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.     

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.     

Consecutive adenine sequences are potential targets in photosensitized DNA damage

Based on direct spectroscopic measurements of hole transfer in DNA and quantification of the yield of DNA oxidative damage, consecutive adenine sequences were found to be a good launching site for photosensitizers to inject a hole in DNA, where the following rapid hole transfer between adenines causes a long-lived charge-separated state leading to DNA oxidative damage. According to the results, the essential requisites for an efficient and/or harmful photosensitizer are determined as follows: to be able to oxidize adenine to trigger hole transfer between adenines, and react rapidly with molecular oxygen following its reduction, avoiding charge recombination and making the reaction irreversible. These results will greatly help us to classify photosensitizers harmful to human health, and to design an improved photosensitizer for biochemical applications.     

Base sequence effects on transport in DNA

Given the success of the polaron model based on solvation in accounting for the width of a hole polaron on an all-adenine (A) sequence on DNA, we extend the calculations to other sequences. We find excellent agreement with the free energy differences measured by Lewis et al. (J. Am. Chem. Soc. 2000, 122, 12037-12038) between a guanine (G) cation and a pair of bases, GG, or a triple of bases, GGG, in all cases surrounded by As, by treating AGGA and AGGGA as solvated polarons. There is additional support for hole polaron formation in DNA from experiments in which oxidative damage due to injected holes is investigated in sequences involving Gs and As. Theory and comparison with transport measurements on repeated sequences involving multiple thymines (Ts) or combinations such as ATs or GCs, where C is cytosine, led to the suggestion that the basic sequences in these cases must be polarons whose wave functions have substantial amplitudes on both chains in a duplex. The size of an electron polaron in DNA is predicted to be similar to that of a hole polaron, approximately 4 or 5 bases. Although experiments have shown that polaron hopping is the dominant mode of charge transport in DNA with repeated sequences such as AGGA, further investigations, particularly of temperature dependence of site energies and transfer integrals, are needed to determine to what extent hole transport takes place by polaron hopping for arbitrary DNA sequences.     

Rational design of a DNA wire possessing an extremely high hole transport ability

DNA is a promising conductive biopolymer. However, there are problems that need to be solved to realize real DNA wires. These include the low efficiency of hole transport and the serious oxidative damage that can occur during hole transport. We have demonstrated a protocol for the design of a DNA wire that can effectively mediate hole transport that is not adversely affected by oxidation during hole transport through the DNA duplex. We have synthesized a stable and effective DNA wire by incorporating a designer nucleobase, benzodeazaadenine derivatives, which have lower oxidation potentials and wider stacking areas but are not decomposed during hole transport.     

Dynamics of inter- and intrastrand hole transport in DNA hairpins

The dynamics of photoinduced electron transfer has been investigated in DNA hairpins possessing a stilbenedicarboxamide (Sa) electron acceptor, a guanine (G) primary donor, and two adjacent guanines (GG) as secondary donors. Hole transport from G to GG across a single A is more rapid than across AA or T by factors of 20 +/- 7 and 40 +/- 15, respectively. Intrastrand hole transport across a single A is more rapid than interstrand transport by a factor of 7 +/- 3.     

Dynamics and energetics of single-step hole transport in DNA hairpins

The dynamics of single-step hole transport processes have been investigated in a number of DNA conjugates possessing a stilbenedicarboxamide electron acceptor, a guanine primary donor, and several secondary donors. Rate constants for both forward and return hole transport between the primary and secondary donor are obtained from kinetic modeling of the nanosecond transient absorption decay profiles of the stilbene anion radical. The kinetic model requires that the hole be localized on either the primary or the secondary donor and not delocalized over both the primary and the secondary donor. Rate constants for hole transport are found to be dependent upon the identity of the secondary donor, the intervening bases, and the location of the secondary donor in the same strand as the primary donor or in the complementary strand. Rate constants for hole transport are much slower than those for the superexchange process used to inject the hole on the primary donor. This difference is attributed to the larger solvent reorganization energy for charge transport versus charge separation. The hole transport rate constants obtained in these experiments are consistent with experimental data for single-step hole transport from other transient absorption studies. Their relevance to long-distance hole migration over tens of base pairs remains to be determined. The forward and return hole transport rate constants provide equilibrium constants and free energies for hole transport equilibria. Secondary GG and GGG donors are found to form very shallow hole traps, whereas the nucleobase deazaguanine forms a relatively deep hole trap. This conclusion is in accord with selected strand cleavage data and thus appears to be representative of the behavior of holes in duplex DNA. Our results are discussed in the context of current theoretical models of hole transport in DNA.     

