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1 RNA with iron(ii) as a cofactor catalyses electron transfer Chiaolong Hsiao, I-Chun Chou, C. Denise Okafor, Jessica C. Bowman, Eric B. O Neill, Shreyas S. Athavale, Anton S. Petrov, Nicholas V. Hud, Roger M. Wartell, Stephen C. Harvey and Loren Dean Williams School of Chemistry and Biochemistry, School of Biology, and NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA NATURE CHEMISTRY 1

2 Table of Contents General Experimental Section... 3 DNA and RNA Synthesis and Purification Single Electron Transfer Reactions Michaelis-Menten Kinetics Michaelis-Menten Data Analysis Control Experiments and Supplemental Figures... 5 RNA Stability in 6 μm Fe 2+ and 50 μm H 2 O Effect of [Fe 2+ ] on RNA stability Effect of RNA concentration on catalysis of electron transfer Effect of prior RNA degradation on catalysis of electron transfer References NATURE CHEMISTRY 2

3 General Experimental Section DNA and RNA Synthesis and Purification. The gene for the Del C209 mutant of the P4-P6 domain of the T. thermophila Group I intron 2 was synthesized by recursive PCR. 3 The 23S rrna and 23S rrna Domain III genes were synthesized as described. 4 The STMV genome was synthesized commercially (MWG Operon). All genes were confirmed by sequencing. All of the large RNAs used here (except the trna) were produced by in vitro transcription (MegaScript T7 Kit, Ambion), minimizing the possibility of contamination by protein-based electron transfer enzymes. RNAs were then precipitated in ethanol/ammonium acetate and lyophilized to powder prior to re-suspension. In vitro produced RNAs were further purified with an RNA Clean and Concentrator TM -25 Kit (Zymo Research). RNA purity and integrity were assayed by denaturing gel electrophoresis, which indicates that the RNAs are not significantly degraded on the timescale of the electron transfer reactions. Nucleic acid concentrations were determined by absorbance at 260 nm, measured with a Thermo Scientific NanoDrop. Nuclease free water (IDT) was used in all experiments involving RNA. Mg 2+ was removed from RNA solutions by heating with divalent cation chelation beads (Hampton Research). Mg 2+ removal was confirmed as described 1. The phenylalanine-specific trna from brewer s yeast [CAS#: ] was obtained from Sigma-Aldrich. Excess salts and other impurities the trna removed with the Zymo RNA Clean and Concentrator Kit. This purification gives an overall 75% recovery yield. Single Electron Transfer Reactions. In 1982, Josephy 5 described the reaction of TMB with H 2 O 2, using a spectrophotometric assay, to demonstrate catalysis of single electron transfer by the enzyme horseradish peroxidase (HRP). In the Josephy TMB/H 2 O 2 assay, TMB is catalytically oxidized at ph 5 (or higher) to a radical cation, forming a blue-colored charge-transfer complex, with absorbance maxima at 370 and 652 nm, and an extinction coefficient of 3.9x10 4 M -1 cm -1 at 652 nm. This TMB/H 2 O 2 reaction has been used broadly for detecting HRP-like catalytic activity (i.e., catalysis of single electron transfer). In recent examples, Jv 6 used TMB/H 2 O 2 to demonstrate HRP-like catalysis by positively-charged gold nanoparticles. Liu 7 used TMB/H 2 O 2 to demonstrate HRP-like catalysis NATURE CHEMISTRY 3

