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Tracking of Proton Transfer Reaction in Supercooled RNA Nucleoside

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  • 1. Tracking of Proton Transfer Reaction in Supercooled RNA Nucleoside Z. Wojnarowska* M. Paluch (presenter)P. Wlodarczyk, M. Dulski, R. Wrzalik Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland C. M. Roland Naval Research Laboratory, Chemistry Division, Code 6120, Washington DC 20375-5342, USA*zwojnaro@us.edu.pl J. Phys. Chem. Lett. 2012, 3, 2288–2292 1
  • 2. Motivation of tautomerizationinvestigationExamples of tautomerization : Importance:  physics  chemistry (chelating agents)  pharmacology (various tautomers-different drug activity) amide-imidic acid tautomerism  molecular biology (noncanonic RNA/DNA tautomers-incorrect base pairing - genetic disease, cancer, or drug resistance) keto-enol tautomerism the same atoms RNA chain but in different Problem: arrangement How to track the proton transfer reaction of RNA nucleoside experimentally? Proprietary and Confidential 2 American Chemical Society
  • 3. Experimental setupExamined sample: β-uridine Measurements: lactam-lactim tautomerismSample preparation: crystal; T<Tm liquid; T=Tm glass; T<Tg dielectric spectrometer (http://www.novocontrol.com/) capacitor filled heating with β-uridine quick cooling (Tm=438 K) Proprietary and Confidential 3 American Chemical Society
  • 4. Results Measurement in a wide Isothermal time-dependent temperature range: dielectric measurement : f max  1 2   T>Tg supercooled liquid state During the sample equilibration:  εs is increasing    s     N   2 Structural relaxation process originates from the cooperative motions Consequently: of the molecule and is related  dipole moment of the sample increases to the glass transition of β-uridine  concentration of isomers with larger Tg  T (   100 s )  324 K dipol moment is getting higher Proprietary and Confidential 4 American Chemical Society
  • 5. Data analysisStep I: Analyzis of kinetic curves Step II: Determination of Ea BDS measurements refractive index measurementsThe isothermal εs=f(t) and n=f(t) dependence Arrhenius equation: reflects the kinetics of the β-uridine tautomerization Ea ln k  ln k0  RT Determination of the rate constants k:  s  A1  exp( k1  t )  A2  exp( k 2  t )  C Proprietary and Confidential 5 American Chemical Society
  • 6. Results interpretationDoes proton transfer during the uridine equilibration involvethe lactam-lactim conversion or its opposite?Experiment: First tautomerization Second tautomerization pathway: pathway: the population of isomers having larger a dipole moment increases during chemical equilibration DFT calculations: for both noncanonical tautomeric structures the dipole moments are higher Δε=216 kJ/mol Δε=182 kJ/mol than that calculated for the Δμ=1.1 D Δμ=1.7 D lactam formconversion of lactam to both Good agreement Lower Ea higher lactims transpires during probability of the time dependent between EaBDS and EaDFT incorrect base measurements pairing Proprietary and Confidential 6 American Chemical Society
  • 7. Biological consequencesof amide-imidic acid conversionDifferent electrostatic potentials on Translation mechanism:the tautomers molecular surfaces: Corectly: mRNA: UCC → tRNA: AGG →serine Consequently: If U in mRNA is replaced by its  different H-bonds formation abilities, noncanonical tautomer:  tautomer 2 is very similar to adenosine, mRNA: UCC (read as ACC) → tRNA: and therefore can mimic this nucleoside UGG →trypsin Proprietary and Confidential 7 American Chemical Society
  • 8. Conclusions The dielectric spectroscopy technique offers a new approach to the study of proton transfer reactions of RNA and DNA M.Paluch compounds, and consequently for Z. Wojnarowska investigations of possible point mutations. C.M. Roland Acknowledgments P. Wlodarczyk The work at NRL was supported by the Office of Naval Research. Z.W. and M.P. are deeply thankful for the financial support received from the National Science Center (Grant MAESTRO2). R. Wrzalik M. DulskiProprietary and Confidential 8American Chemical Society