A comparative picosecond transient infrared study of 1-methylcytosine and 5'-dCMP that sheds further light on the excited states of cytosine derivatives

Ribose and Deoxyribose Group Alter Excited-State Dynamics of 5-Azacytosine in Solution

5-Azacytosine (5-AC) is one of the best interesting noncanonical nucleobases due to its functionalization and structural imitation of natural bases. 5-AC can be used as the scaffold of two important chemotherapeutic medicines, 5-azacytidine and 2'-deoxy-5-azacytidine. Furthermore, increased sensitivity to UV leads to the photochemical effects of 5-AC also attracted attention. Yet, no study has been reported to explore the effect of glycosyl groups on the photophysical and photochemical properties of 5-AC, which can help to reveal the photostability of related actual clinic drugs. In this study, the excited-state dynamics of 5-azacytidine and 2'-deoxy-5-azacytidine are studied by femtosecond transient absorption and quantum-chemical calculations while revisiting that of 5-AC with a wider probe spectral range. It is shown that glycosyl substitution on the N1 position leads to ultrafast excited-state relaxation within several picoseconds in both nucleosides, which is distinct compared with the 17 ps lifetime seen in 5-AC. It is proposed that these changes are due to altering the energy level of the dark nπ* state. Moreover, our results suggest that it should be cautioned to simply replace sugar groups with methyl groups when doing a theoretical calculation study on nucleobases and their derivatives.

The photophysics of protonated cytidine and hemiprotonated cytidine base pair: A computational study

We here study the effect that a lowering of the pH has on the excited state processes of cytidine and a cytidine/cytidine pair in solution, by integrating time-dependent density functional theory and CASSCF/CASPT2 calculations, and including solvent by a mixed discrete/continuum model. Our calculations reproduce the effect of protonation at N3 on the steady-state infrared and absorption spectra of a protonated cytidine (CH+ ), and predict that an easily accessible non-radiative deactivation route exists for the spectroscopic state, explaining its sub-ps lifetime. Indeed, an extremely small energy barrier separates the minimum of the lowest energy bright state from a crossing region with the ground electronic state, reached by out-of-plane motion of the hydrogen substituents of the CC double bond, the so-called ethylenic conical intersection typical of cytidine and other pyrimidine bases. This deactivation route is operative for the two bases forming an hemiprotonated cytidine base pair, [CH·C]+ , the building blocks of I-motif secondary structures, whereas interbase processes play a minor role. N3 protonation disfavors instead the nπ* transitions, associated with the long-living components of cytidine photoactivated dynamics.

Is 1-methylcytosine a faithful model compound for ultrafast deactivation dynamics of cytosine nucleosides in solution?

1-Methylcytosine (1mCyt) is the base for nucleoside N1-methylpseudodeoxycytidine of Hachimoji nucleic acids and a frequently used model compound for theoretical studies on excited states of cytosine nucleosides. However, there is little experimental characterization of spectra and photo-dynamic properties of 1mCyt. Herein, we report a comprehensive investigation into excited state dynamics and effects of solvents on fluorescence dynamics of 1mCyt in both water and acetonitrile. The study employed femtosecond broadband time-resolved fluorescence, transient absorption, and steady-state spectroscopy, along with density functional theory and time-dependent density functional theory calculations. The results obtained provide the first experimental evidence for identifying a dark-natured ∼5.7 ps lifetime nπ* state in the ultrafast non-radiative deactivation with 1mCyt in aqueous solution. This study also demonstrates a significant effect of the solvent on 1mCyt's fluorescence emission, which highlights the crucial role of solute-solvent hydrogen bonding in altering structures and reshaping the radiative as well as nonradiative dynamics of the 1mCyt's ππ* state in the aprotic solvent compared to the protic solvent. The solvent effect exhibited by 1mCyt is distinctive from that known for deoxycytidine, indicating the need for caution in using 1mCyt for modelling the ultrafast dynamics of Cyt nucleosides in solvents with varying properties. Overall, our study unveils a deactivation mechanism that confers a high degree of photo-stability for 1mCyt in solution, shedding light on the molecular basis for solvent-induced effects on the excited state dynamics of nucleobases and derivatives.

