Frederick D. Lewis

Direct measurement of hole transport dynamics in DNA

Our understanding of oxidative damage to double helical DNA and the design of DNA-based devices for molecular electronics is crucially dependent upon elucidation of the mechanism and dynamics of electron and hole transport in DNA. Electrons and holes can migrate from the locus of formation to trap sites, and such migration can occur through either a single-step “superexchange” mechanism or a multistep charge transport “hopping” mechanism. The rates of single-step charge separation and charge recombination processes are found to decrease rapidly with increasing transfer distances, whereas multistep hole transport processes are only weakly distance dependent. However, the dynamics of hole transport has not yet been directly determined. Here we report spectroscopic measurements of photoinduced electron transfer in synthetic DNA that yield rate constants of ∼ 5 × 10 7 s-1 and 5 × 10 6 s-1, respectively, for the forward and return hole transport from a single guanine base to a double guanine base step across a single adenine. These rates are faster than processes leading to strand cleavage, such as the reaction of guanine cation radical with water, thus permitting holes to migrate over long distances in DNA. However, they are too slow to compete with charge recombination in contact ion pairs, a process which protects DNA from photochemical damage.

Donor-bridge-acceptor energetics determine the distance dependence of electron tunneling in DNA

Electron transfer (ET) processes in DNA are of current interest because of their involvement in oxidative strand cleavage reactions and their relevance to the development of molecular electronics. Two mechanisms have been identified for ET in DNA, a single-step tunneling process and a multistep charge-hopping process. The dynamics of tunneling reactions depend on both the distance between the electron donor and acceptor and the nature of the molecular bridge separating the donor and acceptor. In the case of protein and alkane bridges, the distance dependence is not strongly dependent on the properties of the donor and acceptor. In contrast, we show here that the distance decay of DNA ET rates varies markedly with the energetics of the donor and acceptor relative to the bridge. Specifically, we find that an increase in the energy of the bridge states by 0.25 eV (1 eV = 1.602 × 10−19 J) relative to the donor and acceptor energies for photochemical oxidation of nucleotides, without changing the reaction free energy, results in an increase in the characteristic exponential distance decay constant for the ET rates from 0.71 to 1.1 Å−1. These results show that, in the small tunneling energy gap regime of DNA ET, the distance dependence is not universal; it varies strongly with the tunneling energy gap. These DNA ET reactions fill a “missing link” or transition regime between the large barrier (rapidly decaying) tunneling regime and the (slowly decaying) hopping regime in the general theory of bridge-mediated ET processes.

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(-βR), with β = 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.

Hydrophobic self-assembly of a perylenediimide-linked DNA dumbbell into supramolecular polymers.

The self-assembly of DNA dumbbell conjugates possessing hydrophobic perylenediimide (PDI) linkers separated by an eight-base pair A-tract has been investigated. Cryo-TEM images obtained from dilute solutions of the dumbbell in aqueous buffer containing 100 mM NaCl show the presence of structures corresponding to linear end-to-end assemblies of 10-30 dumbbell monomers. The formation of assemblies of this size is consistent with analysis of the UV-vis and fluorescence spectra of these solutions for the content of PDI monomer and dimer chromophores. Assembly size is dependent upon the concentration of dumbbell and salt as well as the temperature. Kinetic analysis of the assembly process by means of salt-jump stopped-flow measurements shows that it occurs by a salt-triggered isodesmic mechanism in which the rate constants for association and dissociation in 100 mM NaCl are 3.2 × 10(7) M(-1)s(-1) and 1.0 s(-1), respectively, faster than the typical rate constants for DNA hybridization. TEM and AFM images of samples deposited from solutions having higher concentrations of dumbbell and NaCl display branched assemblies with linear regions >1 μm in length and diameters indicative of the formation of small bundles of dumbbell end-to-end assemblies. These observations provide the first example of the use of hydrophobic association for the assembly of small DNA duplex conjugates into supramolecular polymers and larger branched aggregates.

