UV-Induced Proton-Coupled Electron Transfer in Cyclic DNA Miniduplexes

The photoactivated dynamics of dGpdC and dCpdG sequences in DNA: a comprehensive quantum mechanical study

Study of alternating DNA GC sequences by different time-resolved spectroscopies has provided fundamental information on the interaction between UV light and DNA, a process of great biological importance. Multiple decay paths have been identified, but their interplay is still poorly understood. Here, we characterize the photophysics of GC-DNA by integrating different computational approaches, to study molecular models including up to 6 bases described at a full quantum mechanical level. Quantum dynamical simulations, exploiting a nonadiabatic linear vibronic coupling (LVC) model, coupled with molecular dynamics sampling of the initial structures of a (GC)5 DNA duplex, provide new insights into the photophysics in the sub-picosecond time-regime. They indicate a substantial population transfer, within 50 fs, from the spectroscopic states towards G → C charge transfer states involving two stacked bases (CTintra), thus explaining the ultrafast disappearance of fluorescence. This picture is consistent with that provided by quantum mechanical geometry optimizations, using time dependent-density functional theory and a polarizable continuum model, which we use to parametrize the LVC model and to map the main excited state deactivation pathways. For the first time, the infrared and excited state absorption signatures of the various states along these pathways are comprehensively mapped. The computational models suggest that the main deactivation pathways, which, according to experiment, lead to ground state recovery on the 10-50 ps time scale, involve CTintra followed by interstrand proton transfer from the neutral G to C-. Our calculations indicate that CTintra is populated to a larger extent and more rapidly in GC than in CG steps and suggest the likely involvement of monomer-like and interstrand charge transfer decay routes for isolated and less stacked CG steps. These findings underscore the importance of the DNA sequence and thermal fluctuations for the dynamics. They will also aid the interpretation of experimental results on other sequences.

Ultrafast Formation of a Delocalized Triplet-Excited State in an Epigenetically Modified DNA Duplex under Direct UV Excitation

Epigenetic modifications impart important functionality to nucleic acids during gene expression but may increase the risk of photoinduced gene mutations. Thus, it is crucial to understand how these modifications affect the photostability of duplex DNA. In this work, the ultrafast formation (<20 ps) of a delocalized triplet charge transfer (CT) state spreading over two stacked neighboring nucleobases after direct UV excitation is demonstrated in a DNA duplex, d(G5fC)9•d(G5fC)9, made of alternating guanine (G) and 5-formylcytosine (5fC) nucleobases. The triplet yield is estimated to be 8 ± 3%, and the lifetime of the triplet CT state is 256 ± 22 ns, indicating that epigenetic modifications dramatically alter the excited state dynamics of duplex DNA and may enhance triplet state-induced photochemistry.

Ultrafast excited state dynamics of pyridine N-oxide derivative in solution; femtosecond fluorescence up-conversion and theoretical calculations

