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.     

Electric polarizability of DNA in aqueous salt solution

Monte Carlo simulations are performed to determine the anisotropy of the electric polarizability of a model DNA fragment in aqueous salt solution. By taking into consideration the participation of coions in the electroneutrality condition, at every simulation step, we obtain a list of counterions constituting the net charge arranged in increasing order of their distance from the DNA and calculate the contribution to the dipole moment from the first n counterions in the list. We define a partial polarizability tensor due to these n counterions to understand the origin of the polarizability in close relation to the solution structure. The ionic distributions are described by the counterion condensation theory. Characteristic features of the electric properties of polyelectrolytes are reproduced. The anisotropy of the electric polarizability Deltaalpha of DNA decreases with the addition of salt, yielding values comparable to experiment. The effect of electrophoretic motion of the polyion is examined by estimating its upper limit.     

Hole transfer in DNA: DNA as a scaffold for hole transfer between two organic molecules

Hole transfer process in ODNs conjugated with two organic molecules, pyrene (Py) and phenothiazine (Ptz) was investigated with the pulse radiolysis measurements. Monitoring the transient absorption of Py⁺ and Ptz⁺, it was shown that the hole transfer rate was dependent on the distance and sequence between Py and Ptz.     

Cation-independent electron transfer between ferricyanide and ferrocyanide ions in aqueous solution

Electron transfer between Fe(CN)(6)(3-) and Fe(CN)(6)(4-) in homogeneous aqueous solution with K(+) as the counterion normally proceeds almost exclusively by a K(+)-catalyzed pathway, but this can be suppressed, and the direct Fe(CN)(6)(3)(-)-Fe(CN)(6)(4-) electron transfer path exposed, by complexing the K(+) with crypt-2.2.2 or 18-crown-6. Fe((13)CN)(6)(4-)-NMR line broadening measurements using either crypt-2.2.2 or (with extrapolation to zero uncomplexed [K(+)]) 18-crown-6 gave consistent values for the rate constant and activation volume (k(0) = (2.4 +/- 0.1) x 10(2) L mol(-1) s(-1) and Delta V(0) = -11.3 +/- 0.3 cm(3) mol(-1), respectively, at 25 degrees C and ionic strength I = 0.2 mol L(-1)) for the uncatalyzed electron transfer path. These values conform well to predictions based on Marcus theory. When [K(+)] was controlled with 18-crown-6, the observed rate constant k(ex) was a linear function of uncomplexed [K(+)], giving k(K) = (4.3 +/- 0.1) x 10(4) L(2) mol(-2) s(-1) at 25 degrees C and I = 0.26 mol L(-1) for the K(+)-catalyzed pathway. When no complexing agent was present, k(ex) was roughly proportional to [K(+)](total), but the corresponding rate constant k(K)' (=k(ex)/[K(+)](total)) was about 60% larger than k(K), evidently because ion pairing by hydrated K(+) lowered the anion-anion repulsions. Ionic strength as such had only a small effect on k(0), k(K), and k(K)'. The rate constants commonly cited in the literature for the Fe(CN)(6)(3-/4-) self-exchange reaction are in fact k(K)'[K(+)](total) values for typical experimental [K(+)](total) levels.     

Proton transfer reactions in aqueous solution of 2-vinylquinoline copolymers

Fluorescence spectra of atactic and isolaclic poly-2-vinylquinoline and copolymers of 2-vinylquinoline and four non fluorescent comonomers have been measured as a function of pH. The homopolymers and the copolymers with pyrrolidone show two band fluorescence spectra; their intensity ratio changes with pH, polymer concentration and excitation wavelength. For the other copolymers the emission of the protonated heterocycle is only a shoulder of the emission of the neutral form. A kinetic scheme has been proposed to explain these results.     

Interaction of DNA fragments with counterions in aqueous solution

Monte Carlo simulation of the hydration of metal ion—DMP⁻ and metal ion—9-methylguanine complexes was performed. A comparative analysis of the results for Na⁺ and K⁺ ions was carried out. The main stages of dissociation were revealed. The energy effects of dissociation were evaluated. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2174–2177, November, 1998.     

A molecular dynamics calculations of hole transfer rates in DNA strands

A computational model, which includes both tunneling and thermal hopping mechanisms, has been applied to study the charge transfer in DNA (GC)n and (AT)n strands. The calculations revealed the crucial role played by the A or G NH2-group vibrations in the hole transfer in both types of strands. Charge-transfer rates in the two strands have been determined based on the molecular dynamics calculations. They are in good agreement with the available experimental data. The modeling approach used here may be employed in the theoretical study of the charge transfer in natural and artificial DNA strands containing AT and GC pairs.     

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.     

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*+.     

