Charge Transfer through the DNA Base Stack

Whether the DNA base pair stack might serve as a medium for efficient, long-range charge transfer has been debated almost since the first proposal of the double-helical structure of DNA. The consequences of long-range radical migration through DNA are important with respect to understanding carcinogenesis and mutagenesis. Double-helical DNA has in its core a stacked array of aromatic heterocyclic base pairs, and this molecular π stack represents a unique system in which to explore the chemistry of electron transfer. We designed a family of metal complexes which bind to DNA by intercalative stacking within the helix; these metallointercalators may be usefully applied in probing DNA-mediated electron transfer. Here we describe a range of electron transfer reactions we carried out which are mediated by the DNA base paired stack. In some cases, DNA serves as a bridge, and spectroscopic analyses permit us to probe how the π stack couples DNA-bound donors and acceptors. These studies point to the sensitivity of coupling to DNA intercalation. However, if the DNA π stack effectively bridges donors and acceptors, the base-pair stack itself might serve not only as a conduit for electron transfer in DNA, but also in reactions initiated from a remote position. We carried out a series of reactions involving oxidative damage to DNA arising from the remotely positioned oxidant on the helix. The implications of long-range charge migration through DNA to effect damage are substantial. As in other DNA-mediated charge transfers, these reactions are highly dependent on DNA intercalation and the integrity of the intervening base-pair stack, but not on molecular distance. Furthermore, a physiologically important DNA lesion, the thymine dimers, can be reversed in a reaction initiated by electron transfer. This repair reaction can also be promoted from a distance as a result of long-range charge migration through the DNA base pair stack.     

Recent developments of charge injection and charge transfer in DNA

The question of whether and how electrons migrate through DNA was a matter of controversial discussion over the last ten years. Today, there is no doubt that long distance charge migration through DNA exists and most scientists explain this process by a multistep hopping mechanism. This feature article presents recent developments of our group on the injection of a positive charge into DNA bases and the transfer of the charge between the DNA bases. The influence of the donor, the nature of the bridge, and the distance between the donor and the acceptor are discussed.     

Direct observation of radical intermediates in protein-dependent DNA charge transport.

Charge migration through the DNA base stack has been probed both spectroscopically, to observe the formation of radical intermediates, and biochemically, to assess irreversible oxidative DNA damage. Charge transport and radical trapping were examined in DNA assemblies in the presence of a site-specifically bound methyltransferase HhaI mutant and an intercalating ruthenium photooxidant using the flash-quench technique. The methyltransferase mutant, which can flip out a base and insert a tryptophan side chain within the DNA cavity, is found to activate long-range hole transfer through the base pair stack. Protein-dependent DNA charge transport is observed over 50 A with guanine radicals formed >10(6) s(-1); hole transport through DNA over this distance is not rate-limiting. Given the time scale and distance regime, such protein-dependent DNA charge transport chemistry requires consideration physiologically.     

双链DNA分子内电荷转移超交换机理

设计并合成了一系列寡聚核苷酸组成的双链DNA分子,通过检测样品中二氨基嘌呤(Ap)荧光峰强度和相对荧光量子产率来研究DNA分子内电荷转移.实验中直接分辨和观测到双链DNA分子内电荷转移超交换机理,超交换机理在近距离起作用；而电荷转移跳跃机理,可能是通过极子运动形式体现.     

Energy contribution of the solvent to the charge migration in DNA

The authors have investigated the interactions of the reaction centers, participating in the charge transfer reaction within the DNA molecule with the phosphate backbones and the solvent molecules, and have estimated the contribution of these interactions into the charge migration in DNA. They have determined the unequal shift of the energy surfaces of the initial and final transition states of the transfer reaction along the energy axis and the dependence of the magnitude of the energy shift on the nature of the reaction centers and the surrounding environment. The nonuniform distribution of the negative charge in the DNA phosphate backbones results in an increase of the positive shift of the energy surface of the DNA base pairs in the center of the structure, where the maximum density of the negative charge is concentrated. Localization of the positive charge on the guanine and the adenine in the DNA base pairs in the oxidized state results in a dependence of the free energy of reaction in the solvent on the pair sequences and their arrangement in the DNA chain. As an example, for the G-C/A-T configuration the positive charges are localized on the same strand that results in a decrease of the free energy of reaction in the solvent for charge migration from G-C to A-T pair by 0.125 eV.     