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.

Photochemical Stability of 5-Methylcytidine Relative to Cytidine: Photophysical Insight for mRNA Therapeutic Applications

5-Methylcytidine (5mCyd) has recently been investigated with renewed interest in its utilization in mRNA therapeutics. However, its photostability following exposure to electromagnetic radiation has been overlooked. This Letter compares the photostability and excited-state dynamics of 5mCyd with those of the canonical RNA nucleoside, cytidine (Cyd), using steady-state and femtosecond transient absorption spectroscopy under physiologic conditions. 5mCyd is shown to have a 5-fold higher fluorescence yield and a 5-fold longer 1ππ* excited-state decay lifetime. Importantly, however, the excited-state population in 5mCyd decays primarily by internal conversion, with a photodegradation rate 3 times smaller than that in Cyd. In Cyd, the population of a 1nπ* state with a lifetime of ca. 45 ps is implicated in the formation 6-hydroxycytidine and other photoproducts.

Revealing the excited-state dynamics of cytidine and the role of excited-state proton transfer process

The high photostability of DNAs and RNAs is inextricably related to the photochemical and photophysical properties of their building blocks, nucleobases and nucleosides, which can dissipate the absorbed UV light energy in a harmless manner. The deactivation mechanism of the nucleosides, especially the decay pathways of cytidine (Cyd), has been a matter of intense debate. In the current study, we employ high-level electronic structure calculations combined with excited state non-adiabatic dynamic simulations to provide a clear picture of the excited state deactivation of Cyd in both gas phase and aqueous solution. In both environments, a barrierless decay path driven by the ring-puckering motion and a relaxation channel with a small energy barrier driven by the elongation motion of CO bond are assigned to <200 fs and sub-picosecond decay time component, respectively. The presence of ribose group has a subtle effect on the dynamic behavior of Cyd in gas phase as the ribose-to-base hydrogen/proton transfer process is energetically inaccessible with a sizable energy barrier of about 1.4 eV. However, this energy barrier is significantly reduced in water, especially when an explicit water molecule is present. Therefore, we argue that the long-lived decay channel found in aqueous solution could be assigned to the Cyd-water intermolecular hydrogen/proton transfer process. The present study postulates a novel scenario toward deep understanding the intrinsic photostability of DNAs and RNAs and provides solid evidence to disclose the long history debate of cytidine excited-state decay mechanism, especially for the assignment of experimentally observed time components.

Unraveling Excited State Dynamics of a Single-Stranded DNA-Assembled Conjugated Polyelectrolyte

Conformational templating of conjugated polyelectrolytes with single-stranded DNAs (ssDNAs) has the prospect of tailoring excited state dynamics for specific optoelectronic applications. We use ultrafast time-resolved infrared spectroscopy to study the photophysics of a cationic polythiophene assembled with different ssDNAs, inducing distinct conformations (flexible disordered structures vs more rigid complexes with increased backbone planarity). Intrachain polarons are always produced upon selective excitation of the polymer, the extent being dependent on backbone torsional order. Polaron formation and decay were monitored through evolution of IR-active vibrational modes that interfere with mid-IR polaron electronic absorption giving rise to Fano-antiresonances. Selective UV excitation of ssDNAs revealed that stacking interactions between thiophene rings and nucleic acid bases can promote the formation of an intermolecular charge transfer complex. The findings inform designers of functional conjugated polymers by identifying that involvement of the scaffold in the photophysics needs to be considered when developing such structures for optoelectronic applications.

Quantum mechanics/molecular mechanics studies on the excited-state decay mechanisms of cytidine aza-analogues: 5-azacytidine and 2'-deoxy-5-azacytidine in aqueous solution

