The Charge Conduction Properties of DNA Holliday Junctions Depend Critically on the Identity of the Tethered Photooxidant Richard P. Fahlman, ² Rajendra D. Sharma, ‡ and Dipankar Sen* ,²,‡ Contribution from Department of Molecular Biology & Biochemistry and Department of Chemistry, Simon Fraser UniVersity, Burnaby, British Columbia V5A 1S6, Canada Received April 5, 2002 Abstract: The mechanism for electrical charge conduction in DNA has been the subject of much recent interest and debate. Many of the measurements of DNA conductivity have been made in aqueous solution, with an aromatic photooxidant moiety such as anthraquinone or a rhodium(III) complex covalently tethered to the DNA. Such studies, however, have given discrepant results, for instance, regarding the relative ability of AT- and GC-rich sequences to conduct charge and the possibility of thymine cyclobutane dimer repair through the DNA from a distance. A recent paper on conduction in DNA immobile four-way junctions using the rhodium photooxidant reported conduction in all four helical arms, contrary to what is known about the three-dimensional structure and stacking of 4-way junctions. We have reexamined conduction in such junctions using rhodium [Rh(phi) 2(byp*)Cl3] as well as the anthraquinone photooxidants, and find that although our rhodium data agree with the previously published work, the anthraquinone data reveal conduction in only two of the four helical arms, consistent with the known tertiary structure of four-way junctions. An electrophoretic investigation revealed the formation of intermolecular aggregates in the rhodium- derivatized junctions, but not in the anthraquinone-labeled junctions. Rhodium-specific aggregation was also observed with simple DNA duplexes under the same experimental conditions. A characteristic property of aggregation was that all participating DNA molecules required the rhodium derivatization, and underivatized molecules did not aggregate with the derivatized ones. It is conceivable that the results reported here will help reconcile the various discrepancies that have been reported from charge conduction experiments carried out on DNA utilizing different photooxidants. Introduction The first conjectures on the potential of DNA to conduct electrical charge date back to nearly forty years ago. 1-2 However, the technologies appropriate to testing such hypoth- eses have not been available until the past decade. The first studies reported divergent conclusions about the efficiency, distance dependence, and rates of observed charge transfer through DNA double helices. A number of studies reported that the aromatic base stacks of a DNA duplex act as an efficient electrical conductor; 3-4 however, other reports concluded that duplex DNA behaved essentially like an insulator. 5-6 Such conflicting observations have stimulated much further study of charge transfer through DNA. To date, the wealth of experi- mental data recorded and evaluated have made it evident that, likely, more than a single mechanism exists for charge transfer through DNA. One possible mechanism is a long-range charge “hopping”, whereby an electron hole migrates through the duplex using the oxidizable guanine bases as “steps” 7 or by a polaron like hopping mechanism. 8 A second prevalent mecha- nism, for rapid, short-range charge transfer, is the single-step superexchange mechanism, where the DNA behaves essen- tially as a molecular wire having a continuous molecular orbital. 9-10 Beyond the issue of the precise mechanism(s) of charge transfer, a consensus has emerged that continuous base-stacking throughout a DNA duplex is important. Efficiency of charge transfer is observed to be lower in duplexes containing either mismatches 11-13 or bulges. 14 However, not all perturbations to the helix have prevented charge transfer, as has been noted in helices containing abasic sites 15 and short, single-stranded overhangs. 16 Nevertheless, even these latter structures have been * To whom correspondence should be addressed: Department of Molecular Biology & Biochemistry, Simon Fraser University, 8888 University Way, Burnaby, British Columbia V5A 1S6, Canada. Tel.: 604- 291-4386. Fax: 604-291-5583. E-mail: sen@sfu.ca. ² Department of Molecular Biology & Biochemistry, Simon Fraser University. ‡ Department of Chemistry, Simon Fraser University. (1) Eley, D. D.; Spivey, D. I. Trans. Faraday Soc. 1962, 58, 411-415. (2) Hoffman, T. A.; Ladik, J. AdV. Chem. Phys. 1964, 7, 84-158. (3) Arkin, M. R.; Stemp, E. D. A.; Holmlin, R. E.; Barton, J. K.; Horrman, A.; Olsen, E. J. C.; Barbara, P. F. Science 1996, 273, 475-480. (4) Murphy, C. J.; Arkin, M. R.; Jenkins, Y.; Ghatlin, N. D.; Bossman, S. H.; Turro, N. J.; Barton, J. K. Science 1993, 262, 1025-1029. (5) Lewis, F. D.; Wu, T.; Zhang, Y.; Letsinger, R. L.; Greenfield, S. R.; Wasielewski, M. R. Science 1997, 277, 673-676. (6) Debije, M. G.; Milano, M. T.; Bernhard, W. A. Angew. Chem., Int. Ed. 1999, 38, 2752-2756. (7) Giese, B. Acc. Chem. Res. 2000, 33, 631-636. (8) Schuster, G. B. Acc. Chem. Res. 2000, 33, 253-260. (9) Turro, N. J.; Barton, J. K. J. Biol. Inorg. Chem. 1998, 3, 201-209. (10) Lewis, F. D.; Letsinger, R. L.; Wasielewski, M. R. Acc. Chem. Res. 2001, 34, 159-170. (11) Kelly, S. O.; Holmlin, R. E.; Stemp, E. D. A.; Barton, J. K. J. Am. Chem. Soc. 1997, 119, 9861-9870. (12) Giese, B.; Wessely, S. Angew. Chem., Int. Ed. 2000, 39, 3490-3491. (13) Boon, E. M.; Ceres, D. M.; Drummond, T. G.; Hill, M. G.; Barton, J. K. Nature Biotech. 2000, 18, 1096-1100. (14) Hall, D. B.; Barton, J. K. J. Am. Chem. Soc. 1997, 119, 5045-5046. Published on Web 09/28/2002 10.1021/ja020495n CCC: $22.00 © 2002 American Chemical Society J. AM. CHEM. SOC. 2002, 124, 12477-12485 9 12477