Reductive electron transfer and transport of excess electrons in DNA

In principle, DNA-mediated charge transfer processes can be categorized as either oxidative hole transfer or reductive electron transfer. In research on DNA damage, major efforts have focused on the investigation of oxidative hole transfer or transport, resulting in insights on the mechanisms. On the other hand, the transport or transfer of excess electrons has a large potential for biomedical applications, mainly for DNA chip technology. Yet the mechanistic details of this type of charge transfer chemistry were unclear. In the last two years this mechanism has been addressed in gamma-pulse radiolysis studies with randomly DNA-bound electron acceptors or traps. The major disadvantage of this experimental setup is that the electron injection and trapping is not site-selective. More recently, new photochemical assays for the chemical and spectroscopic investigation of reductive electron transfer and electron migration in DNA have been published which give new insights into these processes. Based on these results, an electron-hopping mechanism is proposed which involves pyrimidine radical anions as intermediate electron carriers.     

Charge transfer driven by electron correlation: a non-Dyson propagator approach

A hole charge created in a molecular system, for instance, by ionization, can migrate through the system solely driven by electron correlation. This charge transfer due to electron correlation is referred to as charge migration. We introduce in this work a new ab initio method analyzing charge migration due to electron correlation in molecules. This method, a third-order "non-Dyson" propagator approach, aims in the long run, in particular, at the calculation of charge migration in relatively large molecules such as oligopeptides. First results of the new non-Dyson method are compared with a previously used propagator approach.     

Controlling Electron Rebound within Four‐Base π‐Stacks in Z‐DNA by Changing the Sugar Moiety from Deoxy‐ to Ribonucleotide

Charge transfer through DNA is of great interest because of the potential of DNA to be a building block for nanoelectronic sensors and devices. The photochemical reaction of 5‐halouracil has been used for probing charge‐transfer processes along DNA. We previously reported on unique charge transfer following photochemical reaction of 5‐bromouracil within four‐base π‐stacks in Z‐DNA. In this study, we incorporated a guanosine instead of a deoxyguanosine into Z‐DNA, and found that electron transfer occurs in a different mechanism through four‐base π‐stacks.     

Double proton transfer in the isolated and DNA-embedded guanine-cytosine base pair

The energetics and dynamics of double proton transfer (DPT) is investigated theoretically for the Watson-Crick conformation of the guanine-cytosine (GC) base pair. Using semiempirical density functional theory the isolated and DNA-embedded GC pair is considered. Differences in the energetics and dynamics of DPT thus addresses the question of how relevant studies of isolated base pairs are for the understanding of processes occurring in DNA. Two-dimensional potential energy surfaces involving the transferring hydrogen atoms and the proton donors and acceptors are presented for both systems. The DPT reaction is accompanied by a contraction of the distance between the two bases with virtually identical energetic barriers being 18.8 and 18.7 kcal/mol for the isolated and DNA-embedded system, respectively. However, the transition state for DPT in the DNA-embedded GC pair is offset by 0.1 A to larger N-H separation compared to the isolated GC pair. Using activated ab initio molecular dynamics, DPT is readily observed for the isolated base pair with a minimal amount of 21.4 kcal/mol of initial average kinetic energy along the DPT normal mode vector. On a time scale of approximately 100 fs DPT has occurred and the excess energy is redistributed. For the DNA-embedded GC pair considerably more kinetic energy is required (30.0 kcal/mol) for DPT and the process is completed within one hydrogen vibration. The relevance of studies of isolated base pairs and base pair analogs in regard of reactions or properties involving DNA is discussed.     

Mechanism and energetics of intramolecular hydrogen transfer in amide and peptide radicals and cation-radicals

Intramolecular hydrogen transfer in five model amide and peptide radicals and cation-radicals was investigated by combined B3LYP-MP2 calculations. Hypervalent ammonium radicals produced by electron capture in protonated peptides undergo competitive elimination of ammonia, H-atom loss, and H-atom migration to neighboring amide carbonyls. The calculated transition state energies for H-atom migration are slightly but uniformly lower than those for H-atom loss. Transition state theory calculations with inclusion of quantum tunneling effects predict k(H migration)/k(H loss) branching ratios that increase with the ring size of the cyclic transition state for the migration. Intramolecular hydrogen-atom migration in amide and peptide radicals can be described by the proton-coupled electron transfer mechanism. The migrating hydrogen atom shows a negligible spin density and substantial positive charge that are typical of a proton migration. Electron transfer occurs through a pi-orbital system and proceeds in the same (clockwise) or opposite (counterclockwise) direction as the proton motion, depending on the electronic properties of the chain connecting the ammonium group and the amide bond.     

