JBPC  Vol.2 No.3 , August 2011
Spin effects govern DNA/RNA nucleotide polymerization
ABSTRACT
A new radical mechanism of nucleotide polymerization is found. The finding is based on the Car-Parrinello molecular dynamics computations at 310 K with an additional spin-spin coupling term for 31P and 1H atoms and a radical pair spin term included. The mechanism is initiated by a creation of a high-energy spin-separated Mg-ATP complex in a triplet state in which the Mg prefers an uncommon chelation to the O2-O3 oxygens of the ATP. The cleavage of the complex produces the .AMP- and .O- radicals. The latter captures a proton from acidic solution (the Zundel cation) that converts it into the .OH radical. The process agrees with the protoncoupled electron transfer (PCET) mechanism. Through interacting with the HO-C3' group of the deoxyribose/ribose the .OH radical captures its hydrogen atom. The process is accompanied by producing water and the .AMP radical. The .AMP- and .AMP radicals then interact yielding a dimer. The described mechanism is easily generalized for a bigger number of adjoining nucleotides and their type. The radical mechanism is highly sensitive to the .AMP-..OH radical pair spin symmetry and the radius of the .OH diffusion. This confines the operation of the radical mechanism: it is applicable to nucleotide polymerization through the HO-C3’ group of deoxyribose/ribose (DNA/RNA polymerization) and inapplicable through the HO-C2’ group of ribose (RNA) . a result that nature has developed over evolution.

Cite this paper
nullTulub, A. (2011) Spin effects govern DNA/RNA nucleotide polymerization. Journal of Biophysical Chemistry, 2, 300-309. doi: 10.4236/jbpc.2011.23034.
References
[1]   Kirschning, A. (2004) Immobilized catalysis. Springer Verlag, Berlin.

[2]   Harvey, F.L., Berk, A., Keiser, C.A., Krieger, M., Scott, M.P., Bortscher, A. and Ploegh, H. (2008) Molecular cell biology. W. H. Freeman Publishers, New York.

[3]   Metzler, D.E. (1977) The chemical reactions of living cells. Academic Press, New York.

[4]   Cowan, J.A. (1995) Introduction to the biological chemistry of magnesium. VCH, New York.

[5]   Black, C.B. and Cowan, J.A. (1995) Magnesium-de- pendent enzymes in general metabolism. In: Cowan, J.A., Ed., The Biological Chemistry of Magnesium, VCH, New York, pp. 54-87.

[6]   Yang, L., Arora, K., Weard, W.A., Wilson, S.H. and Schlick, T. (2004) Critical role of magnesium ions in DNA polymerase closing and active site assembly. Journal of the American Chemical Society, 126, 8441-8453. doi:10.1021/ja049412o

[7]   Beechero, J.M., Otto, M.R., Bloom, L.B., Eritja, R., Reta-Krantz, L.J. and Goodman, M.F. (1998) Exonuclease-polymerase active site partitioning of primer-template DNA strands and equilibrium Mg2+ binding properties of bacteriophage T4DNA polymerase. Biochemistry, 37, 10144-10155. doi:10.1021/bi980074b

[8]   Kornberg, A. and Baker, T.A. (2005) DNA Replication. 2nd Edition, Nuclear Acid Science Books, New York.

[9]   Tsai, C.S. (2007) Biomacromolecules. Introduction to structure, function and informatics. John Wiley & Sons Inc., Hoboken.

[10]   Mullis, K.B. (1998) The polymerase chain reaction. Nobel Prize lecture: 1993. World Scientific Publication, Singapore.

[11]   Lopus, M., Yenjerla, M. and Wilson L. (2009) Microtubule dynamics (advanced review). In: Wilson, L., Ed., Wiley Encyclopedia of Chemical Biology, Wiley & Sons, New York, 153-168.

