Conformationally Gated Rate Processes in Biological Macromolecules

Femtosecond dynamics of short-range protein electron transfer in flavodoxin

Intraprotein electron transfer (ET) in flavoproteins is important for understanding the correlation of their redox, configuration, and reactivity at the active site. Here, we used oxidized flavodoxin as a model system and report our complete characterization of a photoinduced redox cycle from the initial charge separation in 135-340 fs to subsequent charge recombination in 0.95-1.6 ps and to the final cooling relaxation of the product(s) in 2.5-4.3 ps. With 11 mutations at the active site, we observed that these ultrafast ET dynamics, much faster than active-site relaxation, mainly depend on the reduction potentials of the electron donors with minor changes caused by mutations, reflecting a highly localized ET reaction between the stacked donor and acceptor at a van der Waals distance and leading to a gas-phase type of bimolecular ET reaction confined in the active-site nanospace. Significantly, these ultrafast ET reactions ensure our direct observation of vibrationally excited reaction product(s), suggesting that the back ET barrier is effectively reduced because of the decrease in the total free energy in the Marcus inverted region, leading to the accelerated charge recombination. Such vibrationally coupled charge recombination should be a general feature of flavoproteins with similar configurations and interactions between the cofactor flavin and neighboring aromatic residues.

A Multibox Splitting Scheme: Robust Approximation For ab Initio Molecular Dynamics

In this work, the multibox (M-box) simulation scheme is introduced, which can be considered as a generalization of the QM/MM scheme for multifragment (molecular) systems. This scheme exploits the natural locality of multifragment molecular-based systems by mapping the system into force-coupled block subspaces. Where defined in this way, the entire system can be fully modeled under a quantum mechanical force field. This allows the description of each subspace explicitly by means of a robust electronic structure theory without the requirement for large computational resources. An adequate block-to-block coupling by means of shared subsystem fragments is applied to preserve the long-distance structural correlation in the system during a molecular dynamic (MD) simulation. Since electronic structure descriptions play a central role in the formulation of several parametric models for charge or energy transport, we expect that this space-time correlated scheme can become a reliable computational tool for charge/energy transport/transfer applications. The efficiency of the method is demonstrated by performing statistical and time-resolved analysis using both the multifragment box and full ab initio approaches. We illustrate the method using as examples the melting process of a one-dimensional benzene chain (weak interaction situation) and NVE dynamics for the CnHn polymeric chain (strong interaction situation). We also have extended the threshold of applicability of our model, demonstrating how it can cope with MD simulation with more complex systems and processes.

Electron tunneling through sensitizer wires bound to proteins

We report a quantitative theoretical analysis of long-range electron transfer through sensitizer wires bound in the active-site channel of cytochrome P450cam. Each sensitizer wire consists of a substrate group with high binding affinity for the enzyme active site connected to a ruthenium-diimine through a bridging aliphatic or aromatic chain. Experiments have revealed a dramatic dependence of electron transfer rates on the chemical composition of both the bridging group and the substrate. Using combined molecular dynamics simulations and electronic coupling calculations, we show that electron tunneling through perfluorinated aromatic bridges is promoted by enhanced superexchange coupling through virtual reduced states. In contrast, electron flow through aliphatic bridges occurs by hole-mediated superexchange. We have found that a small number of wire conformations with strong donor-acceptor couplings can account for the observed electron tunneling rates for sensitizer wires terminated with either ethylbenzene or adamantane. In these instances, the rate is dependent not only on electronic coupling of the donor and acceptor but also on the nuclear motion of the sensitizer wire, necessitating the calculation of average rates over the course of a molecular dynamics simulation. These calculations along with related recent findings have made it possible to analyze the results of many other sensitizer-wire experiments that in turn point to new directions in our attempts to observe reactive intermediates in the catalytic cycles of P450 and other heme enzymes.

Effect of curcumin on the amyloid fibrillogenesis of hen egg-white lysozyme

At least twenty human proteins can fold abnormally to form pathological deposits that are associated with several degenerative diseases. Despite extensive investigation on amyloid fibrillogenesis, its detailed molecular mechanisms remain unknown. This study is aimed at exploring the inhibitory activity of curcumin against the fibrillation of hen lysozyme. We found that the formation of amyloid fibrils at pH 2.0 in vitro was inhibited by curcumin in a dose-dependent manner. Moreover, quenching analysis confirmed the existence of an interaction between curcumin and lysozyme, and Van't Hoff analysis indicated that the curcumin-lysozyme interaction is predominantly governed by Van Der Waals force or hydrogen bonding. Curcumin was also found to acquire disaggregating ability on preformed lysozyme fibrils. Finally, we observed that curcumin pre-incubated at 25 degrees C for at least 7 days inhibited lysozyme fibrillogenesis better than untreated curcumin and the enhanced inhibition against HEWL fibrillation might be attributed to the presence of dimeric species.

