A New Mathematical Model for Calculating the Electronic Coupling of a B-DNA Molecule
American Journal of Physical Chemistry
Volume 5, Issue 2, April 2016, Pages: 17-25
Received: Feb. 8, 2016;
Accepted: Feb. 15, 2016;
Published: Mar. 9, 2016
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Dale J. Igram, Center for Computational Nanoscience, Department of Physics and Astronomy, Ball State University, Muncie, IN, USA
Jason W. Ribblett, Department of Chemistry, Ball State University, Muncie, IN, USA
Eric R. Hedin, Center for Computational Nanoscience, Department of Physics and Astronomy, Ball State University, Muncie, IN, USA
Yong S. Joe, Center for Computational Nanoscience, Department of Physics and Astronomy, Ball State University, Muncie, IN, USA
The charge transport properties of DNA have made this molecule very important for use in nanoscale electronics, molecular computing, and biosensoric devices. Early findings have suggested that DNA can behave as a conductor, semiconductor, or an insulator. This variation in electrical behavior is attributed to many factors such as environmental conditions, base sequence, DNA chain length, orientation, temperature, electrode contacts, and fluctuations. To better understand the charge transport characteristics of a DNA molecule, a more thorough understanding of the electronic coupling between base pairs is required. To achieve this goal, two mathematical methods for calculating the electronic interactions between base pairs of a DNA molecule have been developed, which utilize the concepts from Molecular Orbital Theory (MOT) and Electronic Band Structure Theory (EBST). The electronic coupling characteristics of a B-DNA molecule consisting of two Guanine-Cytosine base pairs have been examined for variation in the twist angle between the base pairs, the separation between base pairs, and the separation between base molecules in a given base pair, for both the HOMO and LUMO states. Comparison of results to published literature reveals similar outcomes. The electronic properties (metallic, semi-conducting, insulating) of a B-DNA molecule are also determined.
Dale J. Igram,
Jason W. Ribblett,
Eric R. Hedin,
Yong S. Joe,
A New Mathematical Model for Calculating the Electronic Coupling of a B-DNA Molecule, American Journal of Physical Chemistry.
Vol. 5, No. 2,
2016, pp. 17-25.
M. A. Ratner and J. Jortner, Molecular Electronics, Blackwell, Oxford, UK 1997.
V. Bhalla, R. P. Bajpai, and L.M. Bharadwaj, DNA Electronics, EMBO report 4, 442 – 445 (2003).
C. Mao, T. LaBean, J. H. Reif, and N. C. Seeman, “Logical computation using algorithmic self-assembly of DNA triple-crossover molecules”, Nature, v407, 493 – 496 (2000).
N. C. Seeman, “DNA in a material world”, Nature, v421, 427 – 431 (2003).
C. M. Niemeyer, “Nanoparticles, proteins, and nucleic acids: biotechnology meets materials science”, Angew. Chem. Int. Ed., v40, 4128 – 4158 (2001).
S. J. Park, T. A. Taton, and C. A. Mirkin, “Array-based electrical detection of DNA with nanoparticle probes”, Science, v295, 1503 – 1506 (2002).
S. Steenken, “Purine bases, nucleosides, and nucleotides: aqueous solution redox chemistry and transformation reactions of their radical cations and e- and OH adducts”, Chem. Rev. v89, 503 – 520 (1989).
D. B. Hall and J. K. Barton, “Sensitivity of DNA-mediated electron transfer to the intervening π-stack: A probe for the integrity of the DNA base stack”, J. Am. Chem. Soc., v119, 5045 – 5046 (1997).
H. L Chen and P. Yang, “Progress in the recognition and repair of DNA damage”, Prog. Chem., v14, 239 – 245 (2002).
D. R. Meldrum and M. R. Holl, “Microscale bioanalytical systems”, Science, v297, 1197 – 1198 (2002).
J. Li, D. Stein, C. McMullan, D. Branton, M. J. Aziz, and J. A. Golovchenko, “Ion-beam sculpting at nanometre length scales”, Nature, v412, 166–169 (2001).
D. Wemmer, “Reading DNA”, Nat. Struct. Biol., v5, 169 -171 (1998).
S. F. Nelson, Y. Y Lin, D. J. Gundlach, and T. N. Jackson, “Temperature-independent transport in high-mobility pentacene transistors”, Appl. Phys. Lett. v72, 1854 –1856 (1998).
W. A. Schooneld, J. Vrijmoeth, and T. M. Klapwijk, “Intrinsic charge transport properties of an organic single crystal determined using a multiterminal thin-film transistor”, Appl. Phys. Lett. v73, 3884–3886 (1998).
D. D. Eley, “Organic Semiconductors”, Research, v12, 293–299 (1959).
J. Ladik, “Investigation of the electronic structure of desoxyribonucleic Acid”, Acta Phys. Acad. Sci. Hung., v11, 239 – 257 (1960).
B. Pullmann, and A. Pullmann, “The electronic structure of the purine-pyrimidine pairs of DNA”, Biochim. Biophys. Acta., v36, 343–350 (1959).
