Impact of a single base pair substitution on the charge transfer rate along short DNA hairpins

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 37, 2013, Pages 14867-14871

  Renaud, Nicolas ^a   Berlin, Yuri A ^a   Ratner, Mark A ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

Photoinduced hole transfer; Quantum filling; Stochastic surrogate Hamiltonian

Indexed keywords

ADENINE; CYTOSINE; GUANINE; NANOWIRE; NUCLEIC ACID BASE; THYMINE;

ARTICLE; BASE PAIRING; BINDING SITE; CONFORMATIONAL TRANSITION; DENSITY FUNCTIONAL THEORY; DNA HAIRPIN; DNA SEQUENCE; GENE TRANSFER; IONIZATION; MOLECULAR ELECTRONICS; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; QUANTUM YIELD; STATIC ELECTRICITY; STATISTICS;

PHOTOINDUCED HOLE TRANSFER; QUANTUM FILLING; STOCHASTIC SURROGATE HAMILTONIAN;

BASE PAIRING; DNA; MOLECULAR DYNAMICS SIMULATION; NUCLEIC ACID CONFORMATION; STATIC ELECTRICITY; STOCHASTIC PROCESSES;

EID: 84883767584     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1309139110     Document Type: Article

References (58)

1. Wagenknecht H-A, ed (2006) Charge Transfer in DNA: From Theory to Applications (Wiley-VCH, New York).
2. Schuster GB (2004) Long-Range Charge Transfer in DNA I and II, Topics in Current Chemistry (Springer, Berlin Heidelberg), Vols 236 and 237.
3. Siriwong K, Voityuk AA (2012) Electron transfer in DNA. WIREs Comput Mol Sci 2:780-794.
4. Huang YC, Cheng AKH, Yu H-Z, Sen D (2009) Charge conduction properties of a parallel-stranded DNA G-quadruplex: Implications for chromosomal oxidative damage. Biochemistry 48(29):6794-6804.
5. Kanvah S, et al. (2010) Oxidation of DNA: Damage to nucleobases. Acc Chem Res 43(2):280-287.
6. Okamoto A, Tanaka K, Saito I (2003) Rational design of a DNA wire possessing an extremely high hole transport ability. J Am Chem Soc 125(17):5066-5071. (Pubitemid 36520435)
7. Guo X, Gorodetsky A, Hone J, Barton JK, Nuckolls C (2008) Conductivity of a single DNA duplex bridging a carbon nanotube gap. Nat Nanotechnol 3(3):163.
8. Meggers E, Michel-Beyerle ME, Giese B (1998) Sequence dependent long range hole transport. J Am Chem Soc 120(49):12950-12955. (Pubitemid 29013847)
9. Giese B, Amaudrut J, Köhler AK, Spormann M, Wessely S (2001) Direct observation of hole transfer through DNA by hopping between adenine bases and by tunnelling. Nature 412(6844):318-320. (Pubitemid 32691842)
10. Giese B (2004) Hole injection and hole transfer through DNA: The hopping mechanism. Top Curr Chem 130:151-164.
11. Lewis FD, et al. (2000) Direct measurement of hole transport dynamics in DNA. Nature 406(6791):51-53. (Pubitemid 30460205)
12. Lewis FD, et al. (2000) Dynamics of photoinduced charge separation and charge recombination in synthetic DNA hairpins with stilbenedicarboxamide linkers. J Am Chem Soc 122(12):2889-2902. (Pubitemid 30191049)
13. Lewis FD, Letsinger RL, Wasielewski MR (2001) Dynamics of photoinduced charge transfer and hole transport in synthetic DNA hairpins. Acc Chem Res 34(2):159-170. (Pubitemid 32167865)
14. Kawai K, Takada T, Tojo S, Majima T (2003) Kinetics of weak distance-dependent hole transfer in DNA by adenine-hopping mechanism. J Am Chem Soc 125(23):6842-6843. (Pubitemid 36682763)
15. Jortner J, Bixon M, Langenbacher T, Michel-Beyerle ME (1998) Charge transfer and transport in DNA. Proc Natl Acad Sci USA 95(22):12759-12765. (Pubitemid 28509469)