DNA excited-state dynamics: from single bases to the double helix

Ultraviolet light is strongly absorbed by DNA, producing excited electronic states that sometimes initiate damaging photochemical reactions. Fully mapping the reactive and nonreactive decay pathways available to excited electronic states in DNA is a decades-old quest. Progress toward this goal has accelerated rapidly in recent years, in large measure because of ultrafast laser experiments. Here we review recent discoveries and controversies concerning the nature and dynamics of excited states in DNA model systems in solution. Nonradiative decay by single, solvated nucleotides occurs primarily on the subpicosecond timescale. Surprisingly, excess electronic energy relaxes one or two orders of magnitude more slowly in DNA oligo- and polynucleotides. Highly efficient nonradiative decay pathways guarantee that most excited states do not lead to deleterious reactions but instead relax back to the electronic ground state. Understanding how the spatial organization of the bases controls the relaxation of excess electronic energy in the double helix and in alternative structures is currently one of the most exciting challenges in the field.

Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments

Time-resolved Stokes-shift experiments measure the dynamics of biomolecules and of the perturbed solvent near them on subnanosecond time scales, but molecular dynamics simulations are needed to provide a clear interpretation of the results. Here we show that simulations using standard methods quantitatively reproduce the main features of TRSS experiments in DNA and provide a molecular assignment for the dynamics. The simulations reproduce the magnitude and unusual power-law dynamics of the Stokes shift seen in recent experiments [ Andreatta, D., et al. J. Am. Chem. Soc. 2005, 127, 7270 ]. A polarization model is introduced to eliminate cross-correlations between the different components contributing to the signal. Using this model, well-defined contributions of the DNA, water, and counterion to the experimental signal are extracted. Water is found to have the largest contribution and to be responsible for the power-law dynamics. The counterions have a smaller, but non-negligible, contribution with a time constant of 220 ps. The contribution to the signal of the DNA itself is minor and fits a 30 ps stretched exponential. Both time-averaged and dynamic distributions are calculated. They show a small subset of ions with a different coupling but no other evidence of substates or rate heterogeneity.

Inhibition of Amyloid Fibrillization of Hen Egg-White Lysozymes by Rifampicin and p-Benzoquinone

It has been reported that more than 20 different human proteins can fold abnormally, resulting in the formation of pathological deposits and several lethal degenerative diseases. Despite extensive investigations on amyloid fibril formation, the detailed molecular mechanism remained rather elusive. The current research, utilizing hen egg-white lysozymes as a model system, is aimed at exploring inhibitory activities of two potential molecules against lysozyme fibril formation. We first demonstrated that the formation of lysozyme amyloid fibrils at pH 2.0 was markedly enhanced by the presence of agitation in comparison with its quiescent counterpart. Next, via numerous spectroscopic techniques and transmission electron microscopy, our results revealed that the inhibition of lysozyme amyloid formation by either rifampicin or its analogue p-benzoquinone followed a concentration-dependent fashion. Furthermore, while both inhibitors were shown to acquire an anti-aggregating and a disaggregating activity, rifampicin, in comparison with p-benzoquinone, served as a more effective inhibitor against in vitro amyloid fibrillogenesis of lysozyme. It is our belief that the data reported in this work will not only reinforce the findings validated by others that rifampicin and p-benzoquinone serve as two promising preventive molecules against amyloid fibrillogenesis, but also shed light on a rational design of effective therapeutics for amyloidogenic diseases.