D. D. Eley and D. I. Splivey, “Semicondictivity of organic substances”, Trans. Faraday Soc., v58, 411- 415 (1962).
C. J. Murphy, M. R. Arkin, Y. Jenkins, N. D. Ghatlia, S. H. Bossmann, N. J. Turro, and J. K. Barton, “Long-range photoinduced electron transfer through a DNA helix”, Science, v262, 1025-1029 (1993).
M. R. Arkin, E. D. A. Stemp, R. E. Holmlin, J. K. Barton, A. Hormann, E. J. C. Olson, and P. F. Barbara, “Rates of DNA-mediated electron transfer between metallointercalators”, Science, v273, 475-480 (1996).
C. J. Murphy, M. R. Arkin, N. D. Ghatlial, S. H. Bossmann, N. J. Turro, and J. K. Barton, “Fast photoinduced electron transfer through DNA intercalation”, Proc. Nat. Acad. Sci. v91, 5315-5319 (1994).
K. Wang, J. M. Hamill, B. Wang, C. Guo, S. Jiang, Z. Huang, and B. Xu, “Structure determined charge transport in single DNA molecule break junctions”, Chem. Science, v5, 3425-3431, (2014).
G. I. Livshits, A. Stern, D. Rotem, N. Borovok, G. Eidelshtein, A. Migliore, E. Penzo, S. J. Wind, R. D. Felice, S. S. Skourtis, J. C. Cuevas, L. Gurevich, A. B. Kotlyar, and D. Porath, “Long-range charge transport in single G-quadruplex DNA molecules”, Nature Nanotech., v9, 1040-1046 (2014).
L. Xiang, J. L. Palma, C. Bruot, V. Mujica, M. A. Ratner, and N. Tao, “Intermediate tunneling-hopping regime in DNA charge transport”, Nature Chem. v7, 221–226 (2015).
E. Braun, Y. Eichen, U. Sivan, and G. Ben-Yoseph, “DNA-templated assembly and electrode attachment of a conducting silver wire”, Nature, v391, 775–778 (1998).
A. J. Storm, J. van Noort, S. De Vries, and C. Dekker, “Insulating behavior for DNA molecules between nanoelectrodes at the 100 nm length scale”, Appl. Phys. Lett., v79, 3881–3883 (2001).
D. Porath, A. Bezryadin, S. de Vries, and C. Dekker, “Direct measurement of electrical transport through DNA molecules”, Nature, v403, 635 – 638 (2000).
H. Cohen, C. Nogues, R. Naaman, and D. Porath, “Direct measurement of electrical transport through single DNA molecules of complex sequence”, Proc. Nat. Acad. Sci., v102, 11589 – 11593 (2005).
H. W. Fink and C. Schönenberger, “Electrical conduction through DNA molecules”, Nature, v398, 407 – 410 (1999).
K. H. Yoo, D. H. Ha, J. O. Lee, J. W. Park, J. Kim, J. J. Kim, H. Y. Lee, T. Kawai, and H. Y. Choi, “Electrical conduction through poly(dA)-poly(dT) and poly(dG)-poly(dC) DNA molecules”, Phys. Rev. Lett. v87, 198102(1-4) (2001).
A.Y. Kasumov, M. Kociak, S. Gueron, B. Reulet, V. T. Volkov, D. V. Klinov, and H. Bouchiat, “Proximity-induced superconductivity in DNA”, Science, v291, 280 – 282 (2001).
R. G. Endres, D. L. Cox, and R. R. P. Singh, “Electronic properties of DNA: structural and chemical influence on the quest for high conductance and charge transfer”, e-print cond-mat/0201404, 1-12, (2002).
R. G. Endres, D. L. Cox, and R. R. P. Singh, “The quest for high-conductance DNA”, Rev. Mod. Phys., v76, 195 – 214 (2004).
J. C. Slater and G. F. Koster, “Simplified LCAO method for the periodic potential problem”, Phys. Rev., v94, 1498 – 1524 (1954).
J. P. Lowe and K. A. Paterson, Quantum Chemistry, Elsevier Academic Press, Burlington, MA, 2006.
A. Streitwieser, Molocular Orbital Theory, John Wiley & Sons, Inc., New York, 1961.
R. S. Mulliken, C. A. Rieke, D. Orloff, and H. Orloff, “Formulas and numerical tables for overlap integrals”, Journal of Chemical Physics, v17, 1248 – 1267 (1949).
N. Rosen, “Calculation of interaction between atoms with s-electrons”, Phys. Rev., v38, 255 – 276 (1931).
W. A. Harrison, Electronic Structure and the Properties of Solids, Dover Publications, Inc., New York, 1989.
M. Menon and R. E. Allen, “Simulations of atomic processes at semiconductor surfaces: General method and chemisorption on GaAs (110)”, Phys. Rev. B, v38, 6196 – 6205 (1988).
O. F. Sankey and R. E. Allen, “Atomic forces from electronic energies via the Hellmann-Feynman theorem with application to semiconductor (110) surface relaxation”. Phys. Rev. B, v33, 7164 – 7171 (1986).
N. Lathiotakis and A. N. Andriotis, “The applicability of scaling laws in tight-binding molecular-dynamics”, Solid State Communications, v87, 871 – 875 (1933).