Effect of DNA flanking sequence on charge transport in short DNA duplexes

Biochemistry

Volumn 45, Issue 45, 2006, Pages 13543-13550

  Li, Xi ^a   Peng, Yinghua ^a   Ren, Jinsong ^a   Qu, Xiaogang ^a  

^a CHANGCHUN INSTITUTE OF APPLIED CHEMISTRY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CHARGE TRANSFER; ENZYME KINETICS; FLUORESCENCE; FREE ENERGY; IONIC STRENGTH; REACTION KINETICS; SYNTHESIS (CHEMICAL);

ACTIVE DRUGS; CHARGE TRANSPORT; ENZYMATIC REPAIR; FLANKING SEQUENCE;

DNA;

DAUNORUBICIN; DOUBLE STRANDED DNA; DOXORUBICIN;

AMINO ACID SEQUENCE; ARTICLE; BASE MISPAIRING; CIRCULAR DICHROISM; CROSS LINKING; CYCLIC POTENTIOMETRY; DNA CONFORMATION; DNA FLANKING REGION; DNA SYNTHESIS; FLUORESCENCE; ION TRANSPORT; IONIC STRENGTH; MELTING POINT; OXIDATION REDUCTION REACTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; TRANSPORT KINETICS; ULTRAVIOLET RADIATION;

BASE SEQUENCE; CROSS-LINKING REAGENTS; DAUNORUBICIN; DNA; DOXORUBICIN; ELECTROCHEMISTRY; NUCLEIC ACID HETERODUPLEXES; OSMOLAR CONCENTRATION; SPECTROMETRY, FLUORESCENCE; SPECTROPHOTOMETRY, ULTRAVIOLET; THERMODYNAMICS; ULTRAVIOLET RAYS;

EID: 33750984237     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi061103i     Document Type: Article

References (68)