Computational model of hole transport in DNA

A computational model based on the molecular dynamics (MD) simulation for the hole transport in DNA has been developed and applied to study hole current in DNA strands consisting of different numbers of GC pairs. The approach is based on the hopping mechanism which is thermally activated. The calculations show that the hole hopping intensifies with the temperature and the transport rate increases in agreement with the experimental evidence. It is also determined that the degree of structural ordering in the DNA strand enhances the hole conductivity and reasons are provided why this may occur.     

Crossover from superexchange to hopping as the mechanism for photoinduced charge transfer in DNA hairpin conjugates

The mechanism and dynamics of photoinduced charge separation and charge recombination have been investigated in synthetic DNA hairpins possessing donor and acceptor stilbenes separated by one to seven A:T base pairs. The application of femtosecond broadband pump-probe spectroscopy, nanosecond transient absorption spectroscopy, and picosecond fluorescence decay measurements permits detailed analysis of the formation and decay of the stilbene acceptor singlet state and of the charge-separated intermediates. When the donor and acceptor are separated by a single A:T base pair, charge separation occurs via a single-step superexchange mechanism. However, when the donor and acceptor are separated by two or more A:T base pairs, charge separation occurs via a multistep process consisting of hole injection, hole transport, and hole trapping. In such cases, hole arrival at the electron donor is slower than hole injection into the bridging A-tract. Rate constants for charge separation (hole arrival) and charge recombination are dependent upon the donor-acceptor distance; however, the rate constant for hole injection is independent of the donor-acceptor distance. The observation of crossover from a superexchange to a hopping mechanism provides a "missing link" in the analysis of DNA electron transfer and requires reevaluation of the existing literature for photoinduced electron transfer in DNA.     

The effect of varied ion distributions on long-range DNA charge transport

Long-range oxidative damage to DNA was utilized as a probe to delineate the effects of different ion distributions on DNA charge transport. DNA assemblies were constructed, containing a tethered rhodium intercalating photooxidant, spatially separated from two 5'-GG-3' sites of oxidative damage, with either an A6-tract or a mixed DNA sequence intervening between the guanine doublets; the extent of charge transport was assessed through measurements of the ratio of yields of damage at the guanine doublet distal versus that proximal to the metal binding site. The distal/proximal damage ratios were compared after photooxidation of otherwise identical Rh-tethered assemblies, except for 32P-labeling either at the 5'- or 3'-end; this labeling difference corresponds, in the absence of charge neutralization by condensed counterions, to a shift in negative charge from one end of the duplex to the other. Both with assemblies containing the mixed sequence and the A6-tract, we observed that moving the negative charges to the proximal end of the duplex significantly decreased hole transport to the distal end. We propose that these results reflect variations in the thermodynamic potential at the proximal and distal guanine sites because of the change in charges at the termini of the oligomer. High values for the internal dielectric constant of the stacked base pairs are suggested by these data. Hence, the longitudinal polarizability of DNA may be important to consider in mechanisms for long-range DNA charge transport.     

Kinetics of weak distance-dependent hole transfer in DNA by adenine-hopping mechanism

The kinetics of hole transfer in DNA by adenine-hopping mechanism was investigated by the combined pulse radiolysis-laser flash photolysis method. The hole transfer from Ptz*+* to oxG across the (A)n-bridge preceded by the A-hopping mechanism and the weak distance-dependent hole transfer with the rates faster than 108 s-1 over the distance range of 7-22 A was demonstrated. In contrast, hole transfer from oxG*+ to Ptz followed the single-step super exchange mechanism. Thus, two different processes for the hole transfer across the identical (A)n-bridge in DNA have been demonstrated. The results clearly show that the mechanism of hole transfer in DNA strongly depends on the redox nature of the oxidant, whether it produces only G*+ or both A*+ and G*+.     

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.     

