Exciton states of dynamic DNA double helices: alternating dCdG sequences

The Ubiquity of High-Energy Nanosecond Fluorescence in DNA Duplexes

During the past few years, several studies reported that a significant part of the intrinsic fluorescence of DNA duplexes decays with surprisingly long lifetimes (1-3 ns) at wavelengths shorter than the ππ* emission of their monomeric constituents. This high-energy nanosecond emission (HENE), hardly discernible in the steady-state fluorescence spectra of most duplexes, was investigated by time-correlated single-photon counting. The ubiquity of HENE contrasts with the paradigm that the longest-lived excited states correspond to low-energy excimers/exciplexes. Interestingly, the latter were found to decay faster than the HENE. So far, the excited states responsible for HENE remain elusive. In order to foster future studies for their characterization, this Perspective presents a critical summary of the experimental observations and the first theoretical approaches. Moreover, some new directions for further work are outlined. Finally, the obvious need for computations of the fluorescence anisotropy considering the dynamic conformational landscape of duplexes is stressed.

Deprotonation Dynamics of Guanine Radical Cations†

This review is dedicated to guanine radical cations (G⁺ )^· that are precursors to oxidatively generated damage to DNA. (G⁺ )^· are unstable in neutral aqueous solution and tend to lose a proton. The deprotonation process has been studied by time-resolved absorption experiments in which (G⁺ )^· radicals are produced either by an electron abstraction reaction, using an external oxidant, or by low-energy/low-intensity photoionization of DNA. Both the position of the released proton and the dynamics of the process depend on the secondary DNA structure. While deprotonation in duplex DNA leads to (G-H1)^· radicals, in guanine quadruplexes the (G-H2)^· analogs are observed. Deprotonation in monomeric guanosine proceeds with a time constant of ˜60 ns; in genomic DNA, it is completed within 2 µs; and in guanine quadruplexes, it spans from at least 30 ns to over 50 µs. Such a deprotonation dynamics in four-stranded structures, extended over more than three decades of times, is correlated with the anisotropic structure of DNA and the mobility of its hydration shell. In this case, commonly used second-order reaction models are inappropriate for its description.

Studying the excited electronic states of guanine rich DNA quadruplexes by quantum mechanical methods: main achievements and perspectives

Calculations are providing more and more useful insights into the interaction between light and DNA quadruplexes.

Formation of UV-induced DNA damage contributing to skin cancer development

UV-induced DNA damage plays a key role in the initiation phase of skin cancer. When left unrepaired or when damaged cells are not eliminated by apoptosis, DNA lesions express their mutagneic properties, leading to the activation of proto-oncogene or the inactivation of tumor suppression genes. The chemical nature and the amount of DNA damage strongly depend on the wavelength of the incident photons. The most energetic part of the solar spectrum at the Earth's surface (UVB, 280-320 nm) leads to the formation of cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (64PPs). Less energetic but 20-times more intense UVA (320-400 nm) also induces the formation of CPDs together with a wide variety of oxidatively generated lesions such as single strand breaks and oxidized bases. Among those, 8-oxo-7,8-dihydroguanine (8-oxoGua) is the most frequent since it can be produced by several mechanisms. Data available on the respective yield of DNA photoproducts in cells and skin show that exposure to sunlight mostly induces pyrimidine dimers, which explains the mutational signature found in skin tumors, with lower amounts of 8-oxoGua and strand breaks. The present review aims at describing the basic photochemistry of DNA and discussing the quantitative formation of the different UV-induced DNA lesions reported in the literature. Additional information on mutagenesis, repair and photoprotection is briefly provided.

