DOI: 10.1002/chem.201001978 Investigation of Excess-Electron Transfer in DNA Double-Duplex Systems Allows Estimation of Absolute Excess-Electron Transfer and CPD Cleavage Rates** Danila Fazio, [a] Christian Trindler, [a] Korbinian Heil, [a] Chryssostomos Chatgilialoglu, [b] and Thomas Carell* [a] Introduction Electron injection into DNA is an important process associ- ated with the repair of UV-induced cyclobutane pyrimidine dimer (CPD) and (6–4) lesions. [1, 2] For both DNA lesions, DNA-photolyase repair enzymes are known, which use a light-excited, reduced, and deprotonated flavin as an elec- tron donor to achieve repair through single-electron reduc- tion of the lesions. [1] The injected electron is captured by the UV-induced lesion, which undergoes a fragmentation reac- tion that finally leads to repair. [3] Over the past few years, electron injection into a DNA duplex and movement of an injected excess electron through a DNA duplex have been intensively investigated theoretically and with various DNA- based model compounds. [4–10] It is now clear that an injected (excess) electron can hop through the DNA duplex by using pyrimidine bases as stepping stones. This allows cleavage of CPD lesions located even a few base pairs away from the in- jection site of the excess electron. [11] Even though the princi- ple mechanism of excess-electron transfer, and in particular the distance dependence, [12–18] has been clarified, conflicting data still exist, for example, for the sequence dependence of the transfer reaction. [19–27] In addition, the question of whether excess-electron transfer depends on the transfer di- rection in the DNA duplex has not been satisfactorily inves- tigated. Finally, we are just beginning to understand absolute hopping rates. [19, 21, 28] We believe that some of the problems associated with research on electron transfer in DNA arise because different electron donors and acceptors are used in different experiments. For example, we recently showed that the rate by which a given acceptor reacts with an electron Abstract: To investigate the parameters and rates that determine excess-elec- tron transfer processes in DNA duplex- es, we developed a DNA double- duplex system containing a reduced and deprotonated flavin donor at the junction of two duplexes with either the same or different electron accept- ors in the individual duplex substruc- tures. This model system allows us to bring the two electron acceptors in the duplex substructures into direct compe- tition for injected electrons and this en- ables us to decipher how the kind of acceptor influences the transfer data. Measurements with the electron ac- ceptors 8-bromo-dA (BrdA), 8-bromo- dG (BrdG), 5-bromo-dU (BrdU), and a cyclobutane pyrimidine dimer, which is a UV-induced DNA lesion, allowed us to obtain directly the maximum overall reaction rates of these accept- ors and especially of the T =T dimer with the injected electrons in the duplex. In line with previous observa- tions, we detected that the overall dimer cleavage rate is about one order of magnitude slower than the debromi- nation of BrdU. Furthermore, we pres- ent a more detailed explanation of why sequence dependence cannot be ob- served when a T =T dimer is used as the acceptor and we estimate the abso- lute excess-electron hopping rates. Keywords: cleavage · DNA repair · electron transfer · flavins · nucleo- bases [a] M. Pharm. Chem. D. Fazio, Dr. C. Trindler, Dipl.-Chem. K. Heil, Prof. Dr. T. Carell Department of Chemistry and Biochemistry Ludwig-Maximilians-University Munich Butenandtstrasse 5–13, Haus F, 81377 Munich (Germany) Fax: (+ 49) 89-2180-77756 E-mail: Thomas.Carell@cup.uni-muenchen.de [b] Dr. C. Chatgilialoglu ISOF, Consiglio Nazionale delle Ricerche via P. Gobetti 101, 40129 Bologna (Italy) [**] CPD: cyclobutane pyrimidine dimer Supporting information for this article is available on the WWW under http://dx.doi.org/10.1002/chem.201001978.  2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim Chem. Eur. J. 2011, 17, 206 – 212 206