[12]   Engelhardt, W.A. and Ljubimova, M.N. (1939) Myosine and adenosinetriphosphatase. Nature, 144, 668-669. doi:10.1038/144668b0

[13]   Kachur, T.M., Pilgrim, D.B. (2008) Myosine assembly, maintenance and elongation in muscle: Role of the chaperon unc-45 in myosine thick filament dynamics. International Journal of Molecular Sciences, 8, 1863-1875.

[14]   Cowan, J.A. (2002) Structural and catalytic chemistry of magnesium-dependent enzymes. BioMetals, 15, 225-235. doi:10.1023/A:1016022730880

[15]   Tulub, A.A. (2008) Mg spin affects adenosinetriphosphate activity. PMC Physics B, 1, 1-18.

[16]   Tulub, A.A. (2006) Molecular Dynamics DFT-B3LYP study of guanosinetriphosphate conversion into guanosinemonophosphate upon Mg(2+) chelation of alpha and beta oxygens of the triphosphate tail. Physical Chemistry Chemical Physics, 8, 2187-2192.

[17]   Car, R. and Parrinello, M. (1985) Unified approach to molecular dynamics and density-functional theory. Phy- sical Review Letters, 55, 2471-2474. doi:10.1103/PhysRevLett.55.2471

[18]   Furmanchuk, A., Isayev, O., Shishkin, O.V., Gorb, L. and Leszczynski, J. (2010) Hydration of nucleic acid bases: A Car-Parrinello molecular dynamics approach. Physical Chemistry Chemical Physics, 12, 3363-3375.

[19]   Tulub, A.A. (2009) Magnesium-associated proteins in drug design. AstraZeneca—Annual Reports, Stockholm, London, New York, Tokyo.

[20]   Asher, J.R. and Kaupp, M. (2007) Car-Parrinello molecular dynamics simulations and EPR property calculations in aqueous ubisemiquinone radical ion. Theoretical Chemistry Accounts, 119, 477-487.

[21]   Asher, J.R. and Kaupp, M. (2007) Hyperfine coupling terms of benzosemiquinone radical anion from the Car-Parrinello molecular dynamics. Chemical Physics, 117, 69-79.

[22]   Asher, J.R., Doltsinis, N.L. and Kaupp, M. (2005) Extended Car-Parrinello molecular dynamics and electronic g-tensors study of benzoquinone radical. Magnetic Resonance in Chemistry, 43, 237-247. doi:10.1002/mrc.1669

[23]   Matta, C.F. (2010) Quantum biochemistry. Wiley-VCH Verlag, Weinheim. doi:10.1002/9783527629213

[24]   Freeman, R. (1988) A handbook of nuclear magnetic resonance. Longman Science & Technical Publishing, London.

[25]   Koptyug, I.V., Sluggett, G.W., Ghatlia, N.D., Landis, M.S., Turro, N.J., Ganapathy, S. and Bentrude, W.G. (2000) Magnetic field dependence of the 31P CIDNP in the photolysis of a benzyl phosphate. Evidence for a T--S mechanism. The Journal of Physical Chemistry, 100, 14581-14583. doi:10.1021/jp9619705

[26]   Solov’ev, I.A. and Schulten, K. (2009) Magnetoreception through cryptochrome may involve superoxide. Biophysical Journal, 96, 4804-4813.

[27]   Prabhakar, R., Siegban, P.E.M., Minaev, B.F. and Agren, H. (2002) Activation of triplet dioxygen by glucose oxidase: Spin-orbit coupling in the superoxide ion. The Journal of Physical Chemistry, 106, 3742-3750

[28]   Van Santen, R.A. and Saulet, P. (2009) Computational methods in catalysis and materials science. Wiley-VCH Verlag, Amsterdam. doi:10.1002/9783527625482

[29]   Hutter, J. and Curioni, A. (2005) Car-Parrinello molecular dynamics on massively parallel computers. A European Journal of Chemical Physics and Physical Chemistry, 1, 1-12.

