Ponomarev O.A., Shigaev A.S., Zhukov A.I., Lakhno V.D.
Hole Conductivity in Heterogeneous DNA Fragments
Mathematical Biology & Bioinformatics. 2013;8(1):135-160.
doi: 10.17537/2013.8.135.
References
- Dekker C, Ratner MA. Electronic properties of DNA. Physics World. 2001;14(8):29-33.
- Giese B. Electron transfer in DNA. Current Opinion in Chemical Biology. 2002;6:612-618. doi: 10.1016/S1367-5931(02)00364-2
- Lakhno VD. DNA Nanobioelectronics. International Journal of Quantum Chemistry. 2008;108:1970-1981. doi: 10.1002/qua.21717
- Triberis GP, Dimakogianni M. DNA in the material world: electrical properties and nano-applications. Recent Patents on Nanotechnology. 2009;3:135-153. doi: 10.2174/187221009788490040
- Eley DD, Spivey DI. Semiconductivity of organic substances. Part 9. Nucleic acid in the dry state. Transactions of the Faraday Society. 1962;58:411- 415. doi: 10.1039/tf9625800411
- Kawanishi S, Hiraku Y, Oikawa S. Mechanism of guanine- specific DNA damage by oxidative stress and its role in carcinogenesis and aging. Mutation Research. 2001;488:65-76. doi: 10.1016/S1383-5742(00)00059-4
- Wagenknecht H-A. Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics. Natural Product Reports. 2006;23:973- 1006. doi: 10.1039/b504754b
- Genereux JC, Boal AK, Barton JK. DNA-mediated Charge Transport in Redox Sensing and Signaling. Journal of American Chemical Society. 2010;132:891-905. doi: 10.1021/ja907669c
- Sontz PA, Mui TP, Fuss JO, Tainer JA, Barton JK. DNA charge transport as a first step in coordinating the detection of lesions by repair proteins. Proc. Natl. Acad. Sci. USA. 2012;109:1856-1861. doi: 10.1073/pnas.1120063109
- Sontz PA, Muren NB, Barton JK. DNA Charge Transport for Sensing and Signaling. Accounts of Chemical Research. 2012;45:1792-1800. doi: 10.1021/ar3001298
- Becker D, Sevilla MD. The chemical consequences of radiation damage to DNA. Advances in Radiation Biology. 1993;17:121-180. doi: 10.1016/B978-0-12-035417-7.50006-4
- Sies H, Schulz WA, Steenken S. Adjacent guanines as preferred sites for strand breaks in plasmid DNA irradiated with 193 nm and 248 nm UV laser light. Journal of Photochemistry and Photobiology B. 1996;32:97-102. doi: 10.1016/1011-1344(95)07192-X
- Conwell EM. Charge transport in DNA in solution: The role of polarons. Proc. Natl. Acad. Sci. USA. 2005;102:8795-8799. doi: 10.1073/pnas.0501406102
- Kino K, Sugiyama H. Possible cause of G-C→C-G transversion mutation by guanine oxidation product, imidazolone. Chemistry & Biology. 2001;8:369-378.
- Armitage B. Photocleavage of Nucleic Acids. Chemical Reviews. 1998;98:1171-1200. doi: 10.1021/cr960428+
- Joy A, Ghosh AK, Schuster GB. One-Electron Oxidation of DNA Oligomers That Lack Guanine: Reaction and Strand Cleavage at Remote Thymines by Long-Distance Radical Cation Hopping. Journal of American Chemical Society. 2006;128:5346-5347. doi: 10.1021/ja058758b
- Seidel CAM, Schulz A, Sauer MHM. Nucleobase-Specific Quenching of Fluorescent Dyes. 1. Nucleobase One-Electron Redox Potentials and Their Correlation with Static and Dynamic Quenching Efficiencies. Journal of Physical Chemistry B. 1996;100:5541-5553. doi: 10.1021/jp951507c
- Lewis FD, Wu Y. Dynamics of superexchange photoinduced electron transfer in duplex DNA. Journal of Photochemistry and Photobiology C: Photochemistry Reviews. 2001;2:1-16. doi: 10.1016/S1389-5567(01)00008-9
- Porath D, Bezryadin A, Vries S, Dekker C. Direct measurement of electrical transport through DNA molecules. Nature (London). 2000;403:635-638. doi: 10.1038/35001029
