Ied RNA. The strong assistance was treated with MeNH2 in EtOH (33 , 0.five mL) and MeNH2 in water (40 , 0.5 mL) for 7 h at space temperature. (For RNA containing 5-aminoallyl uridines, the column was 1st treated with ten diethylamine in acetonitrile (20 mL), washed with acetonitrile (20 mL) and dried. Then, the strong support was treated with MeNH2 in EtOH (33 , 1 mL) and NH3 in H2O (28 , 1 mL) for ten min at space temperature and 20 min at 65 .) The supernatant was removed from along with the strong support was washed 3 instances with ethanol/water (1/1, v/v). The supernatant and also the washings have been combined together with the deprotection answer of the residue plus the whole mixture was evaporated to dryness. To get rid of the 2-silyl defending groups, the resulting residue was treated with tetrabutylammonium fluoride trihydrate (TBAF3H2O) in THF (1 M, 1 mL) at 37 overnight. The reaction was quenched by the addition of triethylammonium acetate (TEAA) (1 M, pH 7.4, 1 mL). The volume from the remedy was reduced as well as the solution was desalted having a size exclusion column (GE Healthcare, HiPrep 26/10 Desalting; two.6 ten cm; Sephadex G25) eluating with H2O; the collected fraction was evaporated to dryness and dissolved in 1 mL H2O. Analysis of your crude RNA following deprotection was performed by {ERRĪ² supplier anionexchange chromatography on a Dionex DNAPac PA-100 column (four mm 250 mm) at 80 . Flow rate: 1 mL/min, eluant A: 25 mM Tris Cl (pH 8.0), 6 M urea; eluant B: 25 mM Tris Cl (pH 8.0), 0.5 M NaClO4, six M urea; gradient: 0- 60 B within a within 45 min or 0-40 B in 30 min for short sequences up to 15 nucleotides, UV-detection at 260 nm. Purification of 2-O-(2-Azidoethyl) PLD Formulation modified RNA. Crude RNA items have been purified on a semipreparative Dionex DNAPac PA-100 column (9 mm 250 mm) at 80 with flow price 2 mL/min. Fractions containing RNA had been loaded on a C18 SepPak Plus cartridge (Waters/Millipore), washed with 0.1-0.15 M (Et3NH)+HCO3-, H2O and eluted with H2O/CH3CN (1/1). RNA containing fractions were lyophilized. Analysis on the excellent of purified RNA was performed by anion-exchange chromatography with identical conditions as for crude RNA; the molecular weight was confirmed by LC-ESI mass spectrometry. Yield determination was performed by UV photometrical analysis of oligonucleotide solutions. Mass Spectrometry of 2-O-(2-Azidoethyl) Modified RNA. All experiments were performed on a Finnigan LCQ Advantage MAX ion trap instrumentation connected to an Amersham Ettan micro LC technique. RNA sequences wereArticleanalyzed inside the negative-ion mode with a possible of -4 kV applied for the spray needle. LC: Sample (200 pmol RNA dissolved in 30 L of 20 mM EDTA option; average injection volume: 30 L); column (Waters XTerraMS, C18 2.5 m; 1.0 50 mm) at 21 ; flow price: 30 L/min; eluant A: 8.six mM TEA, one hundred mM 1,1,1,three,3,3-hexafluoroisopropanol in H2O (pH eight.0); eluant B: methanol; gradient: 0-100 B inside a within 30 min; UV-detection at 254 nm. Copper-Catalyzed Azide-Alkyne Cycloaddition (CuAAC) Labeling. 2-O-(2-Azidoethyl) modified RNA (60 nmol) was lyophilized within a 1 mL Eppendorf tube. Then, aqueous solutions of F545 (Acetylene-Fluor 545, Click Chemistry Tools), CuSO4, and sodium ascorbate had been added consecutively; acetonitrile was added as cosolvent36 to reach final concentrations of 1 mM RNA, 2 mM dye, five mM CuSO4, ten mM sodium ascorbate, as well as a H2O/acetonitrile ratio of 4/1 inside a total reaction volume of 60 L. The reaction mixture was degassed and stirred for three to 4 h beneath argon atmosphere at 50 . To monit.