What governs the charge transfer in DNA? The role of DNA conformation and environment

Charge transfer in DNA has received much attention in the last few years due to its role in oxidative damage and repair in DNA and also due to possible applications of DNA in nanoelectronics. Despite intense experimental and theoretical efforts, the mechanism underlying long-range hole transport is still unresolved. This is in particular due to the sensitive dependence of charge transfer on the complex structure and dynamics of DNA and the interaction with the solvent, which could not be addressed adequately in the modeling approaches up to now. In this work, we study the factors governing hole transfer in detail, using a DFT-based fragment-orbital method, which allows to compute the charge transfer parameters along multinanosecond molecular dynamics simulations. Environmental effects are captured using a hybrid quantum mechanics-molecular mechanics (QM/MM) coupling scheme. This methodology allows to analyze several factors responsible for charge transfer in DNA in detail. The fluctuation of counterions, strongly counterbalanced by the surrounding water, leads to large oscillations of onsite energies, which govern the energetics of hole propagation along the DNA strand. In contrast, the electronic couplings depend only on DNA conformation and are not affected by the solvent. In particular, the onsite energies are strongly correlated between neighboring nucleobases, indicating that a conformational-gating type of mechanism may be induced by the collective environmental degrees of freedom.     

Development of donor-acceptor modified DNA hairpins for the investigation of charge hopping kinetics in DNA

Investigation of hole or excess electron hopping in DNA is mostly performed based on yield studies, in which an injector modified DNA duplex is irradiated to continuously inject either holes or electrons into the duplex. Observed is a chemical reaction of a "probe" molecule, which can be either one of the two purine bases or a different trap molecule positioned at various distances. The next step in the field will be the direct time resolution of the hole or electron transfer kinetics in DNA. Herein we describe the development of defined donor-DNA-acceptor systems, with properties that may allow time resolved electron and hole transfer studies in stably folded DNA structures.     

Direct chemical evidence for charge transfer between photoexcited 2-aminopurine and guanine in duplex DNA

Photoexcited 2-aminopurine (Ap*) is extensively exploited as a fluorescent base analogue in the study of DNA structure and dynamics. Quenching of Ap* in DNA is often attributed to stacking interactions between Ap* and DNA bases, despite compelling evidence indicating that charge transfer (CT) between Ap* and DNA bases contributes to quenching. Here we present direct chemical evidence that Ap* undergoes CT with guanine residues in duplex DNA, generating oxidative damage at a distance. Irradiation of Ap in DNA containing the modified guanine, cyclopropylguanosine (CPG), initiates hole transfer from Ap* followed by rapid ring opening of the CPG radical cation. Ring opening accelerates hole trapping to a much shorter time regime than for guanine radicals in DNA; consequently, trapping effectively competes with back electron transfer (BET) leading to permanent CT chemistry. Significantly, BET remains competitive, even with this much faster trapping reaction, consistent with measured kinetics of DNA-mediated CT. The distance dependence of BET is sharper than that of forward CT, leading to an inverted dependence of product yield on distance; at short distances product yield is inhibited by BET, while at longer distances trapping dominates, leading to permanent products. The distance dependence of product yield is distinct from forward CT, or charge injection. As with photoinduced charge transfer in other chemical and biological systems, rapid kinetics for charge injection into DNA need not be associated with a high yield of DNA damage products.     

Effects of reaction rate of radical anion of a photosensitizer with molecular oxygen on the photosensitized DNA damage

Based on the synthesis of DNA modified with photosensitizers, direct spectroscopic measurements of the hole transfer in DNA, and quantification of the yield of the DNA oxidative damage, the reaction rate of the radical anion of the photosensitizer was demonstrated to be critically important in determining the efficiency of photosensitized DNA damage.     