- de Pablo PJ, Moreno-Herrero F, Colchero J, Herrero JG, Herrero P, Baro AM, Ordejon P, Soler JM, Artacho E. Absence of dc-Conductivity in lambda-DNA. Physical Review Letters. 2000;85:4992-4995. doi: 10.1103/PhysRevLett.85.4992
- Fink H-W, Schonenberger C. Electrical conduction through DNA molecules. Nature (London). 1999;398:407-410. doi: 10.1038/18855
- Kasumov AY, Kociak M, Gueron S, Reulet B, Volkov VT, Klinov DV, Bouchiat H. Proximity-induced superconductivity in DNA. Science. 2001;291:280-282. doi: 10.1126/science.291.5502.280
- Shikhovtseva ES, Ponomarev OA. The a-c field influence on conductive channels formation in thread-like structure polymers. Physica A: Statistical Mechanics and its Applications. 1996;231:484-494. doi: 10.1016/0378-4371(96)00100-8
- Yoo K-H, Ha DH, Lee J-O, Park JW, Kim J, Kim JJ, Lee H- Y, Kawai T, Choi HY. Electrical Conduction through Poly(dA)-Poly(dT) and Poly(dG)-Poly(dC) DNA Molecules. Physical Review Letters. 2001;87:198102. doi: 10.1103/PhysRevLett.87.198102
- Schmidt BB, Hettler MH, Schon G. Nonequilibrium polaron hopping transport through DNA. Physical Review B. 2008;77:165337. doi: 10.1103/PhysRevB.77.165337
- Slinker JD, Muren NB, Gorodetsky AA, Barton JK. Multiplexed DNA-modified electrodes. Journal of American Chemical Society. 2010;132:2769-2774. doi: 10.1021/ja909915m
- Slinker JD, Muren NB, Renfrew SE, Barton JK. DNA charge transport over 34 nm. Nature Chemistry. 2011;3:228-233. doi: 10.1038/nchem.982
- Cohen H, Nogues C, Ullien D, Daube S, Naaman Ro, Porath D. Electrical characterization of self-assembled single- and double-stranded DNA monolayers using conductive AFM. Faraday Discussions. 2006;131:367-376. doi: 10.1039/B507706K
- Giese B, Biland A. Recent developments of charge injection and charge transfer in DNA. Chemical Communications. 2002;7:667-672. doi: 10.1039/b111044f
- Murphy CJ, Arkin MR, Jenkins Y, Ghatlia ND, Bossmann SH, Turro NJ, Barton JK. Long-range photoinduced electron transfer through a DNA helix. Science. 1993;262:1025-1029. doi: 10.1126/science.7802858
- Brun AM, Harriman AJ. Dynamics of electron transfer between intercalated polycyclic molecules: effect of interspersed bases. Journal of American Chemical Society. 1992;114:3656-3660. doi: 10.1021/ja00036a013
- Giese B, Wessely S, Spormann M, Lindemann U, Meggers E, Michel-Beyerle ME. On the Mechanism of Long-Range Electron Transfer through DNA. Angewandte Chemie International Edition in English. 1999;38:996-998. doi: 10.1002/(SICI)1521-3773(19990401)38:7<996::AID-ANIE996>3.0.CO;2-4
- Meggers E, Michel-Beyerle ME, Giese B. Sequence Dependent Long Range Hole Transport in DNA. Journal of American Chemical Society. 1998;120:12950-12955. doi: 10.1021/ja983092p
- Jortner J, Bixon M, Langenbacher T, Michel-Beyerle M. Charge transfer and transport in DNA. PNAS. 1998;95:12759-12765. doi: 10.1073/pnas.95.22.12759
- O’Neill MA, Barton JK. DNA Charge Transport: Conformationally Gated Hopping through Stacked Domains. Journal of American Chemical Society. 2004;126:11471-11483. doi: 10.1021/ja048956n
- Genereux JC, Augustyn KE, Davis ML, Shao F, Barton JK. Back-Electron Transfer Suppresses the Periodic Length Dependence of DNA-Mediated Charge Transport across Adenine Tracts. Journal of American Chemical Society. 2008;130:15150-15156. doi: 10.1021/ja8052738
- Lewis FD, Liu X, Liu J, Miller SE, Hayes RT, Wasielewski MR. Direct measurement of hole transport dynamics in DNA. Nature. 2000;406:51-53. doi: 10.1038/35017524
- Lewis FD, Liu X, Liu J, Hayes RT, Wasielewski MR. Dynamics and Equilibria for Oxidation of G, GG, and GGG Sequences in DNA Hairpins. Journal of American Chemical Society. 2000;122:12037-12038. doi: 10.1021/ja002440w
