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.

Triplet Excimer Formation in a DNA Duplex with Silver Ion-Mediated Base Pairs.

The dynamics of excited electronic states in self-assembled structures formed between silver(I) ions and cytosine-containing DNA strands or monomeric cytosine derivatives were investigated by time-resolved infrared (TRIR) spectroscopy and quantum mechanical calculations. The steady-state and time-resolved spectra depend sensitively on the underlying structures, which change with pH and the nucleobase and silver ion concentrations. At pH ∼ 4 and low dC20 strand concentration, an intramolecularly folded i-motif is observed, in which protons, and not silver ions, mediate C-C base pairing. However, at the higher strand concentrations used in the TRIR measurements, dC20 strands associate pairwise to yield duplex structures containing C-Ag+-C base pairs with a high degree of propeller twisting. UV excitation of the silver ion-mediated duplex produces a long-lived excited state, which we assign to a triplet excimer state localized on a pair of stacked cytosines. The computational results indicate that the propeller-twisted motifs induced by metal-ion binding are responsible for the enhanced intersystem crossing that populates the triplet state and not a generic heavy atom effect. Although triplet excimer states have been discussed frequently as intermediates in the formation of cyclobutane pyrimidine dimers, we find neither computational nor experimental evidence for cytosine-cytosine photoproduct formation in the systems studied. These findings provide a rare demonstration of a long-lived triplet excited state that is formed in a significant yield in a DNA duplex, demonstrating that supramolecular structural changes induced by metal ion binding profoundly affect DNA photophysics.

Vibrational relaxation by methylated xanthines in solution: Insights from 2D IR spectroscopy and calculations.

Two-dimensional infrared (2D IR) spectroscopy, infrared pump-infrared probe spectroscopy, and density functional theory calculations were used to study vibrational relaxation by ring and carbonyl stretching modes in a series of methylated xanthine derivatives in acetonitrile and deuterium oxide (heavy water). Isotropic signals from the excited symmetric and asymmetric carbonyl stretch modes decay biexponentially in both solvents. Coherent energy transfer between the symmetric and asymmetric carbonyl stretching modes gives rise to a quantum beat in the time-dependent anisotropy signals. The damping time of the coherent oscillation agrees with the fast decay component of the carbonyl bleach recovery signals, indicating that this time constant reflects intramolecular vibrational redistribution (IVR) to other solute modes. Despite their similar frequencies, the excited ring modes decay monoexponentially with a time constant that matches the slow decay component of the carbonyl modes. The slow decay times, which are faster in heavy water than in acetonitrile, approximately match the ones observed in previous UV pump-IR probe measurements on the same compounds. The slow component is assigned to intermolecular energy transfer to solvent bath modes from low-frequency solute modes, which are populated by IVR and are anharmonically coupled to the carbonyl and ring stretch modes. 2D IR measurements indicate that the carbonyl stretching modes are weakly coupled to the delocalized ring modes, resulting in slow exchange that cannot explain the common solvent-dependence. IVR is suggested to occur at different rates for the carbonyl vs ring modes due to differences in mode-specific couplings and not to differences in the density of accessible states.

Solvent-Dependent Stabilization of a Charge Transfer State is the Key to Ultrafast Triplet State Formation in an Epigenetic DNA Nucleoside.

2'-Deoxy-5-formylcytidine (5fdCyd), a naturally occurring nucleoside found in mammalian DNA and mitochondrial RNA, exhibits important epigenetic functionality in biological processes. Because it efficiently generates triplet excited states, it is an endogenous photosensitizer capable of damaging DNA, but the intersystem crossing (ISC) mechanism responsible for ultrafast triplet state generation is poorly understood. In this study, time-resolved mid-IR spectroscopy and quantum mechanical calculations reveal the distinct ultrafast ISC mechanisms of 5fdCyd in water versus acetonitrile. Our experiment indicates that in water, ISC to triplet states occurs within 1 ps after 285 nm excitation. PCM-TD-DFT computations suggest that this ultrafast ISC is mediated by a singlet state with significant cytosine-to-formyl charge-transfer (CT) character. In contrast, ISC in acetonitrile proceeds via a dark 1 nπ* state with a lifetime of ∼3 ps. CT-induced ISC is not favored in acetonitrile because reaching the minimum of the gateway CT state is hampered by intramolecular hydrogen bonding, which enforces planarity between the aldehyde group and the aromatic group. Our study provides a comprehensive picture of the non-radiative decay of 5fdCyd in solution and new insights into the factors governing ISC in biomolecules. We propose that the intramolecular CT state observed here is a key to the excited-state dynamics of epigenetic nucleosides with modified exocyclic functional groups, paving the way to study their effects in DNA strands.