4 by iron-substituted microparticles. A low ph model system 8 was used here to validate the oxidation of TMB by Fe 2+ /H 2 O 2. At low ph, hydroxyl radical, produced from the decomposition of hydrogen peroxide in the presence of Fe 2+ oxidizes TMB 8. The low ph reaction is noncatalytic in that HRP (or RNA/Fe 2+ as utilized here) are not required. We observe that the low ph non-catalytic oxidation of TMB by H 2 O 2 yields the expected Josephy product, with the same spectral characteristics ( max of 370 and 652 nm), as the higher ph catalytic oxidation of TMB in the presence of Fe 2+ /RNA. For the RNA/Fe 2+ reactions here, 3,3,5,5 -Tetramethylbenzidine (TMB, Sigma-Aldrich) stock solutions were prepared in DMSO. Hydrogen peroxide (30%, Fisher Scientific) stock solutions were prepared in H 2 O. HEPES-TRIS stock buffer solutions were prepared by mixing solutions of HEPES free acid and TRIS free base in H 2 O to achieve ph 7.2. Deoxygenated Fe 2+ solutions were prepared by dissolving a known mass of the FeSO 4-7H 2 O (J.T. Baker) in H 2 O, in a capped tube with a septum, and sparging with argon for two hours. Reactions were prepared by mixing the nucleic acid, TMB, and hydrogen peroxide with HEPES-TRIS buffer, ph 7.2, in a spectrophotometer cell. The absorbance cell was continuously capped by a septum, and reagents were introduced via a syringe under positive argon pressure. Reactions were deoxygenated by sparging with argon for 5 minutes prior to addition of deoxygenated Fe 2+ solution and another 5 minutes of sparging with argon. No reaction is observed in this mixture at ph 7.2. To initiate the reaction, the ph was adjusted to 6.5 by the addition of deoxygenated H 2 SO 4 (aq). Absorbance was recorded with a single-beam USB2000+UV-VIS, Ocean Optics spectrophotometer. The absorbance of the reaction buffer was recorded and subtracted. Data were acquired and analyzed with Logger Pro 3 (Vernier Software Technology). Electron transfer is fully inhibited by excess Mg 2+ (3 mm) or EDTA (5 mm) but not by Na + (10 mm). The final reaction conditions, unless otherwise specified, were: Fe 2+, 6.0 μm; TMB, 500 μm; hydrogen peroxide, 50 μm; HEPES-TRIS, 20 mm, ph 6.5, room temperature. The nucleic acid concentrations were as follows: P4-P6 and STMV genome RNAs, 0.5 μm; 23S rrna, 0.03 μm, ATP (Sigma-Aldrich), 80 um; double-stranded DNA (IDT), 1.0 μm of each strand; 5-mer single stranded RNA (5 -GCACU-3, Dharmacon), 16 um; yeast phenylalanine-trna, 1 um. NATURE CHEMISTRY 4

5 Michaelis-Menten Kinetics. The in vitro transcript of T. thermophilus 23S rrna or P4-P6 Domain RNA, after heat treatment with divalent cation chelation beads, was dissolved in deoxygenated H 2 O and mixed with deoxygenated Fe 2+ (aq). A mixture of TMB/H 2 O 2 in HEPES-TRIS buffer ph 7.2, in a 10 mm rectangular absorbance cell was capped by a septum and deoxygenated for 5 min. Deoxygenated RNA/Fe 2+ solution was added into the deoxygenated TMB/H 2 O 2. To initiate the reaction, the ph was dropped to 6.5 by the addition of deoxygenated H 2 SO 4 (aq). The final concentrations were 0.03 μm 23S rrna or 0.5 μm P6-P6 Domain RNA (strand); Fe 2+, 6 μm; TMB, 500 μm; HEPES-TRIS, 20 mm; H 2 O 2, variable (Figure 2) Michaelis-Menten Data Analysis. For each reaction, the initial time increment during which the velocity was constant was determined by visual inspection. A Bootstrapping Method (using function bootstrap in Matlab R2011b) was employed to generate 1000 bootstrap samples in each constant velocity increment. The initial rate of each reaction is the mean of bootstrap samples. The 95% confidence interval for each initial rate was determined from the 2.5 percentile and the 97.5 percentiles of the bootstrapped samples. The V max and K M values were obtained by nonlinear least squares fitting (lsqcurvefit) with the Michaelis Menten formalism. Control Experiments and Supplemental Figures RNA Stability in 6 μm Fe 2+ and 50 μm H 2 O 2. RNA stability in Fe 2+ /H 2 O 2 solutions under anoxic and oxic conditions was monitored as a function of time by denaturing gel electrophoresis (Figure S1). Oxic and anoxic reaction mixtures were prepared by combining P4-P6 domain RNA (0.5 M) and hydrogen peroxide (50 M) in HEPES-TRIS buffer, ph 7.2, in 1.5 ml eppendorf tubes capped with septa. Anoxic mixtures were sparged with argon, and oxic mixtures were sparged with air. Deoxygenated Fe 2+ (aq) was added to solutions while maintaining positive pressure of argon or air. As in the peroxidase reaction, the ph was dropped to 6.5 by the addition of a calibrated volume of deoxygenated H 2 SO 4 (aq). To quench the RNA degradation reactions, mixtures were transferred (under anoxic conditions) at certain timepoints, to tubes containing chelating beads, and pelleted. The RNA in the anoxic solutions remains essentially intact at around 60 minutes (Figure S1 A). The RNA in the oxic solution is almost fully degraded at 60 minutes (Figure S1 B). This NATURE CHEMISTRY 5