[30]   Rapacioli, M., Barthel, R., Heine, T. and Seifert, G. (2007) Car-Parrinello treatment for an approximate density-functional theory method. Journal of Chemical Physics, 126, 124103-115. doi:10.1063/1.2566510

[31]   Allsopp, N., Follows, J. and Hennecke, M. (2005) Unfolding the IBM & server blue gene solutions. International Business Machines Corporation, IBM Redbooks.

[32]   Doltsinis, N.L. and Marx, D. (2002) Non-adiabatic Car-Parrinello dynamics. Physical Review Letters, 88, 166402-1-4. doi:10.1103/PhysRevLett.88.166402

[33]   Marcus, R.A. (1982) Electron, proton and coupled transfers. Faraday Discussions of the Chemical Society, 74, 7-15. doi:10.1039/dc9827400007

[34]   Reece, S. T. and Nocera, D.C. (2009) Proton-coupled electron transfer in biology. Annual Review of Biochemistry, 78, 673-699. doi:10.1146/annurev.biochem.78.080207.092132

[35]   Kumar, A. and Sevilla, M.D. (2010) Proton-coupled transfer in DNA on formation of radiation-produced radicals. Chemical Reviews, 10, 1021-1043.

[36]   Hammes-Schiffer, S. (2009) Theory of proton-coupled electron transfer in energy conversion processes. Accounts of Chemical Research, 42, 1881-1889. doi:10.1021/ar9001284

[37]   Mayer, J.M. and Rhile, I.J. (2004) Thermodynamics and kinetics of proton-coupled electron transfer: stepwise vs concerted pathways. Biochimica et Biophysica Acta, 16, 51-58.

[38]   Goez, M. (1997) Photochemically induced dynamic nuclear polarization, Advances in Photochemistry, 23, 63-163. doi:10.1002/9780470133545.ch2

[39]   Nakagura, S. and Hyashi, H. (2004) Dynamic spin chemistry. John Wiley & Sons, New York.

[40]   Jones, J.A. and Hore, P.J. (2010) Spin-selective reactions of radical pairs act as quantum measurements. Chemical Physics Letters, 488, 90-93 doi:10.1016/j.cplett.2010.01.063

[41]   Lee, J.J., Oka, T. and Hirada, T. (2010) OH radical in water studied by quantum beats on positron annihilation—The effect of water liquid structures. Journal of Physics: Conference Series, 1, 225-228.

[42]   Wu, Y., Mundy, C.J., Colvin, M.E. and Car, R. (2004) On the mechanism of OH radical induced DNA-base damage: a comparative quantum chemical and Car-Parrinello molecular dynamics study. The Journal of Physical Chemistry A, 108, 2922-2929. doi:10.1021/jp0363592

[43]   Tulub, A.A. (2007) Triplet-singlet spin communication between DNA nucleotides serves the basis for quantum computing. Chemical Physics Letters, 436, 258-262. doi:10.1016/j.cplett.2007.01.054

[44]   Fox-Beyer, B.S., Sun, Z., Balteanu, I., Balay, O.P. and Beyer, M.K. (2005) Hydrogen formatin in the reaction of Zn(H2O)n with HCl. Physical Chemistry Chemical Physics, 7, 981-985.

[45]   Pavlov, M., Siegban, P.E.M. and Sandstrom, M. (1998) Hydration of beryllium, magnesium, calcium, and zinc ions using density functional theory. The Journal of Physical Chemistry A, 102, 219-228. doi:10.1021/jp972072r

[46]   Sobolewski, A.L. and Domcke, W. (2004) Ab initio studies on the photophysics of the guanine-cytosine base pair. Physical Chemistry Chemical Physics, 6, 2763-2771.

[47]   Ohno, K., Esfarjani, K. and Kawazoe, Y. (1999) Computational materials science. From ab initio to Monte Carlo Methods. Springer-Verlag, Berlin.

[48]   Tulub, A.A. (2004) Activation of tubulin assembly into microtubules upon a series of repeated femtosecond laser impulses. Journal of Chemical Physics, 121, 11345- 11350. doi:10.1063/1.1814056

 
 
Top