A single nucleobase tunes nonradiative decay in a DNA-bound silver cluster.

DNA strands are polymeric ligands that both protect and tune molecular-sized silver cluster chromophores. We studied single-stranded DNA C4AC4TC3XT4 with X = guanosine and inosine that form a green fluorescent Ag10 6+ cluster, but these two hosts are distinguished by their binding sites and the brightness of their Ag10 6+ adducts. The nucleobase subunits in these oligomers collectively coordinate this cluster, and fs time-resolved infrared spectra previously identified one point of contact between the C2-NH2 of the X = guanosine, an interaction that is precluded for inosine. Furthermore, this single nucleobase controls the cluster fluorescence as the X = guanosine complex is ∼2.5× dimmer. We discuss the electronic relaxation in these two complexes using transient absorption spectroscopy in the time window 200 fs-400 µs. Three prominent features emerged: a ground state bleach, an excited state absorption, and a stimulated emission. Stimulated emission at the earliest delay time (200 fs) suggests that the emissive state is populated promptly following photoexcitation. Concurrently, the excited state decays and the ground state recovers, and these changes are ∼2× faster for the X = guanosine compared to the X = inosine cluster, paralleling their brightness difference. In contrast to similar radiative decay rates, the nonradiative decay rate is 7× higher with the X = guanosine vs inosine strand. A minor decay channel via a dark state is discussed. The possible correlation between the nonradiative decay and selective coordination with the X = guanosine/inosine suggests that specific nucleobase subunits within a DNA strand can modulate cluster-ligand interactions and, in turn, cluster brightness.

Photoreductive dissolution of cerium oxide nanoparticles and their size-dependent absorption properties.

Cerium oxide has attracted attention recently for its photocatalytic properties, but there are gaps in understanding its performance, especially at low and high pH. UV irradiation of ceria nanoparticles causes electrons from photogenerated electron-hole pairs to localize as small polarons, yielding Ce3+ ions. In pH 10 solution, ceria nanoparticles capped with polyacrylic acid ligands can accumulate large numbers of Ce3+ defects as revealed by strong bleaching of the absorption onset. In contrast, we show that UV irradiation of several-nanometer diameter ceria nanoparticles in acidic (pH < 3) aqueous solution releases Ce3+ ions into solution with a quantum yield that approaches 70% and that varies with excitation wavelength, particle size, and the presence of a hole scavenger (glycerol) on the nanoparticle surface. The instability of Ce3+ at the nanoparticle surface and the ability of electron small polarons to migrate to the surface by hopping strongly suggest that nanoceria is fully oxidized and essentially free of Ce3+ centers at pH < 3. Efficient photoreduction and the excellent stability of unirradiated nanoparticles make it easy to shrink the nanoparticles using only light, while maintaining them in a fully oxidized state. This enables study of the size-dependent absorption properties of ceria nanoparticles that are free of Ce3+ defects. No evidence of quantum confinement is observed, consistent with highly localized excited states. The observed quantum yields of photoreduction are higher than reported for other metal oxides, revealing that a significant fraction of electron-hole pairs are available for driving surface redox reactions, even in fully oxidized particles.

Ultrafast excited state dynamics of silver ion-mediated cytosine-cytosine base pairs in metallo-DNA.