Biphotonic Ionization of DNA: From Model Studies to Cell

Oxidation reactions triggered by low-intensity UV photons represent a minor contribution with respect to the overwhelming pyrimidine base dimerization in both isolated and cellular DNA. The situation is totally different when DNA is exposed to high-intensity UVC radiation under conditions where biphotonic ionization of the four main purine and pyrimidine bases becomes predominant at the expense of singlet excitation processes. The present review article provides a critical survey of the main chemical reactions of the base radical cations thus generated by one-electron oxidation of nucleic acids in model systems and cells. These include oxidation of the bases with the predominant formation of 8-oxo-7,8-dihydroguanine as the result of preferential hole transfer to guanine bases that act as sinks in isolated and cellular DNA. In addition to hydration, other nucleophilic addition reactions involving the guanine radical cation give rise to intra- and interstrand cross-links together with DNA-protein cross-links. Information is provided on the utilization of high-intensity UV laser pulses as molecular biology tools for studying DNA conformational features, nucleic acid-protein interactions and nucleic acid reactivity through DNA-protein cross-links and DNA footprinting experiments.

Radicals generated in alternating guanine-cytosine duplexes by direct absorption of low-energy UV radiation

Recent studies have evidenced that oxidatively damaged DNA, which potentially leads to carcinogenic mutations and aging, may result from the direct absorption of low-energy photons (>250 nm). Herein, the primary species, i.e., ejected electrons and base radicals associated with such damage in duplexes with an alternating guanine-cytosine sequence are quantified by nanosecond transient absorption spectroscopy. The one-photon ionization quantum yield at 266 nm is 1.2 × 10-3, which is similar to those reported previously for adenine-thymine duplexes. This means that the simple presence of guanine, the nucleobase with the lowest ionization potential, does not affect photo-ionization. The transient species detected after 3 μs are identified as deprotonated guanine radicals, which decay with a half-time of 2.5 ms. Spectral assignment is made with the help of quantum chemistry calculations (TD-DFT), which for the first time, provide reference absorption spectra for guanine radicals in duplexes. In addition, our computed spectra predict the changes in transient absorption expected for hole localization as well as deprotonation (to cytosine and bulk water) and hydration of the radical cation.

DNA as UV light-harvesting antenna

The ordered structure of UV chromophores in DNA resembles photosynthetic light-harvesting complexes in which quantum coherence effects play a major role in highly efficient directional energy transfer. The possible role of coherent excitons in energy transport in DNA remains debated. Meanwhile, energy transport properties are greatly important for understanding the mechanisms of photochemical reactions in cellular DNA and for DNA-based artificial nanostructures. Here, we studied energy transfer in DNA complexes formed with silver nanoclusters and with intercalating dye (acridine orange). Steady-state fluorescence measurements with two DNA templates (15-mer DNA duplex and calf thymus DNA) showed that excitation energy can be transferred to the clusters from 21 and 28 nucleobases, respectively. This differed from the DNA-acridine orange complex for which energy transfer took place from four neighboring bases only. Fluorescence up-conversion measurements showed that the energy transfer took place within 100 fs. The efficient energy transport in the Ag-DNA complexes suggests an excitonic mechanism for the transfer, such that the excitation is delocalized over at least four and seven stacked bases, respectively, in one strand of the duplexes stabilizing the clusters. This result demonstrates that the exciton delocalization length in some DNA structures may not be limited to just two bases.

Solvent effects on the excited state characteristics of adenine–thymine base pairs

A systematic analysis of the excited state characteristics of the DNA base pair adenine–thymine in stacked and Watson–Crick hydrogen bonded configurations has been carried out in this study.

Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases

The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.

UV-induced DNA Damage: The Role of Electronic Excited States

The knowledge of the fundamental processes induced by the direct absorption of UV radiation by DNA allows extrapolating conclusions drawn from in vitro studies to the in-vivo DNA photoreactivity. In this respect, the characterization of the DNA electronic excited states plays a key role. For a long time, the mechanisms of DNA lesion formation were discussed in terms of generic "singlet" and "triplet" excited state reactivity. However, since the beginning of the 21(st) century, both experimental and theoretical studies revealed the existence of "collective" excited states, i.e. excited states delocalized over at least two bases. Two limiting cases are distinguished: Frenkel excitons (delocalized ππ* states) and charge-transfer states in which positive and negative charges are located on different bases. The importance of collective excited states in photon absorption (in particular in the UVA spectral domain), the redistribution of the excitation energy within DNA, and the formation of dimeric pyrimidine photoproducts is discussed. The dependence of the behavior of the collective excited states on conformational motions of the nucleic acids is highlighted.