The excited state properties and deactivation pathways of two DNA methylation inhibitors, i.e., 5-azacytidine (5ACyd) and 2'-deoxy-5-azacytidine (5AdCyd) in aqueous solution, are comprehensively explored with the QM(CASPT2//CASSCF)/MM protocol. We systematically map the feasible decay mechanisms based on the obtained excited-state decay paths involving all the identified minimum-energy structures, conical intersections, and crossing points driving the different internal conversion (IC) and intersystem crossing (ISC) routes in and between the 1ππ*, 1nπ*, 3ππ*, 3nπ*, and S0 states. Unlike the 1nπ* state below the 1ππ* state in 5ACyd, deoxyribose group substitution at the N1 position leads to the 1ππ* state becoming the S1 state in 5AdCyd. In 5ACyd and 5AdCyd, the initially populated 1ππ* state mainly deactivates to the S0 state through the direct 1ππ* → S0 IC or mediated by the 1nπ* state. The former nearly barrierless IC channel of 1ππ* → S0 occurs ultrafast via the nearby low-lying 1ππ*/S0 conical intersection. In the latter IC channel of 1ππ* → 1nπ* → S0, the initially photoexcited 1ππ* state first approaches the nearby S2/S1 conical section 1ππ*/1nπ* and then undergoes efficient IC to the 1nπ* state, followed by the further IC to the initial S0 state via the S1/S0 conical intersection 1nπ*/S0. The 1nπ*/S0 conical intersection is estimated to be located 6.0 and 4.9 kcal mol-1 above the 1nπ* state minimum in 5ACyd and 5AdCyd, respectively, at the QM(CASPT2)/MM level. In addition to the efficient singlet-mediated IC channels, the minor ISC routes would populate 1ππ* to T1(ππ*) through 1ππ* → T1 or 1ππ* → 1nπ* → T1. Relatively, the 1ππ* → 1nπ* → T1 route benefits from the spin-orbit coupling (SOC) of 1nπ*/3ππ* of 8.7 cm-1 in 5ACyd and 10.2 cm-1 in 5AdCyd, respectively. Subsequently, the T1 system will approach the nearby T1/S0 crossing point 3ππ*/S0 driving it back to the S0 state. Given the 3ππ*/S0 crossing point located above the T1 minimum and the small T1/S0 SOC, i.e., 8.4 kcal mol-1 and 2.1 cm-1 in 5ACyd and 6.8 kcal mol-1 and 1.9 cm-1 in 5AdCyd, respectively, the slow T1 → S0 would trap the system in the T1 state for a while. The present work could contribute to understanding the mechanistic photophysics and photochemistry of similar aza-nucleosides and their derivatives.

Direct Observation of Excitation Wavelength-Dependent Ultrafast Intersystem Crossing in Cytosine Nucleoside Solution

A triplet excited state can lead to different DNA photolesions, especially in cytosine and its nucleoside/nucleotide as they are hotspots for DNA mutations. However, the triplet state generation mechanism is in controversy, and experimental evidence of ultrafast intersystem crossing (ISC) has not been registered in these molecules. In this work, ultrafast ISC is directly observed in 2'-deoxycytidine (dCyd) solution by using femtosecond transient absorption spectroscopy. Surprisingly, we demonstrate that ISC in dCyd is sensitive to the excitation wavelength, and a spin-vibronic ISC mechanism is proposed. This finding is the last piece of the dCyd excited-state deactivation mechanism puzzle and sets the base for further investigation of triplet state-involved photophysics and photochemistry in dCyd-containing DNA.

The Excited State Dynamics of a Mutagenic Cytidine Etheno Adduct Investigated by Combining Time-Resolved Spectroscopy and Quantum Mechanical Calculations

Joint femtosecond fluorescence upconversion experiments and theoretical calculations provide a hitherto unattained degree of characterization and understanding of the mutagenic etheno adduct 3,N4-etheno-2'-deoxycytidine (εdC) excited state relaxation. This endogenously formed lesion is attracting great interest because of its ubiquity in human tissues and its highly mutagenic properties. The εdC fluorescence is modified with respect to that of the canonical base dC, with a 3-fold increased lifetime and quantum yield at neutral pH. This behavior is amplified upon protonation of the etheno ring (εdCH⁺). Quantum mechanical calculations show that the lowest energy state ππ*1 is responsible for the fluorescence and that the main nonradiative decay pathway to the ground state goes through an ethene-like conical intersection, involving the out-of-plane motion of the C5 and C6 substituents. This conical intersection is lower in energy than the ππ* state (ππ*1) minimum, but a sizable energy barrier explains the increase of εdC and εdCH⁺ fluorescence lifetimes with respect to that of dC.