1. Szent-Györgi, A., Isenberg, I., and Baird, S. J., Jr. (1960) On the electron donating properties of carcinogens, Proc. Natl Acad. Sci. U.S.A. 46, 1444-1449.
2. Fink, H. W., and Schonenberger, C. (1999) Electrical conduction through DNA molecules, Nature 398, 407-410.
3. Wan, C., Fiebig, T., Kelley, S. O., Treadway, C. R., Barton, J., and Zewail, A. H. (2000) Femtosecond dynamics of DNA-mediated electron transfer, Proc. Natl. Acad. Sci. U.S.A. 97, 14052-14055.
4. DeRosa, M. C., Sancar, A., and Barton, J. K. (2005) Electrically monitoring DNA repair by photolyase, Proc. Natl. Acad. Sci. U.S.A. 102, 10788-10792.
5. Hall, D. B., Holmlin, R. E., and Barton, J. K. (1996) Oxidative DNA damage through long-range electron transfer, Nature 382, 731-735.
6. Boon, E. M., Livingston, A. L., Chmiel, N. H., Davis, S. S., and Barton, J. K. (2003) DNA-mediated charge transport for DNA repair, Proc. Natl. Acad. Sci. U.S.A. 100, 12543-12547.
7. Meggers, E., Michel-Beyerle, M. E., and Giese, B. (1998) Sequence dependent long range hole transport in DNA, J. Am. Chem. Soc. 120, 12950-12955.
8. Giese, B. (2000) Long distance charge transport in DNA: The hopping mechanism, Acc. Chem. Res. 33, 631-636.
9. Giese, B., Amaudrut, J., Kohler, 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, 318-320.
10. Bixon, M., Giese, B., Wessely, S., Langenbancher, T., Michel-Beyerle, M. E., and Jortner, J. (1999) Long-range charge hopping in DNA, Proc. Natl. Acad. Sci. U.S.A. 96, 11713-11716.
11. Schuster, G. B. (2000) Long-range charge transfer in DNA: Transient structural distortions control the distance dependence, Acc. Chem. Res. 33, 253-260.
12. Henderson, P. T., Jones, D., Hampikian, G., Kan, Y. Z., and Schuster, G. B. (1999) Long-distance charge transport in duplex DNA: The phonon-assisted polaron-like hopping mechanism, Proc. Natl. Acad. Sci. U.S.A. 96, 8353-8358.
13. Ly, D., Kan, Y. Z., and Schuster, G. B. (1999) Mechanism of charge transport in DNA: Internally-linked anthraquinone conjugates support phonon-assisted polaron hopping, J. Am. Chem. Soc. 121, 9400-9410.
14. Lewis, F. D., Letsinger, R. L., and Wasielewski, M. R. (2001) Dynamics of photoinduced charge transfer and hole transport in synthetic DNA hairpins, Acc. Chem. Res. 34, 159-170.
15. Lewis, F. D., Wu, T. F., Liu, X. Y., Letsinger, R. L., Greenfield, S. R., Miller, S. E., and Wasielewski, M. R. (2000) Dynamics of photoinduced charge separation and charge recombination in synthetic DNA hairpins with stilbenedicarboxamide linkers, J. Am. Chem. Soc. 122, 2889-2902.
16. O'Neill, M. A., and Barton, J. K. (2004) DNA-mediated charge transport chemistry and biology, Top. Curr. Chem. 236, 67-115.
17. Erkkila, K. E., Odom, D. T., and Barton, J. K. (1999) Recognition and reaction of metallointercalators with DNA, Chem. Rev. 99, 2777-2795.
18. Arkin, M. R., Stemp, E. D. A., Holmlin, R. E., Barton, J. K., Hermann, A., Olson, E. J. C., and Barbara, P. F. (1996) Rates of DNA-mediated electron transfer between metallointercalators, Science 273, 475-480.
19. Kelley, S. O., and Barton, J. K. (1999) Electron transfer between bases in double helical DNA, Science 283, 375-381.
20. Kelley, S. O., Jackson, N. M., Hill, M. G., and Barton, J. K. (1999) Long-range electron transfer through DNA films, Angew. Chem., Int. Ed. 38, 941-945.
21. Jackson, N. M., and Hill, M. G. (2001) Electrochemistry at DNA-modified surfaces: New probes for charge transport through the double helix, Curr. Opin. Chem. Biol. 5, 209-215.
22. Kelley, S. O., Barton, J. K., Jackson, N. M., and Hill, M. G. (1997) Electrochemistry of methylene blue bound to a DNA-modified electrode, Bioconjugate Chem. 8, 31-37.
23. Lewis, F. D., Wu, T. F., Zhang, Y. F., Letsinger, R. L., Greenfield, S. R., and Wasielewski, M. R. (1997) Distance-dependent electron transfer in DNA hairpins, Science 277, 673-676.
24. Fukui, K., and Tanaka, K. (1998) Distance dependence of photoinduced electron transfer in DNA, Angew. Chem., Int. Ed. 37, 158-161.
25. Sugiyama, H., and Saito, I. (1996) Theoretical studies of GC-specific photocleavage of DNA via electron transfer: Significant lowering of ionization potential and 5′-localization of HOMO of stacked GG bases in B-form DNA, J. Am. Chem. Soc. 118, 7063-7068.
