Distance-dependent coherent charge transport in DNA: crossover from tunneling to free propagation

Natallia V. Grib, Dmitry A. Ryndyk, Rafael Gutiérrez, Gianaurelio Cuniberti

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DOI: 10.4236/jbpc.2010.12010                

Abstract

Using a tight-binding model, we investigate the influence of intra- and interstand coupling parameters on the charge transport properties in a G-(T)j-GGG DNA sequence and its (G:C)-(T:A)j-(G:C)3 duplex attached to four electrodes. Dependences of the transmission function and of the corresponding conductance of the system on the number of bridging sites were obtained. Simulation results of a recently proposed two-strand superexchange (tunneling) model were reproduced and extended. It is demonstrated that the crossover from strong to weak distance-dependent charge transport is elucidated by a transition from under-barrier tunneling mechanism to free over-barrier propagation in the coherent regime, controlled by temperature and coupling parameters. The role of DNA- electrode coupling has been also considered. It was found that an asymmetry in the DNA-electrode coupling has a drastic effect on the con-ductance leading to an increase in delocaliza-tion of the electronic states in the DNA duplex.

Keywords

DNA; Electron Transport; Modeling of DNA; Electronic Structure of DNA

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Arkin, M.R., Stemp, E.D.A., Holmlin, R.E., Barton, J.K., H?rmann, A., Olson, E.J.C. and Barbara, P.F. (1996) Rates of DNA-mediated electron transfer between metallointer- calators. Science, 273(5274), 475-480.
[2]	Dandliker, P.J., Nú?ez, M.E. and Barton, J.K. (1998) Oxidative charge transfer to repair thymine dimers and damage guanine bases in DNA assemblies containing tethered metallointercalators. Biochemistry, 37(18), 6491- 6502.
[3]	Rajski, S.R., Jackson, B.A. and Barton, J.K. (2000) DNA repair: models for damage and mismatch recognition. Mutation Research, 447(1), 49-72.
[4]	Grib, N.V., Berashevich, J.A. and Borisenko, V.E. (2006) Equivalent electrical network of the DNA molecule. Russian Microelectronics, 35(6), 398-404.
[5]	Bhalla, V., Bajpai, R.P. and Bharadwaj, L.M. (2003) DNA electronics. European Molecular Biology Organization Reports, 4(5), 442-445.
[6]	Niemeyer, C.M. and Adler, M. (2002) Nanomechanical devices based on DNA. Angewandte Chemie Interna- tional Edition, 41(20), 3779-3783.
[7]	Parker, J. (2003) Computing with DNA. European Mole- cular Biology Organization Reports, 4(1), 7-10.
[8]	Rauhe, H., Vopper, G., Feldkamp, U., Banzhaf, W. and Howard, J.C. (2000) Digital DNA molecules. Proceedings of 6th DIMACS Workshop on DNA Based Computers, Leiden, 13-17 June 2000, 1-10.
[9]	Jortner, J., Bixon, M., Langenbacher, T. and Michel- Beyerle, M.E. (1998) Charge transfer and transport in DNA. Proceedings of the National Academy of Sciences of the United States of America, 95(22), 12759-12765.
[10]	Berlin, Y.A., Burin, A.L. and Ranter, M.A. (2000) On the long-range charge transfer in DNA. Journal of Physical Chemistry A, 104(3), 443-445.
[11]	Lewis, F.D., Wu, T., Zhang, Y., Letsinger, R.L., Gree- nfield, S.R. and Wasielewski, M.R. (1997) Distance- dependent electron transfer in DNA hairpins. Science, 277(5326), 673-676.
[12]	Porath, D., Cuniberti, G. and Di Felice, R. (2004) Charge transport in DNA-based devices. Topics in Current Che- mistry, 237, 183-227.
[13]	Gutierrez, R., Porath, D., Cuniberti, G. and Baranowski, S. (2006) Charge transport in disordered solids with app- lications in electronics. John Wiley & Sons Inc., Hoboken.
[14]	Porath, D., Bezryadin, A., De Vries, S. and Dekker, C. (2000) Direct measurement of electrical transport through DNA molecules. Nature, 403(6670), 635-638.
[15]	Xu, B., Zhang, P., Li, X. and Tao, N. (2004) Direct conductance measurement of single DNA molecules in aqueous solution. Nano Letters, 4(6), 1105-1108.
[16]	Cohen, H., Nogues, C., Naaman, R. and Porath, D. (2005) Direct measurement of electrical transport through single DNA molecules of complex sequence. Proceedings of the National Academy of Sciences of the United States of America, 102(33), 11589-11593.
[17]	Cohen, H., Nogues, C., Ullien, D., Daube, S., Naaman, R. and Porath, D. (2006) Electrical characterization of self- assembled single- and double-stranded DNA monolayers using conductive AFM. Faraday Discussions, 131, 367- 376.
[18]	Shapir, E., Cohen, H., Calzolari, A., Cavazzoni, C., Ryn- dyk, D.A., Cuniberti, G., Kotlyar, A.B., Di Felice, R. and Porath, D. (2008) Electronic structure of single DNA mo- lecules resolved by transverse scanning tunnelling spec- troscopy. Nature Materials, 7(1), 68-74.
[19]	Yu, Z.G. and Song, X. (2001) Variable range hopping and electrical conductivity along the DNA double helix. Phy- sical Review Letters, 86(26), 6018-6021.
