Impact of a single base pair substitution on the charge transfer rate along short DNA hairpins.

Numerical studies of hole migration along short DNA hairpins were performed with a particular emphasis on the variations of the rate and quantum yield of the charge separation process with the location of a single guanine:cytosine (G:C) base pair. Our calculations show that the hole arrival rate increases as the position of the guanine:cytosine base pair shifts from the beginning to the end of the sequence. Although these results are in agreement with recent experimental findings, the mechanism governing the charge migration along these sequences is revisited here. Instead of the phenomenological two-step hopping mechanism via the guanine base, the charge propagation occurs through a delocalization of the hole density along the base pair stack. Furthermore, the variations of the charge transfer with the position of the guanine base are explained by the impact of the base pair substitutions on the delocalized conduction channels.

Charge Transport across DNA-Based Three-Way Junctions.

DNA-based molecular electronics will require charges to be transported from one site within a 2D or 3D architecture to another. While this has been shown previously in linear, π-stacked DNA sequences, the dynamics and efficiency of charge transport across DNA three-way junction (3WJ) have yet to be determined. Here, we present an investigation of hole transport and trapping across a DNA-based three-way junction systems by a combination of femtosecond transient absorption spectroscopy and molecular dynamics simulations. Hole transport across the junction is proposed to be gated by conformational fluctuations in the ground state which bring the transiently populated hole carrier nucleobases into better aligned geometries on the nanosecond time scale, thus modulating the π-π electronic coupling along the base pair sequence.

Between superexchange and hopping: an intermediate charge-transfer mechanism in poly(A)-poly(T) DNA hairpins.

We developed a model for hole migration along relatively short DNA hairpins with fewer that seven adenine (A):thymine (T) base pairs. The model was used to simulate hole migration along poly(A)-poly(T) sequences with a particular emphasis on the impact of partial hole localization on the different rate processes. The simulations, performed within the framework of the stochastic surrogate Hamiltonian approach, give values for the arrival rate in good agreement with experimental data. Theoretical results obtained for hairpins with fewer than three A:T base pairs suggest that hole transfer along short hairpins occurs via superexchange. This mechanism is characterized by the exponential distance dependence of the arrival rate on the donor/acceptor distance, k(a) ≃ e(-ßR), with ß = 0.9 Å(-1). For longer systems, up to six A:T pairs, the distance dependence follows a power law k(a) ≃ R(-η) with η = 2. Despite this seemingly clear signature of unbiased hopping, our simulations show the complete delocalization of the hole density along the entire hairpin. According to our analysis, the hole transfer along relatively long sequences may proceed through a mechanism which is distinct from both coherent single-step superexchange and incoherent multistep hopping. The criterion for the validity of this mechanism intermediate between superexchange and hopping is proposed. The impact of partial localization on the rate of hole transfer between neighboring A bases was also investigated.

Exponential distance dependence of photoinitiated stepwise electron transfer in donor-bridge-acceptor molecules: implications for wirelike behavior.

Donor-bridge-acceptor (D-B-A) systems in which a 3,5-dimethyl-4-(9-anthracenyl)julolidine (DMJ-An) chromophore and a naphthalene-1,8:4,5-bis(dicarboximide) (NI) acceptor are linked by oligomeric 2,7-fluorenone (FN(n)) bridges (n = 1-3) have been synthesized. Selective photoexcitation of DMJ-An quantitatively produces DMJ(+•)-An(-•), and An(-•) acts as a high-potential electron donor. Femtosecond transient absorption spectroscopy in the visible and mid-IR regions showed that electron transfer occurs quantitatively in the sequence: DMJ(+•)-An(-•)-FN(n)-NI → DMJ(+•)-An-FN(n)(-•)-NI → DMJ(+•)-An-FN(n)-NI(-•). The charge-shift reaction from An(-•) to NI(-•) exhibits an exponential distance dependence in the nonpolar solvent toluene with an attenuation factor (ß) of 0.34 Å(-1), which would normally be attributed to electron tunneling by the superexchange mechanism. However, the FN(n)(-•) radical anion was directly observed spectroscopically as an intermediate in the charge-separation mechanism, thereby demonstrating conclusively that the overall charge separation involves the incoherent hopping (stepwise) mechanism. Kinetic modeling of the data showed that the observed exponential distance dependence is largely due to electron injection onto the first FN unit followed by charge hopping between the FN units of the bridge biased by the distance-dependent electrostatic attraction of the two charges in D(+•)-B(-•)-A. This work shows that wirelike behavior does not necessarily result from building a stepwise, energetically downhill redox gradient into a D-B-A molecule.

Effects of various halogen anions and cations of alkali metals on energetics of excess charge recombination in stilbene donor-acceptor capped DNA hairpins.