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.

Ultrafast Dynamics of the Two Lowest Bright Excited States of Cytosine and 1-Methylcytosine: A Quantum Dynamical Study

The nonadiabatic quantum dynamics (QD) of cytosine and 1-methylcytosine in the gas phase is simulated for 250 fs after a photoexcitation to one of the first two bright states. The nuclear wavepacket is propagated on the coupled diabatic potential energy surfaces of the lowest seven excited states, including ππ*, nπ*, and Rydberg states along all the vibrational degrees of freedom. We focus in particular on the interplay between the bright and the dark nπ* states, not considering the decay to the ground electronic state. To run these simulations, we implemented an automatic general procedure to parametrize linear vibronic coupling (LVC) models with time-dependent density functional theory (DFT) computations and interfaced it with Gaussian package. The wavepacket was propagated with the multilayer version of the multiconfigurational time dependent Hartree method. Two different density functionals, PBE0 and CAM-B3LYP, which provide a different description of the relative stability of the lowest energy dark states, were used to parametrize the LVC Hamiltonian. Part of the photoexcited population on lowest HOMO-LUMO transition (π_Hπ_L^*) decays within less than 100 fs to a nπ* state which mainly involves a promotion of an electron from the oxygen lone pair to the LUMO (n_Oπ_L^*). The population of the second ππ* state decays almost completely, in <100 fs, not only to π_Hπ_L^* and to n_Oπ_L^* states but also to another nπ_L^* state involving the nitrogen lone pair. The efficiency of the adopted protocol allowed us to check the accuracy of the predictions by repeating the QD simulations with different LVC Hamiltonians parametrized either at the ground-state minimum or at stationary structures of different relevant excited states.

UV-induced hydrogen transfer in DNA base pairs promoted by dark nπ* states

Formation of an excited-state complex enables ultrafast photorelaxation of dark nπ* states in GC and HC base pairs.

Exciton Absorption and Luminescence in i-Motif DNA

We have studied the excited-state dynamics for the i-motif form of cytosine chains (dC)10, using the ultrafast fluorescence up-conversion technique. We have also calculated vertical electronic transition energies and determined the nature of the corresponding excited states in a model tetramer i-motif structure. Quantum chemical calculations of the excitation spectrum of a tetramer i-motif structure predict a significant (0.3 eV) red shift of the lowest-energy transition in the i-motif form relative to its absorption maximum, which agrees with the experimental absorption spectrum. The lowest excitonic state in i-(dC)10 is responsible for a 2 ps red-shifted emission at 370 nm observed in the decay-associated spectra obtained on the femtosecond time-scale. This delocalized (excitonic) excited state is likely a precursor to a long-lived excimer state observed in previous studies. Another fast 310 fs component at 330 nm is assigned to a monomer-like locally excited state. Both emissive states form within less than the available time resolution of the instrument (100 fs). This work contributes to the understanding of excited-state dynamics of DNA within the first few picoseconds, which is the most interesting time range with respect to unraveling the photodamage mechanism, including the formation of the most dangerous DNA lesions such as cyclobutane pyrimidine dimers.

Excited-State Dynamics in the RNA Nucleotide Uridine 5'-Monophosphate Investigated Using Femtosecond Broadband Transient Absorption Spectroscopy

Damage to RNA from ultraviolet radiation induces chemical modifications to the nucleobases. Unraveling the excited states involved in these reactions is essential; however, investigations aimed at understanding the electronic-energy relaxation pathways of the RNA nucleotide uridine 5'-monophosphate (UMP) have not received enough attention. In this Letter, the excited-state dynamics of UMP is investigated in aqueous solution. Excitation at 267 nm results in a trifurcation event that leads to the simultaneous population of the vibrationally excited ground state, a long-lived ¹nπ* state, and a receiver triplet state within 200 fs. The receiver state internally converts to the long-lived ³ππ* state in an ultrafast time scale. The results elucidate the electronic relaxation pathways and clarify earlier transient absorption experiments performed for uracil derivatives in solution. This mechanistic information is important because long-lived nπ* and ππ* excited states of both singlet and triplet multiplicities are thought to lead to the formation of harmful photoproducts.