16. Grozema FC, Berlin YA, Siebbeles LDA (2000) Mechanism of charge migration through DNA: Molecular wire behavior, single-step tunneling or hopping? J Am Chem Soc 122(44):10903-10909.
17. Genereux JC, Wuerth SM, Barton JK (2011) Single-step charge transport through DNA over long distances. J Am Chem Soc 133(11):3863-3868.
18. Grozema FC, et al. (2008) Effect of structural dynamics on charge transfer in DNA hairpins. J Am Chem Soc 130(15):5157-5166. (Pubitemid 351537076)
19. Bixon M, Jortner J (2001) Charge transport in DNA via thermally induced hopping. J Am Chem Soc 123(50):12556- 12567.
20. Berlin YA, Burin AL, Ratner MA (2001) Charge hopping in DNA. J Am Chem Soc 123(2):260-268. (Pubitemid 32062167)
21. Renger T, Marcus RA (2003) Variable-range hopping electron transfer through disordered bridge states: Application to DNA. J Phys Chem 107(41):8404-8419.
22. Bixon M, et al. (1999) Long-range charge hopping in DNA. Proc Natl Acad Sci USA 96(21):11713-11716. (Pubitemid 29502797)
23. Berlin Y, Ratner MA(2005) Intra-molecular electron transfer and electric conductance via sequential hopping: Unified theoretical description. Radiat Phys Chem 74(3):124-131. (Pubitemid 41188292)
24. Hess S, Götz M, Davis WB, Michel-Beyerle M-E (2001) On the apparently anomalous distance dependence of charge-transfer rates in 9-amino-6-chloro-2-methoxyacridine-modified DNA. J Am Chem Soc 123(41):10046-10055. (Pubitemid 32959609)
25. Reid GD, et al. (2002) Femtosecond electron-transfer reactions in mono- and polynucleotides and in DNA. J Am Chem Soc 124(19):5518-5527. (Pubitemid 34506951)
26. Lewis FD, et al. (2002) Donor-bridge-acceptor energetics determine the distance dependence of electron tunneling in DNA. Proc Natl Acad Sci USA 99(20):12536-12541.
27. Lewis FD, et al. (2006) Crossover from superexchange to hopping as the mechanism for photoinduced charge transfer in DNA hairpin conjugates. J Am Chem Soc 128(3):791-800. (Pubitemid 43153028)
28. Murphy CJ, et al. (1993) Long-range photoinduced electron transfer through a DNA helix. Science 262(5136):1025-1029. (Pubitemid 24035038)
29. Hall DB, Holmlin RE, Barton JK (1996) Oxidative DNA damage through long-range electron transfer. Nature 382(6593):731-735. (Pubitemid 26282182)
30. Giese B, et al. (1999) On the mechanism of long-range electron transfer through DNA. Angew Chem Int Ed 38(7):996-998. (Pubitemid 29180984)
31. Takada T, et al. (2004) Charge separation in DNA via consecutive adenine hopping. J Am Chem Soc 126(4):1125-1129. (Pubitemid 38140743)
32. Lewis FD, Daublain P, Cohen B, Vura-Weis J, Wasielewski MR (2008) The influence of guanine on DNA hole transport efficiency. Angew Chem Int Ed 47(20):3798-3800.
33. Lewis FD, et al. (2008) Getting to guanine: Mechanism and dynamics of charge separation and charge recombination in DNA revisited. Photochem Photobiol Sci 7(5):534-539. (Pubitemid 351668120)
34. Vura-Weis J, Wasielewski MR, Thazhathveetil AK, Lewis FD (2009) Efficient charge transport in DNA diblock oligomers. J Am Chem Soc 131(28):9722-9727.
35. Thazhathveetil AK, Trifonov A, Wasielewski MR, Lewis FD (2011) Increasing the speed limit for hole transport in DNA. J Am Chem Soc 133(30):11485-11487.
36. Tainaka K, Fujitsuka M, Takada T, Kawai K, Majima T (2010) Sequence dependence of excess electron transfer in DNA. J Phys Chem B 114(45):14657-14663.