Interference, fluctuation, and alternation of electron tunneling in protein media. 2. Non-condon theory for the energy gap dependence of electron transfer rate

Developing the quantum transition rate theory of Prezhdo and Rossky (J. Chem. Phys. 1997, 107, 5863), we produced a new non-Condon theory of the rate of electron transfer (ET) which happens through a protein medium with conformational fluctuation. The new theory is expressed by a convolution form of the power spectrum for the autocorrelation function of the electronic tunneling matrix element T(DA)(t) with quantum correction and the ordinary Franck-Condon factor. The new theory satisfies the detailed balance condition for the forward and backward ET rates. The ET rate formula is divided into two terms of elastic and inelastic tunneling mechanisms on the mathematical basis. The present theory is applied to the ET from Bph(-) to Q(A) in the reaction center of Rhodobacter sphaeroides. Numerical calculations of T(DA)(t) were made by a combined method of molecular dynamics simulations and quantum chemistry calculations. We showed that the normalized autocorrelation function of T(DA)(t) is almost expressed by exponential forms. The calculated energy gap law of the ET rate is nearly Marcus' parabola in most of the normal region and around the maximum region, but it does not decay substantially in the inverted region, which is called the anomalous inverted region. We also showed that the energy gap law at the high uphill energy gap in the normal region is elevated considerably from the Marcus' parabola, which is called the anomalous normal region. Those anomalous energy gap laws are due to the inelastic tunneling mechanism which works actively at the energy gap far from zero. We presented an empirical formula for easily calculating the non-Condon ET rate, which is usable by many researchers. We provided experimental evidence for the anomalous inverted region which was basically reproduced by the present theory. The present theory was extensively compared with the previous non-Condon theories.

Ultrafast energy transfer and structural dynamics in DNA

Ultrafast structural dynamics concomitant to excitation energy transfer in DNA has been studied using a pair of pyrene-labeled DNA bases. The temporal evolution of the femtosecond pump-probe spectra reveals the existence of two electronic coupling pathways, through-base stack and through-space, which lead to excitation energy transfer and excimer formation even when the labeled DNA bases are separated by one AT base pair. The electronic coupling which mediates through-base stack energy transfer is so strong that a new absorption band arises in the excited-state absorption spectrum within 300 fs. From the analysis of time-dependent spectral shifts due to through-space excimer formation, the local structural dynamics and flexibility of DNA are characterized on the picosecond and nanosecond time scale.

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

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.

Dynamics of electron transport by elastic bending of short DNA duplexes. Experimental study and quantitative modeling of the cyclic voltammetric behavior of 3'-ferrocenyl DNA end-grafted on gold

The dynamics of electron transport within a molecular monolayer of 3'-ferrocenylated-(dT)(20) strands, 5'-thiol end-grafted onto gold electrode surfaces via a short C2-alkyl linker, is analyzed using cyclic voltammetry as the excitation/measurement technique. It is shown that the single-stranded DNA layer behaves as a diffusionless system, due to the high flexibility of the ss-DNA chain. Upon hybridization by the fully complementary (dA)(20) target, the DNA-modified gold electrode displays a highly unusual voltammetric behavior, the faradaic signal even ultimately switching off at a high enough potential scan rate. This remarkable extinction phenomenon is qualitatively and quantitatively justified by the model of elastic bending diffusion developed in the present work which describes the motion of the DNA-borne ferrocene moiety as resulting from the elastic bending of the duplex DNA toward and away from the electrode surface. Its use allows us to demonstrate that the dynamics of electron transport within the hybridized DNA layer is solely controlled by the intrinsic bending elasticity of ds-DNA. Fast scan rate cyclic voltammetry of end-grafted, redox-labeled DNA layers is shown to be an extremely efficient method to probe the bending dynamics of short-DNA fragments in the submillisecond time range. The persistence length of the end-anchored ds-DNA, a parameter quantifying the flexibility of the nanometer-long duplex, can then be straightforwardly and accurately determined from the voltammetry data.

Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model

The internal motions of proteins may serve as a "gate" in some systems, which controls ligand-protein association. This study applies Brownian dynamics simulations in a coarse-grained model to study the gated association rate constants of HIV-1 proteases and drugs. The computed gated association rate constants of three protease mutants, G48V/V82A/I84V/L90M, G48V, and L90M with three drugs, amprenavir, indinavir, and saquinavir, yield good agreements with experiments. The work shows that the flap dynamics leads to "slow gating". The simulations suggest that the flap flexibility and the opening frequency of the wild-type, the G48V and L90M mutants are similar, but the flaps of the variant G48V/V82A/I84V/L90M open less frequently, resulting in a lower gated rate constant. The developed methodology is fast and provides an efficient way to predict the gated association rate constants for various protease mutants and ligands.

Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics

In principle, DNA-mediated charge transfer processes can be categorized as oxidative hole transfer and reductive electron transfer. With respect to the routes of DNA damage most of the past research has been focused on the investigation of oxidative hole transfer or transport. On the other hand, the transport or transfer of excess electrons has a large potential for biomedical applications, mainly for DNA chip technology.

