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Base pair motions control the rates and distance dependencies of reductive and oxidative DNA charge transfer.

ABSTRACT: In 1999, Wan et al. [Proc. Natl. Acad. Sci. USA 96, 6014-6019] published a pioneering paper that established the entanglement between DNA base pair motions and the transfer time of the charge carrier. The DNA assemblies contained an ethidium covalently bound via a flexible alkyl chain to the 5' hydroxyl group of the DNA backbone. Although covalently attached, the loose way in which the ethidium was linked to DNA allowed for large degrees of conformational freedom and thus raised some concern with respect to conformational inhomogeneity. In this letter, we report studies on a different set of ethidium DNA conjugates. In contrast to the "Caltech systems," these conjugates contain ethidium tightly incorporated (as a base pair surrogate) into the DNA base stack, opposite to an abasic site analog. Despite the tight binding, we found that charge transfer from the photoexcited ethidium base pair surrogate across two or more base pairs is several orders of magnitude slower than in case of the DNA systems bearing the tethered ethidium. To further broaden the scope of this account, we compared (oxidative) electron hole transfer and (reductive) electron transfer using the same ethidium chromophore as a charge donor in combination with two different charge acceptors. We found that both electron and hole transfer are characterized by similar rates and distance dependencies. The results demonstrate the importance of nuclear motions and conformational flexibility and underline the presence of a base gating mechanism, which appears to be generic to electronic transfer processes through pi-stacked nucleic acids.

SUBMITTER: Valis L

PROVIDER: S-EPMC1502433 | biostudies-literature | 2006 Jul

REPOSITORIES: biostudies-literature

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Base pair motions control the rates and distance dependencies of reductive and oxidative DNA charge transfer.

Valis Linda L Wang Qiang Q Raytchev Milen M Buchvarov Ivan I Wagenknecht Hans-Achim HA Fiebig Torsten T

Proceedings of the National Academy of Sciences of the United States of America 20060626 27

In 1999, Wan et al. [Proc. Natl. Acad. Sci. USA 96, 6014-6019] published a pioneering paper that established the entanglement between DNA base pair motions and the transfer time of the charge carrier. The DNA assemblies contained an ethidium covalently bound via a flexible alkyl chain to the 5' hydroxyl group of the DNA backbone. Although covalently attached, the loose way in which the ethidium was linked to DNA allowed for large degrees of conformational freedom and thus raised some concern wit ...[more]

PMID: 16801552

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Project description:Three ionization centers make 1,3,5-trimethyl-1,3,5-triazacyclohexane (TMTAC) an interesting model system to study intramolecular charge transfer (CT). Because the molecule assumes a Cs symmetric, axial-equatorial-equatorial (aee) conformation in the ground state, there are two distinct types of the nitrogen atoms. We discovered that either nitrogen atom can be ionized independently so that two molecular cations exist with different (localized) charge distributions in the Franck-Condon region. The initially localized charge can delocalize via CT, provided the molecule acquires a suitable structural geometry. These proper structures are all found to have a common structural motif that supports CT via through-space-interaction. The structural dynamics and the CT process in Rydberg-excited TMTAC, where the molecular ion core closely resembles the ion, were probed by time-resolved Rydberg fingerprint spectroscopy. When TMTAC is excited at 230 nm to the Franck-Condon region of the 3s Rydberg state, the two types of nitrogen atom Rydberg chromophores give rise to distinct binding energy peaks. The sequential molecular responses that follow the Rydberg excitation manifest themselves as time-dependent changes of the binding energy and are observed by ionization at 404 nm. A fast transition with 103 fs time constant was attributed to a motion that leads to a local minimum of the charge-localized state on the Rydberg potential energy surface. Because a large amount of energy is deposited into the vibrational manifolds, the molecule continues to sample the potential energy surface and eventually reaches a dynamic equilibrium between charge-localized and charge-delocalized states. The forward and backward time constants were determined to be 1.02 ps and 4.09 ps, respectively. The binding energy spectrum also reveals the existence of an equilibrium among several charge-delocalized states. Quantum chemical calculations were carried out to find the stable minima of the ground state and the ion state. The binding energies of the Franck-Condon structures and the relaxed ion structures were calculated using the Perdew-Zunger self-interaction corrected DFT (PZ-SIC) method to assign the spectra at time zero and at equilibrium, respectively.

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Base pair motions control the rates and distance dependencies of reductive and oxidative DNA charge transfer.

Publications

Base pair motions control the rates and distance dependencies of reductive and oxidative DNA charge transfer.

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