To better understand the nexus between structure and photophysics in metallo-DNA assemblies, the parallel-stranded duplex formed by the all-cytosine oligonucleotide, dC20, and silver nitrate was studied by circular dichroism (CD), femtosecond transient absorption spectroscopy, and time-dependent-density functional theory calculations. Silver(I) ions mediate Cytosine-Cytosine (CC) base pairs by coordinating to the N3 atoms of two cytosines. Although these silver(I) mediated CC base pairs resemble the proton-mediated CC base pairs found in i-motif DNA at first glance, a comparison of experimental and calculated CD spectra reveals that silver ion-mediated i-motif structures do not form. Instead, the parallel-stranded duplex formed between dC20 and silver ions is proposed to contain consecutive silver-mediated base pairs with high propeller twist-like ones seen in a recent crystal structure of an emissive, DNA-templated silver cluster. Femtosecond transient absorption measurements with broadband probing from the near UV to the near IR reveal an unusually long-lived (>10 ns) excited state in the dC20 silver ion complex that is not seen in dC20 in single-stranded or i-motif forms. This state is also absent in a concentrated solution of cytosine-silver ion complexes that are thought to assemble into planar ribbons or sheets that lack stacked silver(I) mediated CC base pairs. The large propeller twist angle present in metal-mediated base pairs may promote the formation of long-lived charged separated or triplet states in this metallo-DNA.

Ultrafast photoinduced energy and charge transfer: concluding remarks.

The ability to characterize and control the energy and charge transfer events triggered by the photoexcitation of molecules and materials is of fundamental importance to many fields, including the sustainable capture and conversion of solar energy. This article summarizes the papers that were presented and discussed at the recent Faraday discussion meeting on ultrafast photoinduced energy and charge transfer. Ultrafast laser spectroscopy and theory were at the center of discussions on photoinduced phenomena in biological and nanoscale systems of interacting absorbers. Many of the questions that motivate this field of science have occupied scientists for many decades, as a look back to a Faraday discussion meeting that took place 60 years earlier reveals.

Probing eumelanin photoprotection using a catechol:quinone heterodimer model system.

Eumelanin is a natural pigment with photoprotective and radical scavenging characteristics, which are vital for a multitude of living organisms. However, the molecular mechanisms behind these functions remain obscure, in part because eumelanin is a heterogeneous polymer composed of a complex assortment of structural and chemical domains. Despite uncertainty about its precise structure, the functional units of eumelanin are thought to include quinones in various oxidation states. Here, we investigate the photochemistry of a catechol : o-quinone heterodimer as a model system for uncovering the photoprotective roots of eumelanin. Ultrafast transient absorption measurements in the UV to near-IR spectral regions are used to identify the photochemical processes that follow selective excitation of the o-quinone in the heterodimer using 395 nm light. We find that both singlet and triplet o-quinone excited states induce hydrogen atom transfer from the catechol, forming semiquinone radical pairs that persist beyond 2.5 ns, which is the upper time limit accessible by our instrument. Furthermore, the hydrogen atom transfer reaction was found to occur 1000 times faster via the singlet channel. Excited state pathways such as these may be important in eumelanin, where similar hydrogen-bonded interfaces are believed to exist between catechol and o-quinone functional groups.

Effects of Intra- and Intermolecular Hydrogen Bonding on O-H Bond Photodissociation Pathways of a Catechol Derivative.

The catechol functional motif is thought to play both a structural and photochemical role in the ubiquitous natural pigment, eumelanin. Intramolecular and intermolecular hydrogen bonding interactions lead to a variety of geometries involving the two O-H groups in catechol, but its photophysical behavior in these situations has not been comprehensively characterized. Toward this end, we monitor the UV-induced O-H bond photodissociation reaction in an exemplar catechol derivative, 4- tert-butylcatechol, possessing different intramolecular and intermolecular hydrogen bonding geometries using femtosecond transient absorption spectroscopy measurements in the UV-visible and mid-infrared regions following 265 nm photoexcitation. Three different hydrogen bonding arrangements are obtained by tuning solution complexation equilibria of the catechol with the hydrogen bond acceptor, diethyl ether (Et2O), and are verified computationally. We find that intermolecular hydrogen bonding to the free O-H group in catechol increases its first excited singlet state (S1) lifetime by 2 orders of magnitude (i.e., ∼ 16 to 1410 ps), and that O-H bond dissociation is prevented because Et2O is a poor hydrogen atom acceptor. Complexation of both O-H groups with multiple Et2O molecules further elongates the S1 lifetime to 1670 ps due to shifting of the solution equilibria that describe complex formation. Weakening of the characteristic, intramolecular hydrogen bond of the catechol derivative by intermolecular hydrogen bonding to one or more Et2O molecules does not enhance the rate of O-H bond dissociation.

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.