Ultrafast and radiationless electronic excited state decay of uracil and thymine cations: computing the effects of dynamic electron correlation

In this article we characterise the radiationless decay of the first few electronic excited states of the cations of DNA/RNA nucleobases uracil and thymine, including the effects of dynamic electron correlation on energies and geometries (optimised with XMS-CASPT2). In both systems, we find that one state of ²n and another two of ²π⁺ character can be populated following photoionisation, and their different minima and interstate crossings are located. We find strong similarities between uracil and thymine cations: with accessible conical intersections suggesting that depopulation of their electronic excited states takes place on ultrafast timescales in both systems, suggesting that they are photostable in agreement with previous theoretical (uracil⁺) evidence. We find that dynamic electron correlation separates the energy levels of the "3-state" conical intersection (D₂/D₁/D₀)_CI previously located with CASSCF for uracil⁺, which will therefore have a different geometry and higher energy. Simulating the electronic and vibrational absorptions allows us to characterise spectral fingerprints that could be used to monitor these cation photo-processes experimentally.

Ultrafast Excited-State Dynamics of Hydrogen-Bonded Cytosine Microsolvated Clusters with Protic and Aprotic Polar Solvents

Microsolvation effects on the ultrafast excited-state deactivation dynamics of cytosine (Cy) were studied in hydrogen-bonded Cy clusters with protic and aprotic solvents using mass-resolved femtosecond pump-probe ionization spectroscopy. Two protic solvents, water (H₂O) and methanol (MeOH), and one aprotic solvent, tetrahydrofuran (THF), were investigated, and transients of Cy·(H₂O)_1-6, Cy·(MeOH)_1-3, and Cy·THF microsolvated clusters produced in supersonic expansions were measured. With the aid of electronic structure calculations, we assigned the observed dynamics to the low-energy isomers of various Cy clusters and discussed the microsolvation effect on the excited-state deactivation dynamics. With the protic solvents only the microsolvated clusters of Cy keto tautomer were observed. The observed decay time constants of Cy·(H₂O) _n are 0.5 ps for n = 1 and ∼0.2-0.25 ps for n = 2-6. For Cy·(MeOH) _n clusters, the decay time constant for n = 1 cluster is similar to that of the Cy monohydrate, but for n = 2 and 3 the decays are about a factor of 2 slower than the corresponding microhydrates. With the aprotic solvent, THF, hydrogen-bonded complexes of both keto and enol tautomers are present in the beam. The keto-Cy·THF shows a decay similar to that of the keto-Cy monomer, whereas the enol-Cy·THF exhibits a 2-fold slower decay than the enol-Cy monomer, suggesting an increase in the barrier to excited-state deactivation upon binding of one THF molecule to the enol form of Cy.

Fluorescence and Ultrafast Fluorescence Unveil the Formation, Folding Molecularity, and Excitation Dynamics of Homo-Oligomeric and Human Telomeric i-Motifs at Acidic and Neutral pH

i-Motifs are tetraplex DNAs known to be stable at acidic pH. The structure of i-motifs is important in DNA nanotechnology; i-motif-forming sequences with consecutive cytosine (C) molecules are abundant throughout the human genome. There is, however, little information on the structure of C-rich DNAs under physiologically relevant neutral conditions. The electron dynamics of i-motifs, crucial to both biology and materials applications, also remains largely unexplored. In this work, we report a combined femtosecond and nanosecond broadband time-resolved fluorescence (TRF) and steady-state fluorescence investigation on homo-oligomer dC₂₀ , a human telomeric sequence (HTS) 5'-dC₃ (TA₂ C₃ )₃ , and its analogue performed with different excitation at both acidic and neutral pH. Our study provides direct observation of intrinsic fluorescence and the first full probe of the real-time dynamics of the intrinsic fluorescence from i-motifs formed from varied sequences and pH conditions. The results obtained demonstrate concrete evidence for the existence at neutral pH of i-motifs from both dC₂₀ and the HTS. It also identifies that, under neutral conditions, the i-motif from dC₂₀ adopting the bimolecular folding structure is significantly more stable than the HTS i-motif featuring the unimolecular topology. Our femtosecond and nanosecond TRF study unveils excitation dynamics distinctive of the interdigitated architecture of i-motifs with the excited states involved exhibiting deactivation over a remarkably broad timescale through multiple channels involving proton-coupled electron transfer lasting tens of picoseconds, as signified by the solvent kinetic isotope effect, and structure-dependent charge recombination in the hundreds of picoseconds to tens of nanoseconds time regime.