6 experiment indicates that under the reaction conditions of Figure 1 (20 minutes, 6 μm Fe 2+, 50 μm, H 2 O 2, anoxic), the RNA does not significantly degrade. Figure S1: The stability of the T. thermophila Group I intron P4-P6 domain RNA in the presence of Fe 2+ /H 2 O 2 under (A) anoxic conditions, and (B) oxic conditions. This 8M urea, 6% PAGE gel was stained with ethidium bromide. NATURE CHEMISTRY 6

7 Effect of [Fe 2+ ] on RNA stability. RNA stability in Fe 2+ /H 2 O 2 solutions under anoxic conditions, where [Fe 2+ ] is varied, was monitored by denaturing gel electrophoresis (Figure S2). RNA reaction mixtures were prepared by combining P4-P6 domain RNA (0.5 M) and hydrogen peroxide (50 M) in HEPES-TRIS buffer, ph 7.2, in 1.5 ml tubes capped with septa. The mixtures were sparged with argon for 5 minutes followed by the addition of deoxygenated Fe 2+ (aq) (variable concentration) with continuous positive pressure of argon. To mimic the peroxidase reaction conditions, the ph was dropped to 6.5 by addition of Figure S2: The stability of the T. thermophila Group I intron P4-P6 domain RNA with variable [Fe 2+ ] under anoxic conditions in the presence of H 2 O 2. Each reaction was incubated for 15 minutes. This 8M urea, 6% PAGE gel was stained with ethidium bromide. deoxygenated H 2 SO 4 (aq). These RNA degradation reactions were incubated for 15 minutes. To quench the reactions, the mixtures were transferred (under anoxic conditions) to tubes containing chelating beads, and pelleted. These results confirm that under the reactions conditions of Figure 1 (20 minutes, 6 μm Fe 2+, 50 μm H 2 O 2, anoxic), the RNA does not significantly degrade. NATURE CHEMISTRY 7

8 Effect of RNA concentration on catalysis of electron transfer. The RNA/Fe 2+ electron transfer rate increases with [RNA] (Figure S3). Reaction mixtures with P4-P6 domain RNA were prepared as described above (6 μm Fe 2+, 50 μm H 2 O 2, 500 μm TMB under anoxic conditions) except that [RNA] was varied. The initial reaction rate (slope) was determined by linear fitting to the first three minutes of smoothed data. The rate of electron transfer increases with [RNA] while all other components are held fixed. Beyond 0.8 μm (RNA strand) the reaction rate plateaus (not shown), presumably because Fe 2+ becomes limiting. To determine if Fe 2+ chelation by a simple chelator is sufficient for catalysis, we investigated a series of EDTA concentrations and do not observe catalysis with any of them (3, 6, 12 μm EDTA with 6 μm Fe 2+, 50 μm H 2 O 2, 500 μm TMB), data not shown. Figure S3: Rate of electron transfer catalyzed by P4-P6 domain RNA in the presence of 6 μm Fe 2+, 50 μm H 2 O 2, 500 μm TMB under anoxic conditions the effect of RNA concentration. RNA concentration is in units of strands. NATURE CHEMISTRY 8