In this study we have investigated 2-ethylamino-4-nitro-6-methyl pyridine N-oxide (2E6M) molecule that belongs to important group of Proton Coupled Electron Transfer (PCET) compounds where both the charge transfer (CT) and proton transfer processes in excited states may proceed. In this case, this is possible due to the donors and acceptors of electrons and protons in this system, as well as due to the presence of intramolecular {N-H… O [2,566(3) Å}, hydrogen bond.Using stationary and time-resolved spectroscopy, as well as quantum chemical calculations on the DFT and TD DFT B3LYP/6-31G (d,p) level of theory, a partial CT nature of the S₀ → S₁ transition in both tautomeric forms (N and T) has been revealed. Additionally, the excited state intramolecular proton transfer (ESIPT) process shown to be more favorable in apolar and weakly polar solvents than in strongly polar acetonitrile (E_N(S1) > E_T(S1). The displacement of charge from the amine group and the ring to the nitro group has been observed on the changing shapes of the HOMO and LUMO orbitals involved in this transition what further quantitatively allowed to realize the increase in the dipole moment of both forms in the electronic excited state. The calculations show that in two solvents with radically different polarity (heptane, acetonitrile), dipole moments of both forms are very similar [in acetonitrile u_N(S₁) and u_T(S₁) are 11.0 D and 11.5 D, respectively]. Hence, in polar media both forms can be stabilized in a comparable manner. This made it difficult for us to assign a single fluorescent band in acetonitrile to one of the tautomeric forms. However, it seems that due to application of time-resolved spectroscopy, this problem has been clarified. The TCSPC decay curve in acetonitrile with an ultrafast lifetime assigned to the (N) form, along with the femtosecond up-conversion signals that demonstrated only an ultrafast decay without any rise-time of a new excited (T) species, allowed us to conclude that in 2E6M in strongly polar solvent the ESIPT does not occur.The unique fluorescence band origins from the (N) form. In protic solvents, the significant kinetic isotopic effects have provided us with conclusive evidence for the presence of the solvent-assisted ESIPT process. Furthermore, it was noticed that the fluorescence lifetime in D₂O (100-120 fs) estimated from the up-conversion signals is about 40 times shorter relative to methanol. This may suggest that the sine qua non for the ESIPT process in 2E6M in protic solvents is the formation of a complex with a solvent molecule in the hydrogen bridge between the proton donor and proton acceptor, respectively.

Fundamentals of the Intrinsic DNA Fluorescence

The intrinsic fluorescence of nucleic acids is extremely weak compared to that of the fluorescent labels used to probe their structural and functional behavior. Thus, for technical reasons, the investigation of the intrinsic DNA fluorescence was limited for a long time. But with the improvement in spectroscopic techniques, the situation started to change around the turn of the century. During the past two decades, various factors modulating the static and dynamic properties of the DNA fluorescence have been determined; it was shown that, under certain conditions, quantum yields may be up 100 times higher than what was known so far. The ensemble of these studies opened up new paths for the development of label-free DNA fluorescence for biochemical applications. In parallel, these studies have shed new light on the primary processes leading to photoreactions that damage DNA when it absorbs UV radiation.We have been studying a variety of DNA systems, ranging from the monomeric nucleobases to double-stranded and four-stranded structures using fluorescence spectroscopy. The specificity of our work resides in the quantitative association of the steady-state fluorescence spectra with time-resolved data recorded from the femtosecond to the nanosecond timescales, made possible by the development of specific methodologies.Among others, our fluorescence studies provide information on the energy and the polarization of electronic transitions. These are valuable indicators for the evolution of electronic excitations in complex systems, where the electronic coupling between chromophores plays a key role. Highlighting collective effects that originate from electronic interactions in DNA multimers is the objective of the present Account.In contrast to the monomeric chromophores, whose fluorescence decays within a few picoseconds, that of DNA multimers persists on the nanosecond timescale. Even if long-lived states represent only a small fraction of electronic excitations, they may be crucial to the DNA photoreactivity because the probability to reach reactive conformations increases over time, owing to the incessant structural dynamics of nucleic acids.Our femtosecond studies have revealed that an ultrafast excitation energy transfer takes place among the nucleobases within duplexes and G-quadruplexes. Such an ultrafast process is possible when collective states are populated directly upon photon absorption. At much longer times, we discovered an unexpected long-lived high-energy emission stemming from what was coined "HELM excitons". These collective states, whose emission increases with the duplex size, could be responsible for the delayed fluorescence of ππ* states observed for genomic DNA.Most studies dealing with excited-state relaxation in DNA were carried out with excitation in the absorption band peaking at around 260 nm. We went beyond this and also performed the first time-resolved study with excitation in the UVA spectral range, where a very weak absorption tail is present. The resulting fluorescence decays are much slower and the fluorescence quantum yields are much higher than for UVC excitation. We showed that the base pairing of DNA strands enhances the UVA fluorescence and, in parallel, increases the photoreactivity because it modifies the nature of the involved collective excited states.