Direct Measurement of the Dynamics of Hole Hopping in Extended DNA G-Tracts. An Unbiased Random Walk

We report the measurement of distance- and temperature-dependent rate constants for charge separation in capped hairpins in which a stilbene hole acceptor and hole donor are separated by A(3)G(n) diblock polypurine sequences consisting of 3 adenines and 1-19 guanines. The longer diblock systems obey the simplest model for an unbiased random walk, providing a direct measurement of k(hop) = 4.3 × 10(9) s(-1) for a single reversible G-to-G hole hopping step, somewhat faster than the value of 1.2 × 10(9) s(-1) calculated for A-tract hole hopping. The temperature dependence for hopping in A(3)G(13) provides values of E(act) = 2.8 kcal/mol and A = 7 × 10(9) s(-1), consistent with a weakly activated, conformationally gated process.

Charge-Transfer and Spin Dynamics in DNA Hairpin Conjugates with Perylenediimide as a Base-Pair Surrogate

A perylenediimide chromophore (P) was incorporated into DNA hairpins as a base-pair surrogate to prevent the self-aggregation of P that is typical when it is used as the hairpin linker. The photoinduced charge-transfer and spin dynamics of these hairpins were studied using femtosecond transient absorption spectroscopy and time-resolved EPR spectroscopy (TREPR). P is a photooxidant that is sufficiently powerful to quantitatively inject holes into adjacent adenine (A) and guanine (G) nucleobases. The charge-transfer dynamics observed following hole injection from P into the A-tract of the DNA hairpins is consistent with formation of a polaron involving an estimated 3-4 A bases. Trapping of the (A 3-4) (+*) polaron by a G base at the opposite end of the A-tract from P is competitive with charge recombination of the polaron and P (-*) only at short P-G distances. In a hairpin having 3 A-T base pairs between P and G ( 4G), the radical ion pair that results from trapping of the hole by G is spin-correlated and displays TREPR spectra at 295 and 85 K that are consistent with its formation from (1*)P by the radical-pair intersystem crossing mechanism. Charge recombination is spin-selective and produces (3*)P, which at 85 K exhibits a spin-polarized TREPR spectrum that is diagnostic of its origin from the spin-correlated radical ion pair. Interestingly, in a hairpin having no G bases ( 0G), TREPR spectra at 85 K revealed a spin-correlated radical pair with a dipolar interaction identical to that of 4G, implying that the A-base in the fourth A-T base pair away from the P chromophore serves as a hole trap. Our data suggest that hole injection and transport in these hairpins is completely dominated by polaron generation and movement to a trap site rather than by superexchange. On the other hand, the barrier for charge injection from G (+*) back onto the A-T base pairs is strongly activated, so charge recombination from G (or even A trap sites at 85 K) most likely proceeds by a superexchange mechanism.

Dynamics of superexchange photoinduced electron transfer in duplex DNA

Photoinduced electron transfer (PET) in DNA can occur via one of two mechanisms, single-step superexchange and multi-step hole hopping. The dynamics of superexchange charge separation and charge recombination has recently been investigated in several structurally well-defined systems. In each of these systems, an electron acceptor is separated from a guanine or deazaguanine nucleobase donor by a variable number of A:T base pairs. The results of experimental studies on these and related systems are presented and analyzed within the framework of semi-classical electron transfer theory. Comparison of the results with those for other bridge-mediated electron transfer systems indicates that the π-stacked bases of DNA provide a better medium for electron transfer than the sigma bonded pathways of proteins and saturated hydrocarbons but do not function as a molecular wire.

Conformational Control of TT Dimerization in DNA Conjugates. A Molecular Dynamics Study

The paper presents quantum yield results for the [2+2] and 6-4 photodimerization of TT steps in several DNA structures, including hairpins where the context dependence of the photodimerization yield is determined, and it develops a theoretical model that correctly describes the trends in dimerization yield with DNA structure. The DNA conjugates considered include dT(20), dA(20)dT(20), and three alkane-linked hairpins that contain a single TT step. The theoretical modeling of the [2+2] process is based on CASSCF electronic structure calculations for ethylene + ethylene, which show that photoexcitation of low-lying excited states leads to potential surfaces that correlate without significant barriers to a conical intersection with the ground state surface at geometries close to the dimer structure. The primary constraint on dimerization is the distance d between the two double bonds, and it is found that d < 3.52 A leads to quantum yield trends that match the observed trends within a factor of 3. Constraints on the dihedral angle between the two double bonds are not as important, and although it is possible to generate better dimerization yield predictions for some structures by including these constraints, the best overall picture is obtained with no constraint. For 6-4 dimerization, a distance g < 2.87 A and no constraint on dihedral angle provide an accurate description of the yield.