Ladungstransfer durch die DNA: Vom Mechanismus zur Anwendung

DNA charge transfer chemistry has been subject of considerable interest with consequences in the formation of oxidative damage to the DNA which can result in mutagenesis or carcinogenesis. In this article, important examples of spectroscopical and biochemical assays are compared and discussed in terms of the effiencies, rates, and mechanisms. Coupled with the demonstration that such charge transfer can be modulated both negatively and positively by DNA‐binding proteins, these observations therefore suggest the intriguing possibility that DNA‐mediated charge transfer chemistry is biological relevant and may play a role in cellular processes. Additionally, charge transfer chemistry plays a growing role in the recent development of DNA chips detecting mutations or lesions of nucleic acids.     

Reductive Charge Transfer through an RNA Aptamer

The transfer of charges through double helical DNA is a very well investigated bioelectric phenomenon. RNA, on the contrary, has been less studied in this regard. The few available data report on charge transfer through RNA duplex structures mainly composed of homonucleotide sequences. In the light of the RNA world scenarios, it is an interesting question, if charge transfer can be coupled with RNA function. Functional RNAs however, contain versatile structural motifs. Therefore, electron transport also through non-Watson–Crick base-paired regions might be required. We here demonstrate distance-dependent reductive charge transfer through RNA duplexes and through the non-Watson–Crick base-paired region of an RNA aptamer.     

Oxidative charge transport through DNA in nucleosome core particles

Eukaryotic DNA is packaged into nucleosomes, made up of 146 bp of DNA wrapped around a core of histone proteins. We used photoexcited rhodium intercalators to explore DNA charge transport within these assemblies. Although histone proteins inhibit intercalation of the rhodium complex within the core particle, they do not prevent 5'-GG-3' oxidation, the signature of oxidative charge transport through DNA. Moreover, using rhodium intercalators tethered to the 5' terminus of the DNA, we found that guanine bases within the nucleosome can be oxidized from a distance of 24 bp. Histone binding did not affect the pattern and extent of this oxidation. Therefore, although the structure of the nucleosome core particle generally protects DNA from damage by solution-borne molecules, packaging within the nucleosome does not protect DNA from charge transfer damage through the base pair stack.     

Hole polarons in poly(G)-poly(C) and poly(A)-poly(T) DNA molecules

The polaron might play an important role in the process of charge migration through duplex DNA stack. In the present work, we investigate properties of hole polarons in DNA molecules containing identical base pairs, such as poly(G)-poly(C) and poly(A)-poly(T), An extended tight-binding model (extended Su-Schrieffer-Heeger model), which involves the effect of an electric field in the direction of DNA stack, will be introduced. The transfer integral and electron-phonon coupling parameters in this model are obtained according to ab initio calculation for different base pair dimers. Calculations reveal that the polaron in poly(A)-poly(T) has a wider shape and a higher mobility under a specific electric field than that in poly(G)-poly(C) DNA stack.     

Ultrafast Dynamics of Solvation and Charge Transfer in a DNA‐Based Biomaterial

Charge migration along DNA molecules is a key factor for DNA‐based devices in optoelectronics and biotechnology. The association of a significant amount of water molecules in DNA‐based materials for the intactness of the DNA structure and their dynamic role in the charge‐transfer (CT) dynamics is less documented in contemporary literature. In the present study, we have used a genomic DNA–cetyltrimethyl ammonium chloride (CTMA) complex, a technological important biomaterial, and Hoechest 33258 (H258), a well‐known DNA minor groove binder, as fluorogenic probe for the dynamic solvation studies. The CT dynamics of CdSe/ZnS quantum dots (QDs; 5.2 nm) embedded in the as‐prepared and swollen biomaterial have also been studied and correlated with that of the timescale of solvation. We have extended our studies on the temperature‐dependent CT dynamics of QDs in a nanoenvironment of an anionic, sodium bis(2‐ethylhexyl)sulfosuccinate reverse micelle (AOT RMs), whereby the number of water molecules and their dynamics can be tuned in a controlled manner. A direct correlation of the dynamics of solvation and that of the CT in the nanoenvironments clearly suggests that the hydration barrier within the Arrhenius framework essentially dictates the charge‐transfer dynamics.     

On the Mechanism of Long-Range Electron Transfer through DNA

Hopping between bases of similar redox potentials is the mechanism by which charge transport occurs through DNA. This was shown by rate measurements performed with double strands 1 – 3 . This mechanism explains why hole transfer displays a strong sequence dependence, and postulates that electron transfer in unperturbed DNA should not be dependent on the sequence.     