Direct determination of reaction paths and stationary points on potential of mean force surfaces

A simulation approach is introduced for directly determining reaction paths and stationary points on potential of mean force (PMF) surfaces associated with molecular events that occur in complex environments. The nudged elastic band approach was employed to search for steepest descent paths on the PMF surface using the relevant PMF derivatives from a series of local simulations. The steepest descent path on the PMF surface corresponds to the minimum PMF path (i.e. the path with the lowest local PMF barrier), which contains important information about stationary points (e.g. saddle points) on the PMF surface, which in turn can provide useful insights into the thermodynamics and kinetics for the process of interest. By working with the PMF defined in a low-dimensional sub-space rather than a potential energy function of full molecular dimensionality, the main features of the process under study are concisely represented and the orthogonal degrees of freedom are adequately sampled with the appropriate canonical distribution at the desired temperature (e.g. 300 K). Therefore, minimum PMF paths carry statistically meaningful mechanistic information and are complementary to reaction paths of full molecular dimensionality proposed in previous studies. The NEB based path optimization method is direct in the sense that no information regarding the global PMF surface is necessary for the determination of the local reaction path and stationary points along this path. Since only low-dimensional quantities (paths) are searched for, the PMF-path method is expected to scale better in terms of dimension of the PMF sub-space than those aims to fully explore multi-dimensional PMF surfaces. Test applications on simple molecular systems, the alanine di-peptide in vacuum and in solution and a micro-solvated proton-wire, indicate that reliable PMF paths can be determined for both conformational isomerization and chemical reaction processes. However, highly accurate PMF derivatives are required for determining more quantitative observables, such as the free energy profile along the minimum PMF path. Therefore, effective numerical algorithms for calculating local PMF derivatives and systematic protocols for defining the relevant sub-space are the main focus in the near future. Finally, we emphasize that the minimum PMF path defined here includes thermal (e.g. entropic) effects associated with the orthogonal degrees of freedom, but finite kinetic energies associated with the PMF degrees of freedom are not included; this can be improved by adopting a different definition of the reaction path, such as the maximum flux path, on the PMF surface, or thermally sampling all degrees of freedom orthogonal to the one-dimensional path.

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.

Static and dynamic aspects of DNA charge transfer: a theoretical perspective

In this work, we approach the impact of dynamic and static disorder on DNA charge transfer from a theoretical and numerical perspective. Disordered or defect geometries are either realized via molecular dynamics simulations using a classical force field or by experimentally determined DNA bulge structures. We apply a chemically specific, atomically resolved extended Su-Schrieffer-Heeger model to compute the energy parameters relevant to DNA charge transfer. For both models studied here, the effective donor-acceptor couplings--and hence the charge transfer rates--significantly depend upon the geometry. Dynamic disorder leads to a correlation time in this quantity of the order of 30 fs, and the transfer rates universally exhibit a broad, yet well-defined, exponential distribution. For DNA bulges, the angle characterizing the defect controls the charge transfer efficiency. The results are discussed and extensively compared to experimental findings and other calculations.

Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: myosin-II and Ca2+ -ATPase

The structural flexibilities of two molecular machines, myosin and Ca(2+)-ATPase, have been analyzed with normal mode analysis and discussed in the context of their energy conversion functions. The normal mode analysis with physical intermolecular interactions was made possible by an improved implementation of the block normal mode (BNM) approach. The BNM results clearly illustrated that the large-scale conformational transitions implicated in the functional cycles of the two motor systems can be largely captured with a small number of low-frequency normal modes. Therefore, the results support the idea that structural flexibility is an essential part of the construction principle of molecular motors through evolution. Such a feature is expected to be more prevalent in motor proteins than in simpler systems (e.g., signal transduction proteins) because in the former, large-scale conformational transitions often have to occur before the chemical events (e.g., ATP hydrolysis in myosin and ATP binding/phosphorylation in Ca(2+)-ATPase). This highlights the importance of Brownian motions associated with the protein domains that are involved in the functional transitions; in this sense, Brownian molecular machines is an appropriate description of molecular motors, although the normal mode results do not address the origin of the ratchet effect. The results also suggest that it might be more appropriate to describe functional transitions in some molecular motors as intrinsic elastic motions modulating local structural changes in the active site, which in turn gets stabilized by the subsequent chemical events, in contrast with the conventional idea of local changes somehow getting amplified into larger-scale motions. In the case of myosin, for example, we favor the idea that Brownian motions associated with the flexible converter propagates to the Switch I/II region, where the salt-bridge formation gets stabilized by ATP hydrolysis, in contrast with the textbook notion that ATP hydrolysis drives the converter motion. Another useful aspect of the BNM results is that selected low-frequency normal modes have been identified to form a set of collective coordinates that can be used to characterize the progress of a significant fraction of large-scale conformational transitions. Therefore, the present normal mode analysis has provided a stepping-stone toward more elaborate microscopic simulations for addressing critical issues in free energy conversions in molecular machines, such as the coupling and the causal relationship between collective motions and essential local changes at the catalytic active site where ATP hydrolysis occurs.