9 Effect of [Na + ] on catalysis of electron transfer Electron transfer catalyzed by RNA/Fe 2+ is inhibited by high [Na + ] (Figure S4). Reaction mixtures with P4-P6 domain RNA were prepared as described above (6 μm Fe 2+, 50 μm H 2 O 2, 500 μm TMB under anoxic conditions) except that Na + was included. The initial reaction rate (slope) was determined by linear fitting to the first three minutes smoothed data. Figure S4: Rate of electron transfer by the P4-P6 domain RNA in the presence of 6 μm Fe 2+, 50 μm H 2 O 2, 500 μm TMB under anoxic conditions the effect of Na + concentration. NATURE CHEMISTRY 9

10 Effect of prior RNA degradation on catalysis of electron transfer. The rate of electron transfer catalyzed by RNA/Fe 2+ decreases if the RNA has been previously degraded by heat. Reaction solutions with P4-P6 domain RNA were prepared as described above except that the RNA was first degraded by heat. Before the electron transfer reactions, the RNA was incubated at 80 o C in water for 0, 30 min, 60 min, 120 min, or 240 min. As shown in Figure S5 (top), the RNA slowly degrades under these conditions. Integration of the bands on the gel indicates that the heat-induced RNA degradation is 90% complete after 4 hours. Figure S5. (top panel) RNA degradation by heat. The T. thermophila Group I intron P4-P6 domain RNA is degraded by incubation at 80 o C in water for varying lengths of time. This 8M urea, 6% PAGE gel was stained with ethidium bromide. (bottom panel) RNA samples that were degraded by heat before the RNA/Fe 2+ electron-transfer reactions show attenuated catalysis. Heat-induced RNA degradation decreases the rate of catalysis. In a separate experiment, P4-P6 domain RNA in water was partially degraded by the same process, for the same time increments (0, 30 min, 60 min, 120 min, 240 min). The partially degraded RNA from each degradation timepoint was assayed for electron transfer catalysis. Other experimental parameters were held constant. The reaction conditions and methods of data acquisition and analysis were the same as for the experiments described above. The rate of electron transfer is seen to decrease linearly with the extent of heat-induced RNA degradation (Figure 5S, bottom). NATURE CHEMISTRY 10

11 References 1 Athavale, S. S. et al. RNA folding and catalysis mediated by iron (II). PLoS ONE 7, e38024 (2012). 2 Juneau, K., Podell, E., Harrington, D. J. & Cech, T. R. Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA--solvent interactions. Structure. 9, (2001). 3 Bowman, J. C., Azizi, B., Lenz, T. K., Roy, P. & Williams, L. D. Preparation of long templates for RNA in vitro transcription by recursive PCR Vol. 941 in Recombinant and in vitro RNA synthesis (ed G. L. Conn) (Humana Press, 2012). 4 Athavale, S. S. et al. Domain III of the T. thermophilus 23S rrna folds independently to a nearnative state. RNA 18, (2012). 5 Josephy, P. D., Eling, T. & Mason, R. P. The horseradish peroxidase-catalyzed oxidation of 3,5,3',5'-tetramethylbenzidine. Free radical and charge-transfer complex intermediates. J. Biol. Chem. 257, (1982). 6 Jv, Y., Li, B. & Cao, R. Positively-charged gold nanoparticles as peroxidiase mimic and their application in hydrogen peroxide and glucose detection. Chem. Commun. 46, (2010). 7 Liu, X. et al. Bsa-templated mno2 nanoparticles as both peroxidase and oxidase mimics. Analyst 137, (2012). 8 Walling, C. Fentons reagent revisited. Acc Chem Res 8, (1975). NATURE CHEMISTRY 11