Intramolecular proton transfer of serine in aqueous solution. Mechanism and energetics

Serine amino acid in aqueous solution is theoretically studied at the B3PW91/6-31+G^** level using a dielectric continuum solvent model. Neutral and zwitterionic structures in the gas phase and in solution are described and the proton-transfer mechanism is discussed. A neutral conformation in which the carboxyl hydrogen atom is already oriented toward the amino group seems to be the absolute energy minimum in the gas phase and the most stable neutral form in solution. The absolute energy minimum in solution is a zwitterionic form. The energy barrier for proton transfer is predicted to be very small, in particular when zero-point-energy contributions are added. Our calculations allow the dynamic aspects of the ionization mechanism to be discussed by incorporating nonequilibrium effects. Received: 28 June 1999 / Accepted: 13 October 1999 / Published online: 14 March 2000     

DNA diffusion in aqueous solution in presence of suspended particles

Although nanoparticles, which are comparable in size to polymer chains, are widely used as fillers to polymer matrices for developing functional and high performance materials, the dynamics of polymers constrained between solid particles has not been well elucidated. In this study, dynamics of individual polymer under such condition was investigated with fluorescent microscopy using DNA solutions as model systems. For individual T4 and λ DNA molecules in aqueous suspensions of spherical polystyrene particles with diameter of 1 μm, it was found that (i) the radius of gyration of DNA is independent of the particle volume fraction, ?_p, (ii) DNA diffusion is not sensitive to ?_p up to a certain critical ?_p where the average distance between particle surfaces is close to DNA size, and (iii) the DNA diffusion becomes slower at higher ?_p. The diffusion coefficient of DNA was larger, by a factor of 2, in the suspensions at intermediate ?_p than in the corresponding confined geometry (channel/slit between fixed walls), whereas this difference asymptotically vanished with increasing ?_p. This result suggested that the DNA diffusion in the suspensions with intermediate ?_p is accelerated by the particle motion. In fact, the diffusion coefficient measured for DNA in the suspensions was semiquantitatively described by the Rouse constraint‐release model considering the matrix effect on the probe chain diffusion. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 1103–1111, 2009     

Mobility mechanism of hydroxyl radicals in aqueous solution via hydrogen transfer

The hydroxyl radical (OH*) is a highly reactive oxygen species that plays a salient role in aqueous solution. The influence of water molecules upon the mobility and reactivity of the OH* constitutes a crucial knowledge gap in our current understanding of many critical reactions that impact a broad range of scientific fields. Specifically, the relevant molecular mechanisms associated with OH* mobility and the possibility of diffusion in water via a H-transfer reaction remain open questions. Here we report insights into the local hydration and electronic structure of the OH* in aqueous solution from Car-Parrinello molecular dynamics and explore the mechanism of H-transfer between OH* and a water molecule. The relatively small free energy barrier observed (~4 kcal/mol) supports a conjecture that the H-transfer can be a very rapid process in water, in accord with very recent experimental results, and that this reaction can contribute significantly to OH* mobility in aqueous solution. Our findings reveal a novel H-transfer mechanism of hydrated OH*, resembling that of hydrated OH(-) and presenting hybrid characteristics of hydrogen-atom and electron-proton transfer processes, where local structural fluctuations play a pivotal role.     

Theoretical rate constants of super-exchange hole transfer and thermally induced hopping in DNA

Recently, the electronic properties of DNA have been extensively studied, because its conductivity is important not only to the study of fundamental biological problems, but also in the development of molecular-sized electronics and biosensors. We have studied theoretically the reorganization energies, the activation energies, the electronic coupling matrix elements, and the rate constants of hole transfer in B-form double-helix DNA in water. To accommodate the effects of DNA nuclear motions, a subset of reaction coordinates for hole transfer was extracted from classical molecular dynamics (MD) trajectories of DNA in water and then used for ab initio quantum chemical calculations of electron coupling constants based on the generalized Mulliken-Hush model. A molecular mechanics (MM) method was used to determine the nuclear Franck-Condon factor. The rate constants for two types of mechanisms of hole transfer-the thermally induced hopping (TIH) and the super-exchange mechanisms-were determined based on Marcus theory. We found that the calculated matrix elements are strongly dependent on the conformations of the nucleobase pairs of hole-transferable DNA and extend over a wide range of values for the "rise" base-step parameter but cluster around a particular value for the "twist" parameter. The calculated activation energies are in good agreement with experimental results. Whereas the rate constant for the TIH mechanism is not dependent on the number of A-T nucleobase pairs that act as a bridge, the rate constant for the super-exchange process rapidly decreases when the length of the bridge increases. These characteristic trends in the calculated rate constants effectively reproduce those in the experimental data of Giese et al. [Nature 2001, 412, 318]. The calculated rate constants were also compared with the experimental results of Lewis et al. [Nature 2000, 406, 51].     

