Abstract
The paper examines thedynamical behavior of a radical cation(G+*) generated in adouble stranded DNA for differentoligonucleotide sequences. The resonancehole tunneling through an oligonucleotidesequence is studied by the method ofnumerical integration of self-consistentquantum-mechanical equations. The holemotion is considered quantum mechanicallyand nucleotide base oscillations aretreated classically. The results obtaineddemonstrate a strong dependence of chargetransfer on the type of nucleotidesequence. The rates of the hole transferare calculated for different nucleotidesequences and compared with experimentaldata on the transfer from (G+*)to a GGG unit.
Keywords: Hopping, nucleotide pair, superexchange, tunneling
Full Text
The Full Text of this article is available as a PDF (449.7 KB).
References
- 1.Meggers E., Michel-Beyerle M.E., Giese B.J. Sequence Dependent Long Range Hole Transport in DNA. J. Am. Chem. Soc. 1998;120:12950–12955. [Google Scholar]
- 2.Henderson P.T., Jones D., Hampikian G., Kan Y., Schuster G.B. Long-Distance Charge Transport in Duplex DNA: The Phonon-Assisted Polaron-Like Hopping Mechanism. Proc. Natl. Acad. Sci. USA. 1999;96:8353–8358. doi: 10.1073/pnas.96.15.8353. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Ly D., Sanii L., Schuster G.B. Mechanism of Charge Transport in DNA: Internally-Linked Anthraquinone Conjugates Support Phonon-Assisted Polaron Hopping. J. Am. Chem. Soc. 1999;121:9400–9410. [Google Scholar]
- 4.Dekker C., Ratner M.A. Electronic Properties of DNA. Phys. World. 2001;14:29–33. [Google Scholar]
- 5.Fink H.W., Schönenberger C. Electrical Conduction through DNA Molecules. Nature. 1999;398:407–410. doi: 10.1038/18855. [DOI] [PubMed] [Google Scholar]
- 6.Tran P., Alavi B., Gruner G. Charge Transport along the λ-DNA Double Helix. Phys. Rev. Lett. 2000;85:1564–1567. doi: 10.1103/PhysRevLett.85.1564. [DOI] [PubMed] [Google Scholar]
- 7.Porath D., Bezryadin A., de Vries S., Dekker C. Direct Measurement of Electrical Transport through DNA Molecules. Nature. 2000;403:635–638. doi: 10.1038/35001029. [DOI] [PubMed] [Google Scholar]
- 8.Mead T.J., Kayyem J.F. Electron Transfer through DNA Site-Specific Modification of Duplex DNA with Ruthenium Donors and Acceptors. Angew. Chem. Int. Ed. Engl. 1995;34:352–354. [Google Scholar]
- 9.Murphy C.J., Arkin M.R., Jenkins Y., Ghatlia N.D., Bossman S., Turro N.J., Barton J.K. Long-Range Photo-Induced Electron Transfer through a DNA Helix. Science. 1993;262:1025–1029. doi: 10.1126/science.7802858. [DOI] [PubMed] [Google Scholar]
- 10.Ratner M. Electronic Motion in DNA. Nature. 1999;397:480–481. doi: 10.1038/17232. [DOI] [PubMed] [Google Scholar]
- 11.Tubiana M., Dutreux J., Wambersie A. Introduction to Radiobiology. London: Taylor and Franeis; 1990. [Google Scholar]
- 12.Frenkel K. Carcinogen-Mediated Oxidant Formation and Oxidative DNA Damage. Pharmacol. Ther. 1992;53:127–166. doi: 10.1016/0163-7258(92)90047-4. [DOI] [PubMed] [Google Scholar]
- 13.Ames B.N., Shigenaga M.K., Hagen T.M. Oxidants, Antioxidants and the Degenerative Diseases of Aging. Proc. Natl. Acad. Sci. USA. 1993;90:7915–7922. doi: 10.1073/pnas.90.17.7915. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Cadet, J. DNA Damage Caused by Oxidation, Diminution, Ultraviolet Radiation and Photoexcited Psoralens, In: K. Hemminki, A. Pipple, D.E.G. Shuker, F.F. Kadlubar, D. Segerbäck and H. Bartsch (eds.), Dan's DNA Adducts: Identification and Biological Significance, International Agency for Research on Cancer, Lyon, France, IARC Scientific Publications, 125(1994), pp. 245–276. [PubMed]
- 15.Loft S., Poulsen H.E. Cancer Risk and Oxidative DNA Damage in Man. J. Mol. Med. 1996;74:297–312. doi: 10.1007/BF00207507. [DOI] [PubMed] [Google Scholar]
- 16.Gros, F., Tubiana, M., Sarasin, A., Masse, R., Maustacchi, E., Früry-Herard, A. and Rosa, J. (eds.), Colloque 'Risques concerogenes dus aux raycnnements-ionisants', C.R. Acad. Sci. Paris322, Ser III (1999), pp. 81–256.
- 17.Demple B., Harrison L. Repair of Oxidative Damage of DNA: Enzymology and Biology. Annu. Rev. Biochem. 1994;63:915–948. doi: 10.1146/annurev.bi.63.070194.004411. [DOI] [PubMed] [Google Scholar]
- 18.Eley D.D., Spivey D.I. Semiconductivity of Organic Substances. Trans. Faraday Soc. 1962;58:411–415. [Google Scholar]
- 19.Davydov A.S. Solitons and Energy Transfer along ProteinMolecules. J. Theor. Biol. 1977;66:379–387. doi: 10.1016/0022-5193(77)90178-3. [DOI] [PubMed] [Google Scholar]
- 20.Davydov A.S. The Theory of Contraction of Proteins under their Excitation. J. Theor. Biol. 1973;38:559–569. doi: 10.1016/0022-5193(73)90256-7. [DOI] [PubMed] [Google Scholar]
- 21.Scott A. Davydov's Soliton. Phys. Rep. 1992;217:1–68. [Google Scholar]
- 22.Lewis F.D., Wu Y. Dynamics of Superexchange Photoinduced Electron Transfer in Duplex DNA. J. Photochem. Photobiol. 2001;2:1–16. [Google Scholar]
- 23.Voityuk A.A., Rösch N., Bixon M., Jortner J. Electronic Coupling for Charge Transfer and Transport in DNA. J. Phys. Chem. 2000;104:9740–9745. [Google Scholar]
- 24.Borer P.N., Laplante S.R., Kumar A., Zanatta N., Martin A., Hakkinen A., Levy G. C-NMR Relaxation in Three DNA Oligonucleotide Duplexes: Model-Free Analysis of Internal and Overall Motion. Biochemistry. 1994;33:2441–2450. doi: 10.1021/bi00175a012. [DOI] [PubMed] [Google Scholar]
- 25.Grozema F.C., Berlin Y.A., Siebbeles L.D.A. Mechanism of Change Migration through DNA: Molecular Wire Behavior, Single-Step Tunneling or Hopping? J. Am. Chem. Soc. 2000;122:10903–10909. [Google Scholar]
- 26.Grozema F.C., Berlin Y.A., Siebbeles L.D.A. Sequence-Dependent Charge Transfer in Donor-DNA-Acceptor Systems: A Theoretical Study. Int. J. Quant. Chem. 1999;75:1009–1016. [Google Scholar]
- 27.Peyrard, M. and Bishop, A.R. Statistical Mechanics of a Nonlenear Model for DNA Denaturation, Phys. Rev. Lett. 62 (1989), 2755–2758. [DOI] [PubMed]