Stabilization of Mixed Frenkel-Charge Transfer Excitons Extended Across Both Strands of Guanine-Cytosine DNA Duplexes

The photoreactive pathways that may lead to DNA damage depend crucially upon the nature of the excited electronic states. The study of alternating guanine-cytosine duplexes by fluorescence spectroscopy and quantum mechanical calculations identifies a novel type of excited states that can be populated following UVB excitation. These states, denoted High-energy Emitting Long-lived Mixed (HELM) states, extend across both strands and arise from mixing between cytosine Frenkel excitons and guanine-to-cytosine charge transfer states. They emit at energies higher than ππ* states localized on single bases, survive for several nanoseconds, are sensitive to the ionic strength of the solution, and are strongly affected by the structural transition from the B form to the Z form. Their impact on the formation of lesions of the genetic code needs to be assessed.

Computational modeling of photoexcitation in DNA single and double strands

The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.

Electronic excitations in Guanine quadruplexes

Guanine rich DNA strands, such as those encountered at the extremities of human chromosomes, have the ability to form four-stranded structures (G-quadruplexes) whose building blocks are guanine tetrads. G-quadruplex structures are intensively studied in respect of their biological role, as targets for anticancer therapy and, more recently, of their potential applications in the field of molecular electronics. Here we focus on their electronic excited states which are compared to those of non-interacting mono-nucleotides and those of single and double stranded structures. Particular emphasis is given to excited state relaxation processes studied by time-resolved fluorescence spectroscopy from femtosecond to nanosecond time scales. They include ultrafast energy transfer and trapping of ππ* excitations by charge transfer states. The effect of various structural parameters, such as the nature of the metal cations located in the central cavity of G-quadruplexes, the number of tetrads or the conformation of the constitutive single strands, are examined.

Excited state evolution of DNA stacked adenines resolved at the CASPT2//CASSCF/Amber level: from the bright to the excimer state and back

L_a and excimer state population exchange, along the common puckering decay coordinate, explains the longest DNA lifetime component.

Photodynamic behavior of electronic coupling in a N-methylformamide dimer

The role of the bridging water molecules has been studied during the excited state photodynamics of a N-methylformamide dimer in complex with water molecules employing the complete active space self-consistent field (CASSCF) and CAS perturbation theory (CASPT2) methods.

The effect of dimerization on the excited state behavior of methylated xanthine derivatives: a computational study

The behavior of monomers and dimers of methylated xanthine derivatives in their excited states is investigated by means of the ADC(2), CASSCF, and CASPT2 methods. The results of the calculations of stationary points in the ground and excited states, minima on the S0/S1 crossing seams and the relaxation pathways are used to provide the interpretation of experimental observations of the monomer xanthine derivatives. The effect of dimerization on the excited state properties is studied for various relative orientations of the monomers in the dimer complexes in comparison with the relevant monomer species. A significant stabilization in the excited state minima of dimers is observed. These can act as trapping sites. Various types of conical intersections, with both localized and delocalized characters of wavefunctions, have been found, mainly energetically above the lowest bright excited state in the FC region. In addition, structures with the bonds formed between the two monomers were also found on the crossing seams. The possibility of ultrafast relaxation via these conical intersections is discussed.