[20]	Renger, T. and Marcus, R.A. (2003) Variable-range hop- ping electron transfer through disordered bridge states: Application to DNA. Journal of Physical Chemistry A, 107(41), 8404-8419.
[21]	Cuniberti, G., Craco, L., Porath, D. and Dekker, C. (2002) Backbone-induced semiconducting behavior in short DNA wires. Physical Review B, 65(24), (241314)1-4.
[22]	Roche, S. (2003) Sequence dependent DNA-mediated conduction. Physical Review Letters, 91(10), (108101)1-4.
[23]	Wang, H., Lewis, J.P. and Sankey, O.F. (2004) Band-gap tunneling states in DNA. Physical Review Letters, 93(1), (016401)1-4.
[24]	Zhang, W. and Ulloa, S.E. (2004) Extended states in disordered systems: Role of off-diagonal correlations. Physical Review B, 69(15), (153203)1-4.
[25]	Cuenda, S. and Sanchez, A. (2004) Disorder and fluc- tuations in nonlinear excitations in DNA. Fluctuation and Noise Letters, 4(3), L491-L504.
[26]	Fialko, N.S. and Lakhno, V.D. (2000) Nonlinear dyna- mics of excitations in DNA. Physical Letters A, 278(2), 108-111.
[27]	Wang, X.F. and Chakraborty, T. (2006) Charge transfer via a two-strand superexchange bridge in DNA. Physical Review Letters, 97(10), (106602)1-4.
[28]	Giese, B., Amaudrut, J., K?hler, A.-K., Spormann, M. and Wessely, S. (2001) Direct observation of hole transfer through DNA by hopping between adenine bases and by tunnelling. Nature, 412(6844), 318-320.
[29]	Lewis, F.D., Zhu, H., Daublain, P., Cohen, B. and Was- ielewski, M.R. (2006) Hole mobility in DNA A tracts. Angewandte Chemie International Edition, 45(47), 7982- 7985.
[30]	Treadway, C.R., Hill, M.G. and Barton, J.K. (2002) Charge transport through a molecular π-stack: Double helical DNA. Chemical Physics, 281(2-3), 409-428.
[31]	Seidel, A.M., Schulz, A. and Sauer, H.M. (1996) Nucl- eobase-specific quenching of fluorescent dyes. 1. Nucl- eobase one-electron redox potentials and their correlation with static and dynamic quenching efficiencies. Journal of Physical Chemistry, 100(13), 5541-5553.
[32]	Gutiérrez, R., Mandal, S. and Cuniberti, G. (2005) Dis- sipative effects in the electronic transport through DNA molecular wires. Physical Review B, 71(23), (235116)1-9.
[33]	Sugiyama, H. and Saito, I. (1996) Theoretical studies of GG-specific photocleavage of DNA via electron transfer: significant lowering of ionization potential and 5’-local- ization of HOMO of stacked GG bases in B-form DNA. Journal of the American Chemical Society, 118(30), 7063- 7068.
[34]	Endres, R.G., Cox, D.L. and Singh, R.R.P. (2004) Collo- quium: The quest for high-conductance DNA. Reviews of Modern Physics, 76(1), 195-214.
[35]	Senthilkumar, K., Grozema, F.C., Guerra, C.F, Bickel- haupt, F.M., Lewis, F.D., Berlin, Y.A., Ratner, M.A. and Siebbeles, L.D.A. (2005) Absolute rates of hole transfer in DNA. Journal of the American Chemical Society, 127(42), 14894-14903.
[36]	Nitzan, A., Jortner, J., Wilkie, J., Burin, A.L. and Ratner, M.A. (2000) Tunneling time for electron transfer reactions. Journal of Physical Chemistry B, 104(24), 5661-5665.
[37]	Macia, E., Triozon, F. and Roche, S. (2005) Contact- dependent effects and tunneling currents in DNA mole- cules. Physical Review B, 71(11), (113106)1-4.
[38]	Williams, T.T., Odon, D.T. and Barton, J.K. (2000) Vari- ations in DNA charge transport with nucleotide compo- sition and sequence. Journal of the American Chemical Society, 122(37), 9048-9049.
[39]	Sartor, V., Boone, E. and Schuster, G.B. (2001) Long- distance radical cation migration through A/T base pairs in DNA: An experimental test of theory. Journal of Phy- sical Chemistry B, 105(45), 11057-11059.
[40]	De Pablo, P.J., Moreno-Herrero, F., Colchero, J., Gomez- Herrero, J., Herrero, P., Baro, A.M., Ordejon, P., Soler, J.M. and Artacho, E. (2000) Absence of dc-conductivity in λ-DNA. Physical Review Letters, 85(23), 4992-4995.
[41]	Segal, D., Nitzan, A., Davis, W.B., Wasielewski, M.R. and Ratner, M.A. (2000) Electron transfer rates in bridged molecular systems 2. A steady-state analysis of coherent tunneling and thermal transitions. Journal of Physical Chemistry B, 104(16), 3817-3829.
[42]	Valis, L., Wang, Q., Raytchev, M., Buchvarov, I., Wagen- knecth, H.A. and Fiebig, T. (2006) Base pair motions control the rates and distance dependencies of reductive and oxidative DNA charge transfer. Proceedings of the National Academy of Sciences of the United States of America, 103(27), 10192-10195.
[43]	Voityuk, A.A. (2005) Charge transfer in DNA: Hole charge is confined to a single base pair due to solvation effects. Journal of Chemical Physics, 122(20), (204904)1-4.
[44]	Davies, O.R. and Inglesfield, J.E. (2004) Embedding me- thod for conductance of DNA. Physical Review B, 69, (195110)1-4.
[45]	Gutierrez, R., Mohapatra, S., Cohen, H., Porath, D. and Cuniberti, G. (2006) Inelastic quantum transport in a lad- der model: Implications for DNA conduction and com- parison to experiments on suspended DNA oligomers. Physical Review B, 74(23), (235105)1-10.