Photochemical and Photodynamical Properties of Sulfur-Substituted Nucleic Acid Bases

Sulfur-substituted nucleobases (a.k.a., thiobases) are among the world's leading prescriptions for chemotherapy and immunosuppression. Long-term treatment with azathioprine, 6-mercaptopurine and 6-thioguanine has been correlated with the photoinduced formation of carcinomas. Establishing an in-depth understanding of the photochemical properties of these prodrugs may provide a route to overcoming these carcinogenic side effects, or, alternatively, a basis for developing effective compounds for targeted phototherapy. In this review, a broad examination is undertaken, surveying the basic photochemical properties and excited-state dynamics of sulfur-substituted analogs of the canonical DNA and RNA nucleobases. A molecular-level understanding of how sulfur substitution so remarkably perturbs the photochemical properties of the nucleobases is presented by combining experimental results with quantum-chemical calculations. Structure-property relationships demonstrate the impact of site-specific sulfur substitution on the photochemical properties, particularly on the population of the reactive triplet state. The value of fundamental photochemical investigations for driving the development of ultraviolet-A chemotherapeutics is showcased. The most promising photodynamic agents identified thus far have been investigated in various carcinoma cell lines and shown to decrease cell proliferation upon exposure to ultraviolet-A radiation. Overarching principles have been elucidated for the impact that sulfur substitution of the carbonyl oxygen has on the photochemical properties of the nucleobases.

Excited State Decay Pathways of 2'-Deoxy-5-methylcytidine and Deoxycytidine Revisited in Solution: A Comprehensive Kinetic Study by Femtosecond Transient Absorption

Methylated cytosine is proved to have an important role as an epigenetic signal in gene regulation and is often referred to "the fifth base of DNA". A comprehensive understanding of the electronic excited state relaxation in cytosine and its methylated derivatives is crucial for revealing UV-induced photodamage to the biological genome. Because of the existence of multiple closely lying "bright" and "dark" excited states, the decay pathways in these DNA nucleosides are the most complex and the least understood so far. In this study, femtosecond transient absorption with different excitation wavelengths (240-296 nm) was used to study the relaxation of excited electronic states of 5-methylcytosine (5mC) and 2'-deoxy-5-methylcytidine (5mdCyd) in phosphate buffered aqueous solution and in acetonitrile solution. Two distinct nonradiative decay channels were directly observed. The first one is a several picosecond internal conversion channel that involves two bright ππ* states (ππ*₂ and ππ*₁) when ππ*₂ state is initially populated. The second channel contains the lower energy ππ*₁ state and a so far experimental unidentified long-lived state which exhibits a several nanosecond lifetime. The long-lived state can only be accessed by the initially excited ππ*₁ state. Inspired by this new discovery in 5mC and 5mdCyd, we revisited the decay of excited state of 2'-deoxycytidine (dCyd), revealing very similar decay pathways. Additionally, a well-known dark n_Oπ* state (carbonyl lone pair) with ∼30 ps lifetime is present in both decay channels in dCyd. With our detailed experimental results, we successfully reconcile the long history debate of cytosine excited state relaxation mechanism by pointing out that the reason for the complex dynamics under traditional 266 nm excitation is mixed signals from the above-mentioned two distinct decay pathways. Our findings lead to a dramatically different and new picture of electronic energy relaxation in 5mdCyd/dCyd and could help to understand photostability as well as UV-induced photodamage of these nucleotides and related DNAs.

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.

