Femtosecond dynamics of DNA-mediated electron transfer

Abstract

Diverse biophysical and biochemical studies have sought to understand electron transfer (ET) in DNA in part because of its importance to DNA damage and its repair. However, the dynamics and mechanisms of the elementary processes of ET in this medium are not fully understood and have been heavily debated. Two fundamental issues are the distance over which charge is transported and the time-scale on which the transport through the pi-stack of the DNA base pairs may occur. With femtosecond resolution, we report direct observation in DNA of ultrafast ET, initiated by excitation of tethered ethidium (E), the intercalated electron acceptor (A); the electron donor (D) is 7-deazaguanine (Z), a modified base, placed at different, fixed distances from A. The ultrafast ET between these reactants in DNA has been observed with time constants of 5 ps and 75 ps and was found to be essentially independent of the D-A separation (10-17 A). However, the ET efficiency does depend on the D-A distance. The 5-ps decay corresponds to direct ET observed from 7-deazaguanine but not guanine to E. From measurements of orientation anisotropies, we conclude that the slower 75-ps process requires the reorientation of E before ET, similar to E/nucleotide complexes in water. These results reveal the nature of ultrafast ET and its mechanism: in DNA, ET cannot be described as in proteins simply by a phenomenological parameter, beta. Instead, the involvement of the base pairs controls the time scale and the degree of coherent transport.

Figure 1

The DNA assemblies. (a) Molecular models (Insight II) illustrating the E-tethered (red) DNA assemblies (left to right) 5Z, 6Z, and 7Z. The Z base is shown in yellow. Sequences are given below. (b) Structures of guanine (G), Z, and the E-modified tether, as well as an autoradiogram (right) after denaturing 18% PAGE, showing photoinduced damage of an E-modified duplex generated by irradiation at 313 nm of the duplex (10 μM) in 5 mM phosphate/50 mM NaCl, pH 7, 5′ ³²P-labeled on the strand complementary to that containing the tether. Crosslinking occurs at the first two base steps on the 3′ side (near E); see The DNA Assemblies and ref. . The sequence 3′-CGCGCACTTA-5′ also was examined and gave consistent results.

Figure 2

Femtosecond transient absorption of DNA assemblies with 5Z/5G, 6Z/6G, and 7Z/7G after excitation at 500 nm (probed at 400 nm); short (Left) and long (Right) time scales are shown. All samples contained 10 μM duplex DNA in 5 mM phosphate/50 mM NaCl, pH 7. The sequences are displayed with closest position of E indicated.

Figure 3

Femtosecond fluorescence up-conversion of DNA assemblies with 5Z and 5G, detected at 600 nm (Upper) and 670 nm (Lower) in the short (Left) and the long (Right) time range. At the short wavelength, there is a solvent-alone spike around t = 0 (see a), which is absent at the longer wavelength (670 nm). The sample conditions are given in Fig. 2.

Figure 4

Polarization dependence of the time-resolved fluorescence. The decays of the fluorescence anisotropy for 5G (a) and 5Z (c) are shown. Fluorescence decays I_∥ and I_⊥ (polarization of the detection with respect to the excitation) for 5G and 5Z are also given (b and d). The magic angle (54.7°) I(t), deduced from I_∥ and I_⊥ for 5G (see ET Dynamics), is shown for comparison with I_∥. The sample conditions are given in Fig. 2.