Diffusion Approach to Long Distance Charge Migration in DNA: Time-Dependent and Steady-State Analytical Solutions for the Product Yields

In this study we report analytical solutions for both time-dependent and steady-state problems of unbiased charge transfer through a regular DNA sequence via a hopping mechanism. The phenomenon is treated as a diffusion of charge in a one-dimensional array of equally spaced and energetically equivalent temporary trapping sites. The solutions take into account the rates of charge hopping (k), side reactions (k(r)), and charge transfer to a terminal charge acceptor (k(t)). A detailed analysis of the time-dependent problem is performed for the diffusion-controlled regime, i.e., under the assumption that k(t) > k, which is also equivalent to the fast relaxation limit of charge trapping. The analysis shows that the kinetics of charge hopping through DNA is always multiexponential, but under certain circumstances it can be asymptotically approximated by a single-exponential term. In that case, the efficiency of charge transfer can be characterized by a single rate constant k(CT) = 1.23kN(-2) + k(r), where N is the DNA length expressed in terms of the number of equidistant trapping sites and k(r) is the rate of competing chemical processes. The absolute yield of charge transfer under steady-state conditions in general is obtained as Y(infinity) = omega [alpha sinh(alphaN) + omega cosh(alphaN)](-1), where alpha = (2k(r)/k)(1/2) and omega = 2k(t)/k. For the diffusion-controlled regime and small N, in particular, it turns into the known "algebraic" dependence Y(infinity) = [1 + (k(r)/k)N(2)](-1). At large N the solution is asymptotically exponential with the parameter alpha mimicking the tunneling parameter beta in agreement with earlier predictions. Similar equations and distance dependencies have also been obtained for the damage ratios at the intermediate and terminal trapping sites in DNA. The nonlinear least-squares fit of one of these equations to experimental yields of guanine oxidation available from the literature returns kinetic parameters that are in reasonable agreement with those obtained by Bixon et al. [Proc. Natl. Acad. Sci. U.S.A.1999, 96, 11713-11716] by numerical simulations, suggesting that these two approaches are physically equivalent.     

Probing Electronic Symmetry Reduction during Charge Migration via Time-Resolved X-Ray Diffraction

The present work focuses on probing ultrafast charge migration after symmetry-breaking excitation using ultrashort laser pulses. LiCN is chosen as prototypical system because it can be oriented in the laboratory frame and it possesses optically-accessible charge transfer states at low energies. The charge migration is simulated within the hybrid time-dependent density functional theory/configuration interaction framework. Time-resolved electronic current densities and simulated time-resolved x-ray diffraction signals are used to unravel the mechanism of charge migration. Our simulations demonstrate that specific choices of laser polarization lead to a control over the symmetry of the induced charge migration. Moreover, time-resolved x-ray diffraction signals are shown to encode transient symmetry reduction at intermediate times.     

Influence of solvent on the energetics of hole transfer in DNA

We have investigated the contribution of molecular environment to the exchange reactions in the DNA molecule taking into account different geometries of the reaction centers in oxidized and reduced states. We have observed the influence of the ionization potential of the donor and the acceptor on the free energy of the hole transfer reaction in the solvated DNA molecule: A decrease of the free energy occurs if IPA > or = IPD and an increase if IPA < or = IPD. The corresponding decrease of the potential barrier by 0.244 eV for hole migration from (G-C) to (A-T) and increase for migration from (G-C) to (G-C)n in solvent have been determined. The prevalence of oxidation of the redox states in the molecule center in comparison to the molecule sides due to the nonuniform charge distribution along the phosphate backbone was found to be stronger for the non-neutralized backbone than for the neutralized case. The influence of the single counterion on the electrostatic interactions within the solute DNA molecule has been found to be smoothly spread over a long distance approximately 7-8 base pairs. Therefore, each counterion contributes to the oxidation potential of the 7-8 nearest nucleosides and any irregularity due to phosphate neutralization would not significantly modify the potential profile for the hole migration through the DNA molecule.     

A fluorescence aptasensor based on DNA charge transport for sensitive protein detection in serum

A novel fluorescence aptasensor based on DNA charge transport for sensitive protein detection has been developed. A 15nt DNA aptamer against thrombin was used as a model system. The aptamer was integrated into a double strand DNA (dsDNA) that was labeled with a hole injector, naphthalimide (NI), and a fluorophore, Alexa532, at its two ends. After irradiation by UV light, the fluorescence of Alexa532 was bleached due to the oxidization of Alexa532 by the positive charge transported from naphthalimide through the dsDNA. In the presence of thrombin, the binding of thrombin to the aptamer resulted in the unwinding of the dsDNA into ssDNA, which led to the blocking of charge transfer and the strong fluorescence emission of Alexa532. By monitoring the fluorescence signal change, we were able to detect thrombin in homogeneous solutions with high selectivity and high sensitivity down to 1.2 pM. Moreover, as DNA charge transfer is resistant to interferences from biological contexts, the aptasensor can be used directly in undiluted serum with similar sensitivity as that in buffer. This new sensing strategy is expected to promote the exploitation of aptamer-based biosensors for protein assays in complex biological matrixes.