26. Meade, T. J., and Kayyem, J. F. (1995) Electron-transfer through DNA site-specific modification of duplex DNA with ruthenium donors and accepters, Angew. Chem., Int. Ed. 34, 352-354.
27. Holmlin, R. E., Dandliker, P. J., and Barton, J. K. (1997) Charge transfer through the DNA base stack, Angew. Chem., Int. Ed. 36, 2715-2730.
28. Kelly, S. O., and Barton, J. K. (1998) DNA-mediated electron transfer from a modified base to ethidium: π-stacking as a modulator of reactivity, Chem. Biol. 5, 413-425.
29. Hall, D. B., and Barton, J. K. (1997) 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. 119, 5045-5046.
30. Dandliker, P. J., Holmlin, R. E., and Barton, J. K. (1997) Oxidative thymine dimer repair in the DNA helix, Science 275, 1465-1468.
31. Boon, E. M., and Barton, J. K. (2003) DNA electrochemistry as a probe of base pair stacking in A-, B-, and Z-form DNA, Bioconjugate Chem. 14, 1140-1147.
32. Lewis, F. D., Zhang, Y. F., Liu, X. Y., Xu, N., and Letsinger, R. L. (1999) Naphthalenedicarboxamides as fluorescent probes of inter- and intramolecular electron transfer in single strand, hairpin, and duplex DNA, J. Phys. Chem. B 103, 2570-2578.
33. Holmberg, R. C., and Thorp, H. H. (2004) Electrochemical determination of triple helices: Electrocatalytic oxidation of guanine in an intramolecular triplex, Inorg. Chem. 43, 5080-5085.
34. Drummond, T. G., Hill, M. G., and Barton, J. K. (2004) Electron transfer rates in DNA films as a function of tether length, J. Am. Chem. Soc. 126, 15010-15011.
35. Kelly, S. O., Holmlin, R. E., Stemp, E. D. A., and Barton, J. K. (1997) Photoinduced electron transfer in ethidium-modified DNA duplexes: Dependence on distance and base stacking, J. Am. Chem. Soc. 119, 9861-9870.
36. Holmlin, R. E., Tong, R. T., and Barton, J. K. (1998) Long-range triplet energy transfer between metallointercalators tethered to DNA: Importance of intercalation, stacking, and distance, J. Am. Chem. Soc. 120, 9724-9725.
37. Kelley, S. O., Boon, E. M., Barton, J. K., Jackson, N. M., and Hill, M. G. (1999) Single-base mismatch detection based on charge transduction through DNA, Nucleic Acids Res. 27, 4830-4837.
38. Boon, E. M., Jackson, N. M., Wightman, M. D., Kelley, S. O., Hill, M. G., and Barton, J. K. (2003) Intercalative Stacking: A Critical Feature of DNA Charge-Transport Electrochemistry, J. Phys. Chem. B 107, 11805-11812.
39. Qu, X. G., Ren, J. S., Riccell, P. V., Benight, A. S., and Chaires, J. B. (2003) Enthalpy/Entropy Compensation: Influence of DNA Flanking Sequence on the Binding of 7-Amino Actinomycin D to Its Primary Binding Site in Short DNA Duplexes, Biochemistry 42, 11960-11967.
40. Riccelli, P. V., Vallone, P. M., Kashin, I., Faldasz, B. D., Lane, M. J., and Benight, A. S. (1999) Thermodynamic, spectroscopic, and equilibrium binding studies of DNA sequence context effects in six 22-base pair deoxyoligonucleotides, Biochemistry 38, 11197-11208.
41. Fredrik Edfeldt, N. B., Harwood, E. A., Sigurdsson, S. T., Hopkins, P. B., and Reid, B. R. (2004) Sequence context effect on the structure of nitrous acid induced DNA interstrand cross-links, Nucleic Acids Res. 32, 2795-2801.
42. Lindqvist, M., and Graslund, A. (2001) An FTIR and CD study of the structural effects of G-tract length and sequence context on DNA conformation in solution, J. Mol. Biol. 314, 423-432.
43. Eley, D. D., and Spivey, D. I. (1962) Semiconductivity of organic substances. IX. Nucleic acid in the dry state, Trans. Faraday Soc. 55, 411-415.
44. Porath, D., Bezryadin, A., de Vries, S., and Dekker, C. (2000) Direct measurement of electrical transport through DNA molecules, Nature 403, 635-638.
45. Qu, X., Trent, J. O., Fokt, I., Priebe, W., and Chaires, J. B. (2000) Allosteric, chiral-selective drug binding to DNA, Proc. Natl. Acad. Sci. U.S.A. 97, 12032-12037.
46. Qu, X., Wan, C., Becker, H.-C., Zhong, D., and Zewail, A. H. (2001) The anticancer drug-DNA complex: Femtosecond primary dynamics for anthracycline antibiotics function, Proc. Natl. Acad. Sci. U.S.A. 98, 14212-14217.