The S1/S2 exciton interaction in 2-pyridone·6-methyl-2-pyridone: Davydov splitting, vibronic coupling, and vibronic quenching

The excitonic splitting between the S(1) and S(2) electronic states of the doubly hydrogen-bonded dimer 2-pyridone[middle dot]6-methyl-2-pyridone (2PY·6M2PY) is studied in a supersonic jet, applying two-color resonant two-photon ionization (2C-R2PI), UV-UV depletion, and dispersed fluorescence spectroscopies. In contrast to the C(2h) symmetric (2-pyridone)(2) homodimer, in which the S(1) ← S(0) transition is symmetry-forbidden but the S(2) ← S(0) transition is allowed, the symmetry-breaking by the additional methyl group in 2PY·6M2PY leads to the appearance of both the S(1) and S(2) origins, which are separated by Δ(exp) = 154 cm(-1). When combined with the separation of the S(1) ← S(0) excitations of 6M2PY and 2PY, which is δ = 102 cm(-1), one obtains an S(1)/S(2) exciton coupling matrix element of V(AB, el) = 57 cm(-1) in a Frenkel-Davydov exciton model. The vibronic couplings in the S(1)/S(2) ← S(0) spectrum of 2PY·6M2PY are treated by the Fulton-Gouterman single-mode model. We consider independent couplings to the intramolecular 6a(') vibration and to the intermolecular σ(') stretch, and obtain a semi-quantitative fit to the observed spectrum. The dimensionless excitonic couplings are C(6a(')) = 0.15 and C(σ(')) = 0.05, which places this dimer in the weak-coupling limit. However, the S(1)/S(2) state exciton splittings Δ(calc) calculated by the configuration interaction singles method (CIS), time-dependent Hartree-Fock (TD-HF), and approximate second-order coupled-cluster method (CC2) are between 1100 and 1450 cm(-1), or seven to nine times larger than observed. These huge errors result from the neglect of the coupling to the optically active intra- and intermolecular vibrations of the dimer, which lead to vibronic quenching of the purely electronic excitonic splitting. For 2PY·6M2PY the electronic splitting is quenched by a factor of ~30 (i.e., the vibronic quenching factor is Γ(exp) = 0.035), which brings the calculated splittings into close agreement with the experimentally observed value. The 2C-R2PI and fluorescence spectra of the tautomeric species 2-hydroxypyridine·6-methyl-2-pyridone (2HP·6M2PY) are also observed and assigned.

Long-lived fluorescence of homopolymeric guanine-cytosine DNA duplexes

The fluorescence spectrum of the homopolymeric double helix poly(dG) x poly(dC) is dominated by emission decaying on the nanosecond time-scale, as previously reported for the alternating homologue poly(dGdC) x poly(dGdC). Thus, energy trapping over long periods of time is a common feature of GC duplexes which contrast with AT duplexes. The impact of such behaviour on DNA photodamage needs to be evaluated.

Excited-state energies and electronic couplings of DNA base dimers

The singlet excited electronic states of two pi-stacked thymine molecules and their splittings due to electronic coupling have been investigated with a variety of computational methods. Focus has been given on the effect of intermolecular distance on these energies and couplings. Single-reference methods, CIS, CIS(2), EOM-CCSD, TDDFT, and the multireference method CASSCF, have been used, and their performance has been compared. It is found that the excited-state energies are very sensitive to the applied method but the couplings are not as sensitive. Inclusion of diffuse functions in the basis set also affects the excitation energies significantly but not the couplings. TDDFT is inadequate in describing the states and their coupling, while CIS(2) gives results very similar to EOM-CCSD. Excited states of cytosine and adenine pi-stacked dimers were also obtained and compared with those of thymine dimers to gain a more general picture of excited states in pi-stacked DNA base dimers. The coupling is very sensitive to the relative position and orientation of the bases, indicating great variation in the degree of delocalization of the excited states between stacked bases in natural DNA as it fluctuates.

The excited-state lifetimes in a G x C DNA duplex are nearly independent of helix conformation and base-pairing motif

DNA photophysics: Femtosecond transient absorption experiments reveal that excited states produced by UV light in a duplex DNA oligonucleotide decay at essentially the same rate in B and Z helix conformers (see figure).