37. Kawai K, Kodera H, Majima T (2010) Long-range charge transfer through DNA by replacing adenine with diaminopurine. J Am Chem Soc 132(2):627-630.
38. Hush NS, Cheung S (1975) Ionisation potential and donor properties of nucleic bases and related compounds. Chem Phys Lett 34(1):11-14.
39. Mishra D, Pal S (2009) Ionization potential and structure relaxation of adenine, thymine, guanine and cytosine bases and their base pairs: A quantification of reactive sites. J Mol Struct Theochem 902(1-3):96-102.
40. Bar-Haim A, Klafter J (1998) On mean residence and first passage times in finite one-dimensional systems. J Chem Phys 109(13):5187-5193. (Pubitemid 128678689)
41. Senthilkumar K, et al. (2005) Absolute rates of hole transfer in DNA. J Am Chem Soc 127(42):14894-14903. (Pubitemid 41511028)
42. Conwell EM, Rakhmanova SV (2000) Polarons in DNA. Proc Natl Acad Sci USA 97(9):4556-4560. (Pubitemid 30238596)
43. Shao F, O'Neill MA, Barton JK (2004) Long-range oxidative damage to cytosines in duplex DNA. Proc Natl Acad Sci USA 101(52):17914-17919. (Pubitemid 40054049)
44. Henderson PT, Jones D, Hampikian G, Kan Y, Schuster GB (1999) Long-distance charge transport in duplex DNA: The phonon-assisted polaron-like hopping mechanism. Proc Natl Acad Sci USA 96(15):8353-8358. (Pubitemid 29354795)
45. Grozema FC, Siebbeles LDA, Berlin YA, Ratner MA (2002) Hole mobility in DNA: Effects of static and dynamic structural fluctuations. ChemPhysChem 3(6):536-539.
46. Grozema FC, et al. (2009) Effect of GC base pairs on charge transfer through DNA hairpins: The importance of electrostatic interactions. J Am Chem Soc 131(40):14204-14205.
47. Renaud N, Berlin YA, Lewis FD, Ratner MA (2013) Between superexchange and hopping: An intermediate charge-transfer mechanism in poly(A)-poly(T) DNA hairpins. J Am Chem Soc 135(10):3953-3963.
48. O'Neill MA, Barton JK (2004) DNA charge transport: Conformationally gated hopping through stacked domains. J Am Chem Soc 126(37):11471-11483. (Pubitemid 39244963)
49. Barnett RN, Cleveland CL, Joy A, Landman U, Schuster GB (2001) Charge migration in DNA: Ion-gated transport. Science 294(5542):567-571. (Pubitemid 32999548)
50. Voityuk AA, Siriwong K, Rosch N (2001) Charge transfer in DNA. Sensitivity of electronic couplings to conformational changes. Phys Chem Chem Phys 3(24):5421-5425.
51. Katz G, Gelman D, Ratner MA, Kosloff R (2008) Stochastic surrogate Hamiltonian. J Chem Phys 129(3):034108.
52. Katz G, Ratner MA, Kosloff R (2010) Control by decoherence: Weak field control of an excited state objective. New J Phys 12:015003.
53. Renaud N, Ratner MA, Mujica V (2011) A stochastic surrogate Hamiltonian approach of coherent and incoherent exciton transport in the Fenna-Matthews-Olson complex. J Chem Phys 135(7):075102.
54. Renaud N, et al. (2012) Quantum interferences and electron transfer in photosystem I. J Phys Chem A 117(29):5899-5908.
55. Ouchi M, Badi N, Lutz J-F, Sawamoto M (2011) Single-chain technology using discrete synthetic macromolecules. Nat Chem 3(12):917-924.
56. Sergeyev S, Pisula W, Geerts YH (2007) Discotic liquid crystals: A new generation of organic semiconductors. Chem Soc Rev 36(12):1902- 1929.
57. Voityuk AA (2005) Charge transfer in DNA: Hole charge is confined to a single base pair due to solvation effects. J Chem Phys 122(20):204904.
58. Basko DM, Conwell EM (2002) Effect of solvation on hole motion in DNA. Phys Rev Lett 88(9):098102.