- Lewis FD, Zuo X, Liu J, Hayes RT, Wasielewski MR. Dynamics of Inter- and Intrastrand Hole Transport in DNA Hairpins. Journal of American Chemical Society. 2002;124:4568-4569. doi: 10.1021/ja0177859
- Lewis FD, Liu J, Liu X, Zuo X, Hayes RT, Wasielewski MR. Dynamics and Energetics of Hole Trapping in DNA by 7- Deazaguanine. Angewandte Chemie International Edition. 2002;41:1026-1028. doi: 10.1002/1521-3773(20020315)41:6<1026::AID-ANIE1026>3.0.CO;2-T
- Lewis FD, Liu X, Zuo X, Hayes RT, Wasielewski MR. Dynamics and Energetics of Single-Step Hole Transport in DNA Hairpins. Journal of American Chemical Society. 2003;125:4850-4861. doi: 10.1021/ja029390a
- Shigaev AS, Ponomarev OA, Lakhno VD. A new approach to microscopic modeling of a hole transfer in heteropolymer DNA. Chemical Physics Letters. 2011;513:276-279. doi: 10.1016/j.cplett.2011.07.080
- Kelley SO, Barton JK. Electron transfer between bases in double helical DNA. Science. 1999;283:375-381. doi: 10.1126/science.283.5400.375
- Genereux JC, Wuerth SM, Barton JK. Single-step Charge Transport through DNA over Long Distances. Journal of American Chemical Society. 2011;133:3863-3868. doi: 10.1021/ja107033v
- Mickley Conron SM, Thazhathveetil AK, Wasielewski MR, Burin AL, Lewis FD. Direct Measurement of the Dynamics of Hole Hopping in Extended DNA G-Tracts. An Unbiased Random Walk. Journal of American Chemical Society. 2010;132:14388-14390. doi: 10.1021/ja106991f
- Holstein T. Studies of polaron motion: Part I. The molecular-crystal model. Annals of Physics. 1959;8:325-342. doi: 10.1016/0003-4916(59)90002-8
- Kubo R. Statistical-Mechanical Theory of Irreversible Processes. I. General Theory and Simple Applications to Magnetic and Conduction Problems. Journal of the Physical Society of Japan. 1957;12:570-586. doi: 10.1143/JPSJ.12.570
- Peyrard M, Bishop AR. Statistical Mechanics of a Nonlinear Model for DNA Denaturation. Physical Review Letters. 1989;62:2755-2758. doi: 10.1103/PhysRevLett.62.2755
- Voityuk AA, Rosch N, Bixon M, Jortner J. Electronic Coupling for Charge Transfer and Transport in DNA. Journal of Physical Chemistry B. 2000;104:9740- 9745. doi: 10.1021/jp001109w
- Debije MG, Milano MT, Bernhard WA. DNA Responds to Ionizing Radiation as an Insulator, Not as a “Molecular Wire”. Angewandte Chemie International Edition. 1999;38:2752-2756. doi: 10.1002/(SICI)1521-3773(19990917)38:18<2752::AID-ANIE2752>3.0.CO;2-U
- Lundin U, McKenzie RH. Temperature dependence of polaronic transport through single molecules and quantum dots. Physical Review B. 2002;66:075303. doi: 10.1103/PhysRevB.66.075303
- Lakhno VD, Sychyov VV. Modeling of the hole transfer dynamics in the tetramer GAGG. Biophysics. 2004;49:430-433.
- Kubarev S.I., Ponomarev O.A. The effects of dynamic binding in statistical physics. Moscow: Nauka, 1992. 141 p. (in Russ.).
- Yakushevich LV. Nonlinear DNA dynamics: a new model. Physics Letters A. 1989;136:413-417. doi: 10.1016/0375-9601(89)90425-8
- Dauxois T, Peyrard M, Bishop AR. Entropy-driven DNA denaturation. Physical Review E. 1993;47: R44-R47. doi: 10.1103/PhysRevE.47.R44
- Choi CH, Kalosakas G, Rasmussen KO, Hiromura M, Bishop AR, Usheva A. DNA dynamically directs its own transcription initiation. Nucleic Acids Research. 2004;32:1584- 1590. doi: 10.1093/nar/gkh335
- Kalosakas G, Ransmussen KO, Bishop AR, Choi CH, Usheva A. Sequence-specific thermal fluctuations identify start sites for DNA transcription. Europhysics Letters. 2004;68:127-133. doi: 10.1209/epl/i2004-10167-8
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