Excited-State Dynamics of a DNA Duplex in a Deep Eutectic Solvent Probed by Femtosecond Time-Resolved IR Spectroscopy.

To better understand how the solvent influences excited-state deactivation in DNA strands, femtosecond time-resolved IR (fs-TRIR) pump-probe measurements were performed on a d(AT)9·d(AT)9 duplex dissolved in a deep eutectic solvent (DES) made from choline chloride and ethylene glycol in a 1:2 mol ratio. This solvent, known as ethaline, is a member of a class of ionic liquids capable of solubilizing DNA with minimal disruption to its secondary structure. UV melting analysis reveals that the duplex studied here melts at 18 °C in ethaline compared to 50 °C in aqueous solution. Ethaline has an excellent transparency window that facilitates TRIR measurements in the double-bond stretching region. Transient spectra recorded in deuterated ethaline at room temperature indicate that photoinduced intrastrand charge transfer occurs from A to T, yielding the same exciplex state previously detected in aqueous solution. This state decays via charge recombination with a lifetime of 380 ± 10 ps compared to the 300 ± 10 ps lifetime measured earlier in D2O solution. The TRIR data strongly suggest that the long-lived exciplex forms exclusively in the solvated duplex, and not in the denatured single strands, which appear to have little, if any, base stacking. The longer lifetime of the exciplex state in the DES compared to aqueous solution is suggested to arise from reduced stabilization of the charge transfer state, resulting in slower charge recombination on account of Marcus inverted behavior.

Decay Pathways of Thymine Revisited.

The decay of electronically excited states of thymine (Thy) and thymidine 5'-monophosphate (TMP) was studied by time-resolved UV/vis and IR spectroscopy. In addition to the well-established ultrafast internal conversion to the ground state, a so far unidentified UV-induced species is observed. In D2O, this species decays with a time constant of 300 ps for thymine and of 1 ns for TMP. The species coexists with the lowest triplet state and is formed with a comparably high quantum yield of about 10% independent of the solvent. The experimentally determined spectral signatures are discussed in the light of quantum chemical calculations of the singlet and triplet excited states of thymine.

Crystallization kinetics of cerium oxide nanoparticles formed by spontaneous, room-temperature hydrolysis of cerium(iv) ammonium nitrate in light and heavy water.

A stable sol of cerium oxide nanoparticles forms spontaneously when cerium(iv) ammonium nitrate (CAN) is dissolved in room-temperature water at mM concentrations. Electron microscopy experiments reveal the formation of highly crystalline cerium oxide particles several nm in diameter and suggest that they are formed from amorphous particles that are similar in size. Under the low pH conditions of the experiments, the nanoparticles form a stable dispersion and show no evidence of aggregation, even many months after synthesis. The absence of particles large enough to scatter light significantly makes it possible to observe the crystallization kinetics through dramatic changes in the UV-visible absorption spectra that occur during solution aging. Measurements show that the cerium oxide nanocrystals are formed roughly an order of magnitude more slowly in D2O than in H2O solution. This large solvent kinetic isotope effect (kH/kD ∼ 10), which is reported here for the first time for the crystallization of a solid metal oxide phase, indicates a rate-determining proton transfer reaction, which is assigned to the conversion of hydroxy to oxo bridges. In D2O solution, the absorption per mole of cerium ions increases by over 400% at 290 nm as the weakly absorbing precursor phase is transformed into nanocrystalline cerium oxide. An isosbestic point is detected at 368 nm, and the absorption spectra can be modeled throughout aging by the sum of spectra of just two interconverting species. Preliminary ultrafast transient absorption experiments confirm that the optical properties of the amorphous precursors differ greatly from those of the final, nanocrystalline phase. Crystallization of CeO2 from CAN in water has much in common with the crystallization of iron oxides from iron(iii) salts, including the importance of non-classical nucleation and growth pathways. It is an outstanding system for studying the poorly understood events that cause molecularly solvated ions to self-assemble into nanocrystals, following hydrolysis. At the same time, the strong susceptibility of CAN to spontaneously form CeO2 nanocrystals under the mildest of reaction conditions indicates that caution is needed when working with this common sacrificial oxidant.

Ultrafast Excited-State Deactivation of the Bacterial Pigment Violacein.

