Photoinduced short-range electron transfer in DNA with fluorescent DNA bases: lessons from ethidium and thiazole orange as charge donors

Abstract

Charge transfer processes through the double helix of DNA cover a broad range of mechanistic models ranging from superexchange to hopping mechanisms. Over the last decade, these processes were studied by our group in a photoinduced fashion since (i) the starting time for the charge transfer is clearly defined by the absorption of the photon and (ii) photoexcitation delivers the necessary driving force to the DNA system. It is a prerequisite to modify oligonucleotides synthetically with suitable organic fluorophores that serve as photoinducable charge donors. In the first part of this perspective article we summarize our recent advances in the area of DNA-mediated reductive electron transfer processes over short ranges using synthetic DNA-donor-acceptor systems. The second part of this article focuses on ethidium as the photoinducable charge donor. Ethidium-modified DNA can be used to compare oxidative hole transfer with reductive electron transfer since the type of charge transfer can be controlled by choosing the right charge acceptor. Recent results showed that an efficient charge transfer through DNA using covalently bound ethidium is strongly influenced mainly by DNA dynamics but also by several other parameters that affect the electronic coupling between charge donor and acceptor.

DNA-Multichromophore Systems

“…143, 313 On the other hand, ethidium and thiazole orange have lower oxidation potentials than all the natural nucleobases and thus were used as charge donors to 5-nitroindole and 7-deazaguanine. 138, 314, 315 …”

Acceleration of Long‐Range Photoinduced Electron Transfer through DNA by Hydroxyquinolines as Artificial Base Pairs

“…The Hq–Hq pair was combined with a DNA‐based donor–acceptor system consisting of: 1) 6‐ N , N ‐dimethylaminopyrene conjugated to 2′‐deoxyuridine (Ap–dU) as photoinducable electron donor,12 and 2) methyl viologen attached to the 2′‐position of uridine (Mv–U) as electron acceptor (Figure 1). 4c The oxidation potential of the nucleoside conjugate Ap–dU is E 0 1/2 (ox)=0.88 V (vs. NHE); together with E 00 =3.1 V photoexcited Ap*–dU is an approximately 400 mV stronger photoreductant for DNA than our previously applied pyrene conjugates 12. 13…”

“…Ap–dU and Hq can be incorporated into oligonucleotides via their phosphoramidites as DNA building blocks (Scheme ) 12. Due to the instability of Mv under typical DNA workup conditions, it was attached to 2′‐propargylated uridine via postsynthetic copper(I)‐catalyzed cycloaddition (Mv–U) 4c. To study the first step of electron transfer from Ap–dU to Hq, we synthesized DNA1–DNA3 lacking the final electron acceptor Mv–U and bearing the photoinducable electron donor Ap–dU at a distance from two to four intervening base pairs to the Hq–Hq pair.…”

Distance dependence of hole transfer rates from G radical cations to GGG traps in DNA

“…Fluctuations affect the electronic parameters governing charge transfer and the resulting properties 4,21,22,[27][28][29][30][31] and may be responsible for the obtained quantitative deviations from the experimental results. Note however that our calculations do not contain any adjustable parameters and, further, correspond to zero temperature, thus ignoring thermal fluctuations of the DNA average structure.…”