Interaction of UV radiation with DNA helices

Recent experimental and theoretical investigations dealing with model DNA double helices, composed of either adenine–thymine (A–T) or guanine–cytosine (G–C) base pairs, and G quadruplexes shed some light on the excited states populated by photon absorption and their relaxation, energy transfer among bases, and one-photon ionization. These studies revealed that the Franck–Condon excited states of DNA helices cannot be considered as the sum of their monomeric constituents because electronic coupling induces delocalization of the excitation over a few bases. Energy transfer takes place via intraband scattering in less than 100 fs. The fluorescence lifetimes of DNA helices detected by fluorescence upconversion and corresponding mainly to ππ* transitions are longer than that of an equimolar mixture of nucleotides; the only exception was observed for alternating G–C polymers. Moreover, nanosecond flash photolysis experiments showed that organization of bases within single and double helices may lead to a lowering of their ionization potential. Finally, the first determination regarding the time-scale needed for the formation of T dimers, the (6–4) adducts, was determined for the single strand (dT)20.

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.

Ultrafast excited-state dynamics of RNA and DNA C tracts

The excited-state dynamics of the RNA homopolymer of cytosine and of the 18-mer (dC)(18) were studied by steady-state and time-resolved absorption and emission spectroscopy. At pH 6.8, excitation of poly(rC) by a femtosecond UV pump pulse produces excited states that decay up to one order of magnitude more slowly than the excited states formed in the mononucleotide cytidine 5'-monophosphate under the same conditions. Even slower relaxation is observed for the hemiprotonated, self-associated form of poly(rC), which is stable at acidic pH. Transient absorption and time-resolved fluorescence signals for (dC)(18) at pH 6.8 are similar to ones observed for poly(rC) near pH 4, indicating that hemiprotonated structures are found in DNA C tracts at neutral pH. In both systems, there is evidence for two kinds of emitting states with lifetimes of ~100 ps and slightly more than 1 ns. The former states are responsible for the bulk of emission from the hemiprotonated structures. Evidence suggests that slow electronic relaxation in these self-complexes is the result of vertical base stacking. The similar signals from RNA and DNA C tracts suggest a common base-stacked structure, which may be identical with that of i-motif DNA.

Effect of the GC content of DNA on the distribution of UVB-induced bipyrimidine photoproducts

Solar UV radiation is a major mutagen that damages DNA through the formation of dimeric photoproducts between adjacent thymine and cytosine bases. A major effect of the GC content of the genome is thus anticipated, in particular in prokaryotes where this parameter significantly varies among species. We quantified the formation of UV-induced photolesions within both isolated and cellular DNA of bacteria of different GC content. First, we could unambiguously show the favored formation of cytosine-containing photoproducts with increasing GC content (from 28 to 72%) in isolated DNA. Thymine-thymine cyclobutane dimer was a minor lesion at high GC content. This trend was confirmed by an accurate and quantitative analysis of the photochemical data based on the exact dinucleotide frequencies of the studied genomes. The observation of the effect of the genome composition on the distribution of photoproducts was then confirmed in living cells, using two marine bacteria exhibiting different GC content. Because cytosine-containing photoproducts are highly mutagenic, it may be predicted that species with genomes exhibiting a high GC content are more susceptible to UV-induced mutagenesis.

Lattice theory of ultrafast excitonic and charge-transfer dynamics in DNA

We propose a lattice fermion model suitable for studying the ultrafast photoexcitation dynamics of ordered chains of deoxyribonucleic acid (DNA) polymers. The model includes both parallel (intrachain) and perpendicular (cross-chain) terms as well as diagonal cross-chain terms coupling neighboring bases. The general form of our Hamiltonian is borrowed from lattice fermion models of quantum chromodynamics. The band structure for this model can be determined analytically, and we use this as a basis for computing the singly excited states of the poly(dA)poly(dT) DNA duplex using configuration interaction singles. Parameters for the model are taken from various literature sources and our own ab initio calculations. Results indicate that the excited states consist of a low energy band of dark charge-separated states followed by separate bands of delocalized excitonic states which have weak mixing between the thymidine and adenosine sides of the DNA chain. We then propose a lattice exciton model based upon the transition dipole-dipole couplings between bases and compare the analytical results for the survival probability of an initially localized exciton to exact numerical results. The results herein underscore the competing role of excitonic and charge-transfer dynamics in these systems.