Proton-Coupled Electron Transfer for Photoinduced Generation of Two-Electron Reduced Species of Quinone

Purpose-built molecules that follow the fundamental process of photosynthesis have significance in developing better insight into the natural photosynthesis process. Quinones have a significant role as electron acceptors in natural photosynthesis, and their reduction is assisted through H-bond donation or protonation. The major challenge in such studies is to couple the multielectron and proton-transfer process and to achieve a reasonably stable charge-separated state for the elucidation of the mechanistic pathway. We have tried to address this issue through the design of a donor-acceptor-donor molecular triad (2RuAQ) derived from two equivalent [Ru(bpy)₃]²⁺ derivatives and a bridging anthraquinone moiety (AQ). Photoinduced proton-coupled electron transfer (PCET) for this molecular triad was systematically investigated in the absence and presence of hexafluoroisopropanol and p-toluenesulfonic acid (PTSA) using time-resolved absorption spectroscopy in the ultrafast time domain. Results reveal the generation of a relatively long-lived charge-separated state in this multi-electron transfer reaction, and we could confirm the generation of AQ^2- and Ru^III as the transient intermediates. We could rationalize the mechanistic pathway and the dynamics associated with photoinduced processes and the role of H-bonding in stabilizing charge-separated states. Transient absorption spectroscopic studies reveal that the rates of intramolecular electron transfer and the mechanistic pathways associated with the PCET process are significantly different in different solvent compositions having different polarities. In acetonitrile, a concerted PCET mechanism prevails, whereas the stepwise PCET reaction process is observed in the presence of PTSA. The results of the present study represent a unique model for the mechanistic diversity of PCET reactions.

Vibrations of the guanine-cytosine pair in chloroform: an anharmonic computational study

We compute at the anharmonic level the vibrational spectra of the Watson-Crick dimer formed by guanosine (G) and cytidine (C) in chloroform, together with those of G, C and the most populated GG dimer. The spectra for deuterated and partially deuterated GC are also computed. We use DFT calculations, with B3LYP and CAM-B3LYP as reference functionals. Solvent effects from chloroform are included via the Polarizable Continuum Model (PCM), and by performing tests on models including up two chloroform molecules. Both B3LYP and CAM-B3LYP calculations reproduce the shape of the experimental spectra well in the fingerprint region (1500-1700 cm-1) and in the N-H stretching region (2800-3600 cm-1), with B3LYP providing better quantitative agreement with experiments. According to our calculations, the N-H amido streching mode of G falls at ∼2900 cm-1, while the N-H amino of G and C falls at ∼3100 cm-1 when hydrogen-bonded, or ∼3500 cm-1 when free. Overtone and combination bands strongly contribute to the absorption band at ∼3300 cm-1. Inclusion of bulk solvent effects significantly increases the accuracy of the computed spectra, while solute-solvent interactions have a smaller, though still noticeable, effect. Some key aspects of the anharmonic treatment of strongly vibrationally coupled supermolecular systems and the related methodological issues are also discussed.

Oxidative Addition of Singlet Oxygen to Model Building Blocks of the Aerucyclamide A Peptide: A First-Principles Approach

Singlet oxygen (¹O₂) is a significant source of biodamage in living organisms. ¹O₂ is a highly reactive excited electronic-state spin-configuration of molecular oxygen and is usually prepared via organic molecule sensitization. Despite the wealth of experimental studies on the ¹O₂-induced oxidation of several bio-organic molecules, the detailed mechanism of the oxidation process is largely unknown. Using high-level quantum chemical methods, we compute the potential energy profiles of the various electronic states associated with the [4 + 2]-cycloaddition reaction of O₂ with a class of model peptide precursors that are based on derivatives of oxazole and thiazole. Experiments have shown that such oxazole/thiazole-based model peptides show a favorable reaction with ¹O₂. Upon increasing the molecular complexity, the bimolecular rate constant decreases and is attributed to the π-perturbing effects of the substituent of the oxazole/thiazole moiety. Our theoretical predictions are in excellent agreement with the experimental measurements and reveal a deep insight into the myriad electronic states that may hinder/promote the reaction of a given bio-organic molecule with ¹O₂.