DNA hairpin conjugates with a stilbenedicarboxamide (Sa) hole donor and a stilbenediether (Sd) hole acceptor are considered as model systems for studying charge recombination (CR) of excess charges in DNA. Using the method of thermodynamic integration, we estimated the relative free energies of this process in hairpins with three adenine:thymine pairs between Sa and Sd surrounded by 1 M aqueous solutions of ionic compounds M(+)Cl(-) (M = Li, Na, K) and Na(+)X(-) (X = F, Cl, Br, I). The values of this quantity were calculated with respect to the free energy for the same hairpin in the 1 M NaCl aqueous solution. Based on the results obtained, we conclude that halogen anions have no significant influence on the rate of the CR reaction. By contrast, cations of other alkali metals can considerably change the potential barrier of the process, thus affecting the reaction rate. Different results obtained for cations and anions were attributed to the fundamental distinction in the electrostatic interactions of M(+) and X(-) species with negatively charged phosphate groups of the hairpin. In addition, our results show that the relative free energy of CR is larger for cations that are able to be closer to Sd and Sa structural units. The latter correlation suggests that the replacement of Na(+) by cations of other alkali metals enables one to change the CR rate modifying it in either direction.

Effect of GC base pairs on charge transfer through DNA hairpins: the importance of electrostatic interactions.

DNA hairpins in which an electron donor and an electron acceptor are attached to the ends are excellent model systems for the study of charge transfer in weakly coupled pi-stacked systems. In this communication we report on a computational study of the effect of the base pair sequence in these DNA hairpins on the kinetics of charge transfer. We show that the rate of charge transfer strongly depends on the actual position of a GC base pair in a sequence that otherwise only contains AT base pairs. This can be explained by evaluating the energy landscape through which the charge travels. It is shown that including the electrostatic interaction between electron and hole can explain the experimentally observed dependence on the position of the GC in the DNA. We conclude that electrostatic interactions are important to consider when explaining the charge transfer kinetics in GC containing DNA sequences.

Effect of structural dynamics on charge transfer in DNA hairpins.

We present a theoretical study of the positive charge transfer in stilbene-linked DNA hairpins containing only AT base pairs using a tight-binding model that includes a description of structural fluctuations. The parameters are the charge transfer integral between neighboring units and the site energies. Fluctuations in these parameters were studied by a combination of molecular dynamics simulations of the structural dynamics and density functional theory calculations of charge transfer integrals and orbital energies. The fluctuations in both parameters were found to be substantial and to occur on subpicosecond time scales. Tight-binding calculations of the dynamics of charge transfer show that for short DNA hairpins (<4 base pairs) the charge moves by a single-step superexchange mechanism with a relatively strong distance dependence. For longer hairpins, a crossover to a fluctuation-assisted incoherent mechanism was found. Analysis of the charge distribution during the charge transfer process indicates that for longer bridges substantial charge density builds up on the bridge, but this charge density is mostly confined to the adenine next to the hole donor. This is caused by the electrostatic interaction between the hole on the AT bridge and the negative charge on the hole donor. We conclude both that the relatively strong distance dependence for short bridges is mostly due to this electrostatic interaction and that structural fluctuations play a critical role in the charge transfer, especially for longer bridge lengths.

Artificial genetic selection for an efficient translation initiation site for expression of human RACK1 gene in Escherichia coli.

In bacterial expression systems, translation initiation is usually the rate limiting and the least predictable stage of protein synthesis. Efficiency of a translation initiation site can vary dramatically depending on the sequence context. This is why many standard expression vectors provide very poor expression levels of some genes. This notion persuaded us to develop an artificial genetic selection protocol, which allows one to find for a given target gene an individual efficient ribosome binding site from a random pool. In order to create Darwinian pressure necessary for the genetic selection, we designed a system based on translational coupling, in which microorganism survival in the presence of antibiotic depends on expression of the target gene, while putting no special requirements on this gene. Using this system we obtained superproducing constructs for the human protein RACK1 (receptor for activated C kinase).

Deep-hole transfer leads to ultrafast charge migration in DNA hairpins.

Charge transport through the DNA double helix is of fundamental interest in chemistry and biochemistry, but also has potential technological applications such as for DNA-based nanoelectronics. For the latter, it is of considerable interest to explore ways to influence or enhance charge transfer. In this Article we demonstrate a new mechanism for DNA charge transport, namely 'deep-hole transfer', which involves long-range migration of a hole through low-lying electronic states of the nucleobases. Here, we demonstrate, in a combined experimental and theoretical study, that it is possible to achieve such transfer behaviour by changing the energetics of charge injection. This mechanism leads to an enhancement in transfer rates by up to two orders of magnitude and much weaker distance dependence. This transfer is faster than relaxation to the lowest-energy state, setting this mechanism apart from those previously described. This opens up a new direction to optimize charge transfer in DNA with unprecedented charge-transfer rates.