The photophysical properties of the natural pigment violacein extracted from an Antarctic organism adapted to high exposure levels of UV radiation were measured in a combined steady-state and time-resolved spectroscopic study for the first time. In the low-viscosity solvents methanol and acetone, violacein exhibits low fluorescence quantum yields on the order of 10-4, and femtosecond transient absorption measurements reveal excited-state lifetimes of 3.2 ± 0.2 and 4.5 ± 0.2 picoseconds in methanol and acetone, respectively. As solvent viscosity is increased, both the fluorescence quantum yield and excited-state lifetime of this intensely colored pigment increase dramatically and stimulated emission decays 30-fold more slowly in glycerol than in methanol at room temperature. Excited-state deactivation is suggested to occur via a molecular-rotor mechanism in which torsion about an interring bond leads to a conical intersection with the ground state.

Efficient UV-induced charge separation and recombination in an 8-oxoguanine-containing dinucleotide.

During the early evolution of life, 8-oxo-7,8-dihydro-2'-deoxyguanosine (O) may have functioned as a proto-flavin capable of repairing cyclobutane pyrimidine dimers in DNA or RNA by photoinduced electron transfer using longer wavelength UVB radiation. To investigate the ability of O to act as an excited-state electron donor, a dinucleotide mimic of the FADH2 cofactor containing O at the 5'-end and 2'-deoxyadenosine at the 3'-end was studied by femtosecond transient absorption spectroscopy in aqueous solution. Following excitation with a UV pulse, a broadband mid-IR pulse probed vibrational modes of ground-state and electronically excited molecules in the double-bond stretching region. Global analysis of time- and frequency-resolved transient absorption data coupled with ab initio quantum mechanical calculations reveal vibrational marker bands of nucleobase radical ions formed by electron transfer from O to 2'-deoxyadenosine. The quantum yield of charge separation is 0.4 at 265 nm, but decreases to 0.1 at 295 nm. Charge recombination occurs in 60 ps before the O radical cation can lose a deuteron to water. Kinetic and thermodynamic considerations strongly suggest that all nucleobases can undergo ultrafast charge separation when π-stacked in DNA or RNA. Interbase charge transfer is proposed to be a major decay pathway for UV excited states of nucleic acids of great importance for photostability as well as photoredox activity.

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

The excited-state dynamics of two cyclic DNA miniduplexes, each containing just two base pairs, are investigated using time-resolved infrared spectroscopy. As in longer DNA duplexes, intrastrand electron transfer induced by UV excitation triggers interstrand proton transfer in the alternating miniduplex containing two out-of-phase G·C base pairs. The resulting excited state decays on a time scale of several tens of picoseconds. This state is absent when one of the two G residues is substituted by 8-oxo-7,8-dihydroguanine, a modification that is suggested to disrupt base stacking, while maintaining base pairing. These findings demonstrate that a nucleobase tetramer arranged as two stacked base pairs accurately captures the interplay between intrastrand and interstrand decay channels. The similar signals seen in the miniduplexes and longer sequences suggest that excited states in the latter rapidly localize on two adjacent base pairs.

Subnanosecond Emission Dynamics of AT DNA Oligonucleotides.

UV radiation creates excited electronic states in DNA that can decay to mutagenic photoproducts. When excited states return to the electronic ground state, photochemical injury is avoided. Understanding of the available relaxation pathways has advanced rapidly during the past decade, but there has been persistent uncertainty, and even controversy, over how to compare results from transient absorption and time-resolved emission experiments. Here, emission from single- and double-stranded AT DNA compounds excited at 265 nm was studied in aqueous solution using the time-correlated single photon counting technique. There is quantitative agreement between the emission lifetimes ranging from 50 to 200 ps and ones measured in transient absorption experiments, demonstrating that both techniques probe the same excited states. The results indicate that excitations with lifetimes of more than a few picoseconds are weakly emissive excimer and charge transfer states. Only a minute fraction of excitations persist beyond 1 ns in AT DNA strands at room temperature.

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.

Photoinduced long-lived charge transfer excited states in AT-DNA strands.

The IR spectrum of a charge transfer (CT) excited electronic state in DNA has been computed for the first time, enabling assignment of the long-lived component of the transient IR spectrum of a d(AT)9 single strand to an A → T CT state. Experimentally, the CT state lifetime is much shorter than in the double strand, and our calculations explain this result using Marcus Theory.