47. Gewirtz, D. A. (1999) A critical evaluation of the mechanisms of action proposed for the antitumor effects of the anthracycline antibiotics adriamycin and daunorubicin, Biochem. Pharmacol. 57, 727-741.
48. Oliveira-Brett, A. M., Vivan, M., Fernandes, I. R., and Piedade, J. A. P. (2002) Electrochemical detection of in situ adriamycin oxidative damage to DNA, Talanta 56, 959-970.
49. Chu, X., Shen, G. L., Jiang, J. H., Kang, T. F., Xiong, B., and Yu, R. Q. (1998) Voltammetric studies of the interaction of daunomycin anticancer drug with DNA and analytical applications, Anal. Chim. Acta 373, 29-38.
50. Pang, D. W., Zhang, M., Wang, Z. L., Qi, Y. P., Cheng, J. K., and Liu, Z. Y. (1996) Modification of glassy carbon and gold electrodes with DNA, J. Electroanal. Chem. 403, 183-188.
51. Leng, F. F., Savkur, R., Fokt, I., Przewloka, T., Priebe, W., and Chaires, J. B. (1996) Base Specific and regioselective chemical Cross-Linking of daunorubicin to DNA, J. Am. Chem. Soc. 118, 4731-4737.
52. Szulawska, A., Gniazdowski, M., and Czyz, M. (2005) Sequence specificity of formaldehyde-mediated covalent binding of anthracycline derivatives to DNA, Biochem. Pharmacol. 69, 7-18.
53. Yang, X. L., and Wang, A. H. J. (1999) Structure studies of atom-specific anticancer drugs acting on DNA, Pharmacol. Ther. 83, 181-215.
54. Zhang, H., Yu, H., Ren, J., and Qu, X. (2006) Reversible B-Z DNA transition under the low salt condition and non-B form polydApolydT selectivity by a cubane-like europium-L-aspartic acid complex, Biophys. J. 90, 3203-3207.
55. Zhang, H., Yu, H., Ren, J., and Qu, X. (2006) PolydA and polyrA self-structured by a europium and amino acid complex, FEBS Lett. 580, 3726-3730.
56. Mergny, J. L., and Lacroix, L. (2003) Analysis of thermal melting curves, Oligonucleotides 13, 515-537.
57. Qu, X., Chou, J., Lu, T., Dong, S., Zhou, C., and Cotton, T. M. (1995) Promoter effect of halogen anions on the direct electro-chemical reaction of cytochrome c at gold electrodes, J. Electroanal. Chem. 381, 81-85.
58. Qu, X., Lu, T., Dong, S., Zhou, C., and Cotton, T. M. (1994) Electrochemical reaction of cytochrome c at gold electrodes modified with thiophen containing one functional group, Bioelectrochem. Bioenerg. 34, 153-156.
59. Vasiliskov, V. A., Prokopenko, D. V., and Mirzabekov, A. D. (2001) Parallel multiplex thermodynamic analysis of coaxial base stacking in DNA duplex by oligodeoxyribonucleotide microchips, Nucleic Acids Res. 29, 2303-2313.
60. Yakovchuk, P., Protozanova, E., and Frank-Kamenetskii, M. D. (2006) Base-stacking and base-pairing contributions into thermal stability of the DNA double helix, Nucleic Acids Res. 34, 564-574.
61. Roll, C., Ketterle, C., Faibis, V., Fazakerley, G. V., and Boulard, Y. (1998) Conformations of nicked and gapped DNA structures by NMR and molecular dynamic simulations in water, Biochemistry 37, 4059-4070.
62. Benight, A. S., Gallo, F. J., Paner, T. M., Bishop, K. D., Faldasz, B. D., and Lane, M. J. (1995) Advances in Biophysical Chemistry, Vol. 5, pp 1-55, JAI Press Inc., Greenwich, CT.
63. Qu, X., and Chaires, J. B. (2000) Analysis of drug-DNA binding data, Methods Enzymol. 321, 353-369.
64. Sarapuu, A., Vaik, K., Schiffrin, D. J., and Tammeveski, K. (2003) Electrochemical reduction of oxygen on anthraquinone-modified glassy carbon electrodes in alkaline solution, J. Electroanal. Chem. 541, 23-29.
65. Bard, A. J., and Faulkner, L. R. (2001) Electrochemical Methods: Fundamentals and Applications, 2nd ed., Wiley & Sons, New York.
66. Laviron, E. (1979) General Expression of the Linear Potential Sweep Voltammogram in the case of Diffusionless Electrochemical Systems, J. Electroanal. Chem. 101, 19-28.
67. Napper, A. M., Liu, H. Y., and Waldeck, D. H. (2001) The nature of electronic coupling between ferrocene and gold through alkanethiolate monolayers on electrodes: The importance of chain composition, interchain coupling, and quantum interference, J. Phys. Chem. B 105, 7699-7707.
68. Wang, J., Ozsoz, M., Cai, X. H., Rivas, G., Shiraishi, H., Grant, D. H., Chicharro, M., Fernandes, J., and Palecek, E. (1998) Interactions of antitumor drug daunomycin with DNA in solution and at the surface, Bioelectrochem. Bioenerg. 45, 33-40.