Electrogenerated chemiluminescence induced by sequential hot electron and hole injection into aqueous electrolyte solution

Hole injection into aqueous electrolyte solution is proposed to occur when oxide-coated aluminum electrode is anodically pulse-polarized by a voltage pulse train containing sufficiently high-voltage anodic pulses. The effects of anodic pulses are studied by using an aromatic Tb(III) chelate as a probe known to produce intensive hot electron-induced electrochemiluminescence (HECL) with plain cathodic pulses and preoxidized electrodes. The presently studied system allows injection of hot electrons and holes successively into aqueous electrolyte solutions and can be utilized in detecting electrochemiluminescent labels in fully aqueous solutions, and actually, the system is suggested to be quite close to a pulse radiolysis system providing hydrated electrons and hydroxyl radicals as the primary radicals in aqueous solution without the problems and hazards of ionizing radiation. The analytical power of the present excitation waveforms are that they allow detection of electrochemiluminescent labels at very low detection limits in bioaffinity assays such as in immunoassays or DNA probe assays. The two important properties of the present waveforms are: (i) they provide in situ oxidation of the electrode surface resulting in the desired oxide film thickness and (ii) they can provide one-electron oxidants for the system by hole injection either via F- and F⁺-center band of the oxide or by direct hole injection to valence band of water at highly anodic pulse amplitudes.     

Long-lived charge-separated state leading to DNA damage through hole transfer

The hole transfer causes the long-lived charge-separated state in DNA during the photosensitized one-electron oxidation of DNA. The combination of the transient absorption measurement and DNA damage quantification by HPLC clearly demonstrated that the yield of the DNA damage correlates well with the lifetime of the charge-separated state.     

Complexation of DNA with cationic gemini surfactant in aqueous solution

Interactions between DNA and the cationic gemini surfactant trimethylene-1,3-bis(dodecyldimethylammonium bromide) (12-3-12) in aqueous solution have been investigated by UV-vis transmittance, zeta potential, and fluorescence emission spectrum. Complexes of DNA and gemini surfactant are observed in which the negative charges of DNA are neutralized by cationic surfactants effectively. The DNA-induced micelle-like structure of the surfactant due to the electrostatic and hydrophobic interactions is determined by the fluorescence spectrum of pyrene. It is found that the critical aggregation concentration (CAC) for DNA/12-3-12 complexes depends little on the addition of sodium bromide (NaBr) because of the counterbalance salt effect. However, at high surfactant concentration, NaBr facilitates the formation of larger DNA/surfactant aggregates. Displacement of ethidium bromide (EB) by surfactant evidently illustrates the strong cooperative binding between surfactant and DNA. In contrast to that in the absence of surfactant, the added NaBr at high surfactant concentration influences not only the binding of surfactant with DNA, but also the stability of DNA/EB complex.     

Mechanism of charge separation in DNA by hole transfer through consecutive adenines

To investigate the mechanism of charge separation in DNA with consecutive adenines adjacent to a photosensitizer (Sens), a series of naphthalimide (NI) and 5-bromouracil ((br)U)-modified DNAs were prepared, and the quantum yields of formation of the charge-separated states (Phi) upon photo-excitation of the Sens NI in DNA were measured. The Phi was modulated by the incorporation site of (br)U, which changes the oxidation potential of its complementary A through hydrogen bonding and the hole-transfer rates between adenines. The results were interpreted as charge separation by means of the initial charge transfer between NI in the singlet excited state and the second- and third-nearest adenine to the NI. In addition, the oxidation of the A nearest to NI leads to the rapid charge recombination within a contact ion pair. This suggests that the charge-separation process can be refined to maximize the Phi by putting a redox-inactive spacer base pair between a photosensitizer and an A-T stretch.     

CASSCF/CAS-PT2 study of hole transfer in stacked DNA nucleobases

CASSCF and CAS-PT2 calculations are performed for the ground and excited states of radical cations consisting of two and three nucleobases. The generalized Mulliken-Hush approach is employed for estimating electronic couplings for hole transfer in the pi-stacks. We compare the CASSCF results with data obtained within Koopmans' approximation. The calculations show that an excess charge in the ground and excited states in the systems is quite localized on a single base both at the CASSCF level and in Koopmans' picture. However, the CASSCF calculations point to a larger degree of localization and, in line with this, smaller transition dipole moments. The agreement between the CAS-PT2 corrected energy gaps and the values estimated with Koopmans' theorem is better, with the CAS-PT2 calculations giving somewhat smaller gaps. Overall, both factors result in smaller CASSCF/CAS-PT2 couplings, which are reduced by up to 40% of the couplings calculated using Koopmans' approximation. The tabulated data can be used as benchmark values for the electronic couplings of stacked nucleobases. For the base trimers, comparison of the results obtained within two- and three-state models show that the multistate treatment should be applied to derive reliable estimates. Finally, the superexchange approach to estimate the donor acceptor electronic coupling in the stacks GAG and GTG is considered.