Hydrophobic dimerization and thermal dissociation of perylenediimide-linked DNA hairpins

The structure and properties of hairpin-forming bis(oligonucleotide) conjugates possessing perylenediimide (PDI) chromophores as hairpin linkers have been investigated using a combination of spectroscopic and computational methods. These conjugates exist predominantly as monomer hairpins at room temperature in the absence of added salt and as head-to-head hairpin dimers in the presence of >50 mM NaCl. The hairpin dimer structure is consistent with the results of small-angle X-ray scattering in aqueous solution and molecular dynamics simulation. The structure of the nonconjugated PDI dimer in water is investigated using potential of mean force calculations. The salt dependence is attributed to increased cation condensation in the hairpin dimer vs monomer. Upon heating at low salt concentrations, the hairpin dimer undergoes sequential dissociation to form the monomer hairpin followed by conversion to a random coil structure; whereas at high salt concentrations both dissociation processes occur over the same temperature range. The monomer and dimer hairpins have distinct spectroscopic properties both in the ground state and excited singlet state. The UV and CD spectra provide evidence for electronic interaction between PDI and the adjacent base pair. Low fluorescence quantum yields are observed for both the monomer and dimer. The transient absorption spectrum of the dimer undergoes time-dependent spectral changes attributed to a change in the PDI-PDI torsional angle from ca. 20 degrees in the Franck-Condon singlet state to ca. 0 degrees in the relaxed singlet state, a process which occurs within ca. 40 ps.

Electron hopping among cofacially stacked perylenediimides assembled by using DNA hairpins

The self-assembly of redox-active molecules into ordered arrays capable of rapid, long-distance charge transport is important for the development of functional nanomaterials for organic electronics. In this regard, DNA shows great promise as a structural scaffold for the helical arrangement of chromophores and other (semi)conducting materials. Base substitutions and modifications, sugar modifications, and noncovalent interactions have all been used for the construction of such DNA-based structures. Perylenediimides (PDIs), which have the advantages of strong absorptivity, high fluorescence quantum yields, high photochemical and thermal stability, strong hydrophobic p–p stacking interactions, and semiconducting properties, have been incorporated in a variety of structures. Recently, Wagner and Wagenknecht reported the preparation of a PDI derivative, P (Figure 1), which is readily incorporated into an oligonucleotide and serves as a base-pair surrogate when located opposite an abasic site in a duplex structure. The incorporation of P in opposite complementary oligonucleotides has been shown to result in the formation of stable duplexes in which the P units are located in a zipperlike fashion within the hydrophobic interior of the resulting duplex. 17] The stacking of P units within the duplex resulted in an excimer-like state following photoexcitation. We report herein the results of our investigation of intramolecular electron hopping within a series of synthetic DNA hairpins 1–4 (Figure 1). These hairpins possess compact 3’-CCA loop regions connecting poly(T)–poly(A) stems containing a single P moiety located opposite an abasic site (1), two P moieties located opposite abasic sites and attached either to the same strand (in 2s) or to opposite strands (in 2o), or three or four P moieties positioned adjacent to one another but on opposite strands in a zipperlike fashion (in 3 and 4). The EPR spectra of the singly reduced duplexes were consistent with electron hopping between two sites in both dimers (the hairpins containing two P moieties) and the trimer 3, and among three sites in the tetramer 4. Herein, we discuss the origin and implications of partial electron sharing. Oligonucleotides containing P were synthesized by the method of Wagner and Wagenknecht; the CCA linker in hairpins 1–4 has been employed previously in the synthesis of stable minihairpins. 17, 18] The characterization of 1–4, including mass spectrometry and circular dichroism (CD), is described in the Supporting Information. An intensity reversal was observed in the UV/Vis absorption spectra for the 0!0 and 0!1 transitions in 2–4 with respect to those of 1 (Figure 2). This result indicates that the p-stacked P chromophores are exciton-coupled. Moreover, the A0!0/A0!1 ratio for the vibronic bands decreased as the number of P units increased, and there was a notable difference between dimers 2s and 2o, presumably as a result of the conformational changes imposed by the attachment of the two P units to either one strand or opposite strands within the duplex. Upon the partial chemical reduction of P with sodium dithionite, peaks corresponding to the radical anion appeared at 727, 815, and 980 nm, whereas the vibronic progression in the visible region decreased in intensity (see Figure S1 in the Supporting Information). The Figure 1. DNA hairpin structures.