Experimental and theoretical studies on thymine photodimerization mediated by oxidatively generated DNA lesions and epigenetic intermediates

Combined spectroscopic and computational studies reveal that, in spite of their structural similarities, 5-formyluracil and 5-formylcytosine photosensitize cyclobutane thymine dimers through two different types of mechanisms.

Electron transfer in photoexcited pyrrole dimers

Following on from previous experimental and theoretical work [Neville et al., Nat. Commun. 7, 11357 (2016)], we report the results of a combined electronic structure theory and quantum dynamics study of the excited state dynamics of the pyrrole dimer following excitation to its first two excited states. Employing an exciton-based analysis of the Ã(π3s/σ^*) and B̃(π3s/3p/σ^*) states, we identify an excited-state electron transfer pathway involving the coupling of the Ã(π3s/σ^*) and B̃(π3s/3p/σ^*) states and driven by N-H dissociation in the B̃(π3s/3p/σ^*) state. This electron transfer mechanism is found to be mediated by vibronic coupling of the B̃ state, which has a mixed π3s/3p Rydberg character at the Franck-Condon point, to a high-lying charge transfer state of the πσ^* character by the N-H stretch coordinate. Motivated by these results, quantum dynamics simulations of the excited-state dynamics of the pyrrole dimer are performed using the multiconfigurational time-dependent Hartree method and a newly developed model Hamiltonian. It is predicted that the newly identified electron transfer pathway will be open following excitation to both the Ã(π3s/σ^*) and B̃(π3s/3p/σ^*) states and may be the dominant relaxation pathway in the latter case.

Exploring ultraviolet photoinduced charge-transfer dynamics in a model dinucleotide of guanine and thymine

An understanding of the initial photoexcited states of DNA is essential to unravelling deleterious photoinduced chemical reactions and the intrinsic ultrafast photoprotection of the genetic code for all life. In our combined experimental and theoretical study, we have elucidated the primary non-radiative relaxation dynamics of a model nucleotide of guanine and thymine (2'-deoxyguanosine 3'-monophosphate 5'-thymidine, d(GpT)) in buffered aqueous solution. Experimentally, we unequivocally demonstrate that the Franck-Condon excited states of d(GpT) are significantly delocalised across both nucleobases, and mediate d(G⁺pT^-) exciplex product formation on an ultrafast (<350 fs) timescale. Theoretical studies show that the nature of the vertical excited states is very dependent on the specific geometry of the dinucleotide, and dictate the degree of delocalised, charge-transfer or localised character. Our mechanism for prompt exciplex formation involves a rapid change in electronic structure and includes a diabatic surface crossing very close to the Franck-Condon region mediating fast d(G⁺pT^-) formation. Exciplexes are quickly converted back to neutral ground state molecules on a ∼10 ps timescale with a high quantum yield, ensuring the photostability of the nucleotide sequence.

Excited-state dynamics of mononucleotides and DNA strands in a deep eutectic solvent

The photophysics of several mono- and oligonucleotides were investigated in a deep eutectic solvent for the first time. The solvent glyceline, prepared as a 1 : 2 mole ratio mixture of choline chloride and glycerol, was used to study excited-state deactivation in a non-aqueous solvent by the use of steady-state and time-resolved spectroscopy. DNA strands in glyceline retain the secondary structures that are present in aqueous solution to some degree, thus enabling a study of the effects of solvent properties on the excited states of stacked bases and stacked base pairs. The excited-state lifetime of the mononucleotide 5'-AMP in glyceline is 630 fs, or twice as long as in aqueous solution. Even slower relaxation is seen for 5'-TMP in glyceline, and a possible triplet state with a lifetime greater than 3 ns is observed. Circular dichroism spectra show that the single strand (dA)18 and the duplex d(AT)9·d(AT)9 adopt similar structures in glyceline and in aqueous solution. Despite having similar conformations in both solvents, femtosecond transient absorption experiments reveal striking changes in the dynamics. Excited-state decay and vibrational cooling generally take place more slowly in glyceline than in water. Additionally, the fraction of long-lived excited states in both oligonucleotide systems is lower in glyceline than in aqueous solution. For a DNA duplex, water is suggested to favor decay pathways involving intrastrand charge separation, while the deep eutectic solvent favors interstrand deactivation channels involving neutral species. Slower solvation dynamics in the viscous deep eutectic solvent may also play a role. These results demonstrate that the dynamics of excitations in stacked bases and stacked base pairs depend not only on conformation, but are also highly sensitive to the solvent.