Conformationally Gated Charge Transfer in DNA Three-Way Junctions.

Molecular structures that direct charge transport in two or three dimensions possess some of the essential functionality of electrical switches and gates. We use theory, modeling, and simulation to explore the conformational dynamics of DNA three-way junctions (TWJs) that may control the flow of charge through these structures. Molecular dynamics simulations and quantum calculations indicate that DNA TWJs undergo dynamic interconversion among "well stacked" conformations on the time scale of nanoseconds, a feature that makes the junctions very different from linear DNA duplexes. The studies further indicate that this conformational gating would control charge flow through these TWJs, distinguishing them from conventional (larger size scale) gated devices. Simulations also find that structures with polyethylene glycol linking groups ("extenders") lock conformations that favor CT for 25 ns or more. The simulations explain the kinetics observed experimentally in TWJs and rationalize their transport properties compared with double-stranded DNA.

DNA base pair stacks with high electric conductance: a systematic structural search.

We report a computational search for DNA π-stack structures exhibiting high electric conductance in the hopping regime, based on the INDO/S calculations of electronic coupling and the method of data analysis called k-means clustering. Using homogeneous poly(G)-poly(C) and poly(A)-poly(T) stacks as the simplest structural models, we identify the configurations of neighboring G:C and A:T pairs that allow strong electronic coupling and, therefore, molecular electric conductance much larger than the values reported for the corresponding reference systems in the literature. A computational approach for modeling the impact of thermal fluctuations on the averaged dimer structure was also proposed and applied to the [(G:C),(G:C)] and [(A:T),(A:T)] duplexes. The results of this work may provide guidance for the construction of DNA devices and DNA-based elements of nanoscale molecular circuits. Several factors that cause changes of step parameters favorable to the formation of the predicted stack conformation with high electric conductance of DNA molecules are also discussed; favorable geometries may enhance the conductivity by factors as large as 15.

Effect of electrostatic interactions and dynamic disorder on the distance dependence of charge transfer in donor-bridge-acceptor systems.

Using a tight-binding model of charge transport in systems with static and dynamic disorder, we present a theoretical study of the positive charge transfer in molecular assemblies that involve a hole donor and an acceptor connected by fluorene and phenyl bridges. Two parameters that determine the rate of charge transfer within the proposed model are the charge transfer integral between neighboring units and the site energies. Fluctuations in the values of the charge transfer integral and the energy landscape for hole transport were calculated by taking into account variations of the dihedral angle between neighboring units and electrostatic interaction of positive charge moving along the bridge and the negative charge that remains on the hole donor. Analysis of the dynamics of hole transfer and the distribution of the positive charge during this process allows the conclusion that the rapid fall of the hole transfer rate coefficient observed in experiments with short bridges (three and four structural units for systems with fluorene and phenyl bridges, respectively) can be attributed to the electrostatic interaction. This interaction is responsible for the formation of the effective barrier between donor and acceptor with the height that increases as the number of structural bridge units remains less than 3 (fluorene bridge) or 4 (phenyl bridge). For longer bridges, however, the effective barrier changes only weakly and now the charge transport is mostly dominated by the fluctuation-assisted incoherent hole migration along the bridge. The latter mechanism exhibits much weaker dependence of the rate coefficient on the bridge length in agreement with the available experimental results.

Absolute rates of hole transfer in DNA.

Absolute rates of hole transfer between guanine nucleobases separated by one or two A:T base pairs in stilbenedicarboxamide-linked DNA hairpins were obtained by improved kinetic analysis of experimental data. The charge-transfer rates in four different DNA sequences were calculated using a density-functional-based tight-binding model and a semiclassical superexchange model. Site energies and charge-transfer integrals were calculated directly as the diagonal and off-diagonal matrix elements of the Kohn-Sham Hamiltonian, respectively, for all possible combinations of nucleobases. Taking into account the Coulomb interaction between the negative charge on the stilbenedicarboxamide linker and the hole on the DNA strand as well as effects of base pair twisting, the relative order of the experimental rates for hole transfer in different hairpins could be reproduced by tight-binding calculations. To reproduce quantitatively the absolute values of the measured rate constants, the effect of the reorganization energy was taken into account within the semiclassical superexchange model for charge transfer. The experimental rates could be reproduced with reorganization energies near 1 eV. The quantum chemical data obtained were used to discuss charge carrier mobility and hole-transport equilibria in DNA.