Dynamic nature of the intramolecular electronic coupling mediated by a solvent molecule: a computational study

We present a combined Molecular Dynamics/Quantum Chemical study of the solvent-mediated electronic coupling between an electron donor and acceptor in a C-clamp molecule. We characterize the coupling fluctuations due to the solvent motion for different solvents (acetonitrile, benzene, 1,3-diisopropyl-benzene) for the charge separation and the charge recombination processes. The time scale for solvent-induced coupling fluctuation is approximately 0.1 ps. The effect of these fluctuations on the observed rate is discussed using a recently developed theoretical model. We show that, while the microscopic charge transfer process is very complicated and its computational modeling very subtle, the macroscopic phenomenology can be captured by the standard models. Analyzing the contribution to the coupling given by different solvent orbitals, we find that many solvent orbitals mediate the electron transfer and that paths through different solvent orbitals can interfere constructively or destructively. A relatively small subset of substrate-solvent configurations dominate contributions to solvent-mediated coupling. This subset of configurations is related to the electronic structure of the C-clamp molecule.

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.

2-Aminopurine: a probe of structural dynamics and charge transfer in DNA and DNA:RNA hybrids

Spectroscopic techniques are employed to probe relationships between structural dynamics and charge transfer (CT) efficiency in DNA duplexes and DNA:RNA hybrids containing photoexcited 2-aminopurine (Ap). To better understand the variety of interactions and reactions, including CT, between Ap and DNA, the fluorescence behavior of Ap is investigated in a full series of redox-inactive as well as redox-active assemblies. Thus, Ap is developed as a dual reporter of structural dynamics and base-base CT reactions in nucleic acid duplexes. CD, NMR, and thermal denaturation profiles are consistent with the family of DNA duplexes adopting a distinct conformation versus the DNA:RNA hybrids. Fluorescence measurements establish that the d(A)-r(U) tract of the DNA:RNA hybrid exhibits enhanced structural flexibility relative to that of the d(A)-d(T) tract of the DNA duplexes. The yield of CT from either G or 7-deazaguanine (Z) to Ap in the assemblies was determined by comparing Ap emission in redox-active G- or Z-containing duplexes to otherwise identical duplexes in which the G or Z is replaced by inosine (I), the redox-inactive nucleoside analogue. Investigations of CT not only demonstrate efficient intrastrand base-base CT in the DNA:RNA hybrids but also reveal a distance dependence of CT yield that is more shallow through the d(A)-r(U) bridge of the A-form DNA:RNA hybrids than through the d(A)-d(T) bridge of the B-form DNA duplexes. The shallow distance dependence of intrastrand CT in DNA:RNA hybrids correlates with the increased conformational flexibility of bases within the hybrid duplexes. Measurements of interstrand base-base CT provide another means to distinguish between the A- and B-form helices. Significantly, in the A-form DNA:RNA hybrids, a similar distance dependence is obtained for inter- and intrastrand reactions, while, in B-DNA, a more shallow distance dependence is evident with interstrand CT reactions. These observations are consistent with evaluations of intra- and interstrand base overlap in A- versus B-form duplexes. Overall, these data underscore the sensitivity of CT chemistry to nucleic acid structure and structural dynamics.

DNA photocleavage by a supramolecular Ru(II)-viologen complex

A novel Ru(II) complex possessing two sequentially linked viologen units, Ru-V(1)-V(2)(6+), was synthesized and characterized. Upon excitation of the Ru(II) unit (lambda(exc) = 532 nm, fwhm approximately 10 ns), a long-lived charge-separated (CS) state is observed (tau = 1.7 micros) by transient absorption spectroscopy. Unlike Ru(bpy)(3)(2+), which cleaves DNA upon photolysis through the formation of reactive oxygen species, such as (1)O(2) and O(2)(-), the photocleavage of plasmid DNA by Ru-V(1)-V(2)(6+) is observed both in air and under N(2) atmosphere (lambda(irr) > 395 nm).