Isotopic substitution affects excited state branching in a DNA duplex in aqueous solution

Changing the solvent from H2O to D2O dramatically affects the branching of the initial excited electronic states in an alternating G·C DNA duplex into two distinct decay channels. The slower, multisite PCET channel that deactivates more than half of all excited states in D2O becomes six times weaker in H2O.

Recent advances in bioinspired proton-coupled electron transfer

Fundamental aspects of PCET continue to attract attention. Understanding this reaction type is desirable for small-molecule activation and solar energy conversion.

Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA

The intrinsic photostability of nucleic acids is intimately related to evolution of life, while its understanding at the molecular and electronic levels remains a challenge for modern science. Among the different decay pathways proposed in the last two decades, the excited-state hydrogen transfer between guanine-cytosine base pairs has been identified as an efficient non-reactive channel to dissipate the excess of energy provided by light absorption. The present work studies the dynamics of such phenomena taking place in a (dG)·(dC) B-DNA homopolymer in water solution using state-of-the-art molecular modelling and simulation methods. A dynamic effect that boosts the photostability of the inter-strand hydrogen atom transfers, inherent to the Watson-Crick base pairing, is unveiled and ascribed to the energy released during the proton transfer step. Our results also reveal a novel mechanism of DNA decay named four proton transfer (FPT), in which two protons of two adjacent G-C base pairs are transferred to form a biradical zwitterionic intermediate. Decay of the latter intermediate to the ground state triggers the transfer of the protons back to the guanine molecules recovering the Watson-Crick structure of the tetramer. This FPT process is activated by the close interaction of a nearby Na+ counterion with the oxygen atoms of the guanine nucleobases and hence represents a photostable channel operative in natural nucleic acids.

How nature covers its bases

The response of nucleobases to UV radiation depends on structure in subtle ways, as revealed by gas-phase experiments.

Fluorescence quenching of the N-methylquinolinium cation by pairs of water or alcohol molecules

The proposed mechanism involves an electron transfer from H₂O/ROH to the excited quinolinium, concerted with proton transfer to the second hydroxy molecule.

Photoactivated proton coupled electron transfer in DNA: insights from quantum mechanical calculations

The energetics of the two main proton coupled electron transfer processes that could occur in DNA are determined by means of time dependent-DFT calculations, using the M052X functional and the polarizable continuum model to include solvent effect.

Protocol for the Solid-phase Synthesis of Oligomers of RNA Containing a 2'-O-thiophenylmethyl Modification and Characterization via Circular Dichroism

Solid-phase synthesis has been used to obtain canonical and modified polymers of nucleic acids, specifically of DNA or RNA, which has made it a popular methodology for applications in various fields and for different research purposes. The procedure described herein focuses on the synthesis, purification, and characterization of dodecamers of RNA 5'-[CUA CGG AAU CAU]-3' containing zero, one, or two modifications located at the C2'-O-position. The probes are based on 2-thiophenylmethyl groups, incorporated into RNA nucleotides via standard organic synthesis and introduced into the corresponding oligonucleotides via their respective phosphoramidites. This report makes use of phosphoramidite chemistry via the four canonical nucleobases (Uridine (U), Cytosine (C), Guanosine (G), Adenosine (A)), as well as 2-thiophenylmethyl functionalized nucleotides modified at the 2'-O-position; however, the methodology is amenable for a large variety of modifications that have been developed over the years. The oligonucleotides were synthesized on a controlled-pore glass (CPG) support followed by cleavage from the resin and deprotection under standard conditions, i.e., a mixture of ammonia and methylamine (AMA) followed by hydrogen fluoride/triethylamine/N-methylpyrrolidinone. The corresponding oligonucleotides were purified via polyacrylamide electrophoresis (20% denaturing) followed by elution, desalting, and isolation via reversed-phase chromatography (Sep-pak, C18-column). Quantification and structural parameters were assessed via ultraviolet-visible (UV-vis) and circular dichroism (CD) photometric analysis, respectively. This report aims to serve as a resource and guide for beginner and expert researchers interested in embarking in this field. It is expected to serve as a work-in-progress as new technologies and methodologies are developed. The description of the methodologies and techniques within this document correspond to a DNA/RNA synthesizer (refurbished and purchased in 2013) that uses phosphoramidite chemistry.