Robust charge transport in DNA double crossover assemblies

BACKGROUND: Multiple-stranded DNA assemblies, encoded by sequence, have been constructed in an effort to self-assemble nanodevices of defined molecular architecture. Double-helical DNA has been probed also as a molecular medium for charge transport. Conductivity studies suggest that DNA displays semiconductor properties, whereas biochemical studies have shown that oxidative damage to B-DNA at the 5'-G of a 5'-GG-3' doublet can occur by charge transport through DNA up to 20 nm from a photo-excited metallointercalator. The possible application of DNA assemblies, in particular double crossover (DX) molecules, in electrical nanodevices prompted the design of a DNA DX assembly with oxidatively sensitive guanine moieties and a tethered rhodium photo-oxidant strategically placed to probe charge transport. RESULTS: DX assemblies support long-range charge transport selectively down the base stack bearing the intercalated photo-oxidant. Despite tight packing, no electron transfer (ET) crossover to the adjacent base stack is observed. Moreover, the base stack of a DX assembly is well-coupled and less susceptible than duplex DNA to stacking perturbations. Introducing a double mismatch along the path for charge transport entirely disrupts long-range ET in duplex DNA, but only marginally decreases it in the analogous stack within DX molecules. CONCLUSIONS: The path for charge transport in a DX DNA assembly is determined directly by base stacking. As a result, the two closely packed stacks within this assembly are electronically insulated from one another. Therefore, DX DNA assemblies may serve as robust, insulated conduits for charge transport in nanoscale devices.     

Direct measurement of the dynamics of excess electron transfer through consecutive thymine sequence in DNA

Charge transfer in DNA is an essential process in biological systems because of its close relation to DNA damage and repair. DNA is also an important material used in nanotechnology for wiring and constructing various nanomaterials. Although hole transfer in DNA has been investigated by various researchers and the dynamic properties of this process have been well established, the dynamics of a negative charge, that is, excess electron, in DNA have not been revealed until now. In the present paper, we directly measured the rate of excess electron transfer (EET) through a consecutive thymine (T) sequence in nicked-dumbbell DNAs conjugated with a tetrathiophene derivative (4T) as an electron donor and diphenylacetylene (DPA) as an electron acceptor at both ends. The selective excitation of 4T by a femtosecond laser pulse caused the excess electron injection into DNA, and led to EET in DNA by a consecutive T-hopping mechanism, which eventually formed the DPA radical anion (DPA(?-)). The rate constant for the process of EET through consecutive T was determined to be (4.4 ± 0.3) × 10(10) s(-1) from an analysis of the kinetic traces of the ΔO.D. during the laser flash photolysis. It should be emphasized that the EET rate constant for T-hopping is faster than the rate constants for oxidative hole transfers in DNA (10(4) to 10(10) s(-1) for A- and G-hopping).     

DNA logic gates

A conceptually new logic gate based on DNA has been devised. Methoxybenzodeazaadenine ((MD)A), an artificial nucleobase which we recently developed for efficient hole transport through DNA, formed stable base pairs with T and C. However, a reasonable hole-transport efficiency was observed in the reaction for the duplex containing an (MD)A/T base pair, whereas the hole transport was strongly suppressed in the reaction using a duplex where the base opposite (MD)A was replaced by C. The influence of complementary pyrimidines on the efficiency of hole transport through (MD)A was quite contrary to the selectivity observed for hole transport through G. The orthogonality of the modulation of these hole-transport properties by complementary pyrimidine bases is promising for the design of a new molecular logic gate. The logic gate system was executed by hole transport through short DNA duplexes, which consisted of the "logic gate strand", containing hole-transporting nucleobases, and the "input strand", containing pyrimidines which modulate the hole-transport efficiency of logic bases. A logic gate strand containing multiple (MD)A bases in series provided the basis for a sharp AND logic action. On the other hand, for OR logic and combinational logic, conversion of Boolean expressions to standard sum-of-product (SOP) expressions was indispensable. Three logic gate strands were designed for OR logic according to each product term in the standard SOP expression of OR logic. The hole-transport efficiency observed for the mixed sample of logic gate strands exhibited an OR logic behavior. This approach is generally applicable to the design of other complicated combinational logic circuits such as the full-adder.     

DNA hole transport on an electrode: application to effective photoelectrochemical SNP typing

A useful feature of DNA is that long-range hole transport through DNA is readily achieved. Photostimulated long-range hole transport through DNA has prospective use in the development of a conceptually new electrochemical single-nucleotide polymorphism (SNP) typing method for use as a versatile platform for gene diagnostics and pharmacogenetics. We have applied artificial DNAs designed for photostimulated long-range hole transport through DNA to SNP typing. By hybridizing photosensitizer-equipped DNA probes, immobilized on gold working electrodes, with a target DNA strand containing an SNP site, we observed a cathodic photocurrent, which markedly changed depending on the nature of the base at the specific site. The use of a combination of hole-transporting bases constitutes a very powerful method for a single-step electrochemical assay applicable to SNP typing of all types of sequences.