Italy). Inosine 3′‐5′‐cyclic monophoshate sodium salt was supplied by (Merck, Germany). Anti‐p‐PDE4A and anti‐p‐PDE5 were supplied by Fabgennix (Frisco, TX, USA). Anti‐PDE4A was supplied by ProteinTech (Manchester, UK). Anti‐PDE5 was supplied by Santa Cruz Biotechnology (Heidelberg, Germany). Anti‐eNOS was supplied by BD Transduction Laboratories (USA). Anti‐β‐actin was supplied by Merck (Germany). ODQ, U46619, FR 139317 and BQ788 were supplied by Tocris (Bristol, UK).
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3

Quantitative Analysis of Nucleotides

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Adenosine, Adenosine Monophosphate (AMP), Adenosine triphosphate (ATP), Guanosine, Guanosine monophosphate (GMP), guanosine triphosphate (GTP), Inosine, Inosine monophosphate (IMP), and Inosine triphosphate (ITP) were purchased from Sigma Aldrich, St. Louis, MO; isotopic internal standards for each, (Ribose 13C5) were from Cambridge Isotope Laboratories, Andover, MA.
Analytical grade reagents were purchased from Fisher Scientific, Fairlawn, NJ, (acetonitrile, methanol, formic acid, potassium chloride, phosphoric acid, and ammonium hydroxide). Ammonium acetate 5 M solution was purchased from Ambion® and alkaline phosphatase was purchased from Sigma Aldrich, St. Louis. Ultrapure (UP) water was prepared in house from deionized water with a Barnstead Nanopure System (Thermo Fisher Scientific, Waltham, MA). Other supplies included Waters Sep-Pak Accell Plus QMA Cartridge, 3 cc (500 mg) (Waters Corporation, Milford, MA) and Varian Bond-Elut LRC Phenylboronic Acid (PBA) Cartridge 100mg/10 mL (Agilent, Santa Clara, CA). PAXgene® tubes were from Qiagen, Valencia, CA.
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4

Quantitative Analysis of Nucleotides

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Adenosine, Adenosine Monophosphate (AMP), Adenosine triphosphate (ATP), Guanosine, Guanosine monophosphate (GMP), guanosine triphosphate (GTP), Inosine, Inosine monophosphate (IMP), and Inosine triphosphate (ITP) were purchased from Sigma Aldrich, St. Louis, MO; isotopic internal standards for each, (Ribose 13C5) were from Cambridge Isotope Laboratories, Andover, MA.
Analytical grade reagents were purchased from Fisher Scientific, Fairlawn, NJ, (acetonitrile, methanol, formic acid, potassium chloride, phosphoric acid, and ammonium hydroxide) as well as Whatman® 903 DBS cards, bags and desiccant for DBS preparation and storage. Ammonium acetate 5M solution was purchased from Ambion® and alkaline phosphatase was purchased from Sigma Aldrich, St. Louis. Ultrapure (UP) water was prepared in house from deionized water with a Barnstead Nanopure System (Thermo Fisher Scientific, Waltham, MA). Other supplies included Waters Sep-Pak Accell Plus QMA Cartridge, 3cc (500mg) (Waters Corporation, Milford, MA) and Varian Bond-Elut LRC Phenylboronic Acid (PBA) Cartridge 100mg/10mL (Agilent, Santa Clara, CA). Blood products for lysed cellular matrix were obtained from Bonfils, Denver CO. Cell preparation tubes (CPT) and dipotassium EDTA tubes were purchased from Becton, Dickinson and Company, Franklin Lakes, NJ.
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5

Redox Reactions and Nucleotides Assay

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Hexaammineruthenium(III) chloride (Ru(NH3)6 2+/3+ ), potassium ferricyanide (Fe(CN)6 3-/4-), ammonium iron(II) sulfate hexahydrate (Fe 2+/3+ ), uridylic acid (UMP) and inosine triphosphate (ITP) were purchased from Sigma-Aldrich.
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6

Tailing A24 RNA with Poly(U) Polymerase

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To test for tailing 32 P-labeled A24 as a substrate using residues (ATP, CTP, GTP, UTP or ITP) a reaction containing labeled A24 RNA, 0.5mM NTP, 50mM NaCl, 10mM MgCl 2 , 10 mM Tris-Cl pH 7.9, 1mM DTT, 500 ug/ml Bovine Serum Albumin (BSA), and 0.6 units of NEB poly(U) polymerase in a final volume of 5ul was incubated at 37°C for 30 minutes. The standard reaction for adding homopolymers to the 3′ends of model mRNAs and yeast RNA preparations using Cid1 poly(U) polymerase is as follows: RNA (various amounts) in 0.1mM EDTA in volumes up to 2.95uL is denatured at 95°C for 2 minutes then placed on ice for 2 minutes. The RNA is added to a reaction containing 4mM NTP (ATP, CTP, GTP, UTP or ITP) 50mM NaCl, 13.5mM MgCl 2 , 10 mM Tris-Cl pH 7.9, 1mM DTT, 500 ug/ml BSA, and 0.6 units of NEB poly(U) polymerase in a final volume of 7.5ul and incubated at 37°C for 1 hour. To test for incorporation of modified U residues, 200fmol MYL6(A+) RNA was incubated with 1mM concentration of modified UTP analog or a combination of 0.5mM modified UTP analog and 0.5mM UTP following the standard poly(U) polymerase reaction.
Inosine triphosphate was purchased from Sigma. Modified UTP analogs were purchased from TriLink, Inc.
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