Indications of 5' to 3' Interbase Electron Transfer as the First Step of Pyrimidine Dimer Formation Probed by a Dinucleotide Analog

Pyrimidine dimers are the most common DNA lesions generated under UV radiation. To reveal the molecular mechanisms behind their formation, it is of significance to reveal the roles of each pyrimidine residue. We thus replaced the 5'-pyrimidine residue with a photochemically inert xylene moiety (X). The electron-rich X can be readily oxidized but not reduced, defining the direction of interbase electron transfer (ET). Irradiation of the XpT dinucleotide under 254 nm UV light generates two major photoproducts: a pyrimidine (6-4) pyrimidone analog (6-4PP) and an analog of the so-called spore photoproduct (SP). Both products are formed by reaction at C4=O of the photo-excited 3'-thymidine (T), which indicates that excitation of a single "driver" residue is sufficient to trigger pyrimidine dimerization. Our quantum-chemical calculations demonstrated that photo-excited 3'-T accepts an electron from 5'-X. The resulting charge-separated radical pair lowers its energy upon formation of interbase covalent bonds, eventually yielding 6-4PP and SP.

Is UV-Induced Electron-Driven Proton Transfer Active in a Chemically Modified A·T DNA Base Pair?

Transient electronic and vibrational absorption spectroscopies have been used to investigate whether UV-induced electron-driven proton transfer (EDPT) mechanisms are active in a chemically modified adenine-thymine (A·T) DNA base pair. To enhance the fraction of biologically relevant Watson-Crick (WC) hydrogen-bonding motifs and eliminate undesired Hoogsteen structures, a chemically modified derivative of A was synthesized, 8-(tert-butyl)-9-ethyladenine (8tBA). Equimolar solutions of 8tBA and silyl-protected T nucleosides in chloroform yield a mixture of WC pairs, reverse WC pairs, and residual monomers. Unlike previous transient absorption studies of WC guanine-cytosine (G·C) pairs, no clear spectroscopic or kinetic evidence was identified for the participation of EDPT in the excited-state relaxation dynamics of 8tBA·T pairs, although ultrafast (sub-100 fs) EDPT cannot be discounted. Monomer-like dynamics are proposed to dominate in 8tBA·T.

Life in the light: nucleic acid photoproperties as a legacy of chemical evolution

Photophysical investigations of the canonical nucleobases that make up DNA and RNA during the past 15 years have revealed that excited states formed by the absorption of UV radiation decay with subpicosecond lifetimes (i.e., <10(-12) s). Ultrashort lifetimes are a general property of absorbing sunscreen molecules, suggesting that the nucleobases are molecular survivors of a harsh UV environment. Encoding the genome using photostable building blocks is an elegant solution to the threat of photochemical damage. Ultrafast excited-state deactivation strongly supports the hypothesis that UV radiation played a major role in shaping molecular inventories on the early Earth before the emergence of life and the subsequent development of a protective ozone shield. Here, we review the general physical and chemical principles that underlie the photostability, or "UV hardiness", of modern nucleic acids and discuss the possible implications of these findings for prebiotic chemical evolution. In RNA and DNA strands, much longer-lived excited states are observed, which at first glance appear to increase the risk of photochemistry. It is proposed that the dramatically different photoproperties that emerge from assemblies of photostable building blocks may explain the transition from a world of molecular survival to a world in which energy-rich excited electronic states were eventually tamed for biological purposes such as energy transduction, signaling, and repair of the genetic machinery.