Solute-Solvent Interactions and Excited-State Symmetry Breaking: Beyond the Dipole-Dipole and the Hydrogen-Bond Interactions

Symmetry breaking of the excited state of a linear quadrupolar acceptor-donor-acceptor molecule was investigated using time-resolved infrared spectroscopy in 55 solvents allowing the influence of several solute-solvent interactions to be examined separately. No symmetry breaking was found in nonpolar solvents irrespective of their refractive index, indicating that differences in dispersion interactions between the two arms of the molecule do not suffice to induce an asymmetric distribution of the excitation. However, symmetry breaking was observed in nondipolar but quadrupolar solvents like benzene to an extent that can be as large as that found in medium dipolar solvents like THF. Whereas larger symmetry breaking occurs in the most dipolar solvents, the strongest are observed in protic solvents due to hydrogen bonding. Strong evidence of the formation of halogen bonds in the excited state is also presented, confirming the idea of symmetry-breaking-induced asymmetrical photochemistry.

Water–chromophore electron transfer determines the photochemistry of cytosine and cytidine

Irradiation of aqueous cytidine may result in a water–chromophore electron transfer process which explains numerous experimental observations, including photodamage.

Effects of ionization on stability of 1-methylcytosine - DFT and PCM studies

Consequences of ionization were studied by quantum-chemical methods (DFT and PCM) for 1-methylcytosine (MC)—a model of the nucleobase cytosine (C) connected with sugar in DNA. For calculations, three prototropic tautomers (one amino and two imino forms) and two imino zwitterions were considered, including conformational or configurational isomerism of exo heterogroups. Ionization and interactions between neighboring groups affect intramolecular proton-transfers, geometric and thermodynamic parameters, and electron delocalization for individual isomers. We discovered that an imino isomer is present in the isomeric mixture in the highest amount for positively ionized MC. Its contribution in neutral and negatively ionized MC is considerably smaller. Acid-base parameters for selected radical ions were estimated in the gas phase and compared to those of neutral MC. Gas-phase acidity of radical cations is close to that of the conjugate acid of MC, and gas-phase basicity of radical anions is close to that of the conjugate base of MC. Various routes of amino-imino conversion between neutral and ionized isomers were considered. Energetic-barrier for intramolecular proton-transfer in MC is close to that in the parent system—formamidine.

Remarkable effects of solvent and substitution on the photo-dynamics of cytosine: a femtosecond broadband time-resolved fluorescence and transient absorption study

Cytosine (Cyt) among all the nucleic acid bases features the most complex and least understood nonradiative deactivation, a process that is crucially important for its photostability. Herein, the excited state dynamics of Cyt and a series of its N1- and C5-derivatives, including the full set of Cyt nucleosides and nucleotides in DNA and RNA and the nucleosides of 5-methyl cytosine, 5-methylcytidine and 2'-deoxy-5-methylcytidine, have been investigated in water and in methanol employing femtosecond broadband time-resolved fluorescence coupled with fs transient absorption spectroscopy. The results reveal remarkable state-specific effects of the substitution and solvent in tuning distinctively the timescales and pathways of the nonradiative decays. For Cyt and the N1-derivatives, the nonradiative deactivations occur in a common two-state process through three channels, two from the light-absorbing ππ* state with respectively the sub-picosecond (∼0.2 ps) and the picosecond (∼1.5 ps) time constant, and the third is due to an optically dark nπ* state with the lifetime ranging from several to hundreds of picoseconds depending on solvents and substitutions. Compared to Cyt, the presence of the ribose or deoxyribose moiety at the N1 position of N1-derivatives facilitates the formation of the nπ* at the sub-picosecond timescale and at the same time increases its lifetime by ∼4-6 times in both water and methanol. In sharp contrast, the existence of the methyl group at the C5 position of the C5-derivatives eliminates completely the sub-picosecond ππ* channel and the channel due to the nπ*, but on the other hand slows down the decay of the ππ* state which after relaxation exhibits a single time constant of ∼4.1 to ∼7.6 ps depending on solvents. Varying the solvent from water to methanol accelerates only slightly the decay of the ππ* state in all the compounds; while for Cyt and its N1-derivatives, this change of solvent also retards strongly the nπ* channel, prolongs its lifetime from such as ∼7.7 ps in water to ∼52 ps in methanol for Cyt and from ∼30 ps in water to ∼186 ps in methanol for deoxycytidine. The spectral signatures we obtained for the ππ* and the nπ* states allow unambiguous evidence for clarifying uncertainties in the excited states of Cyt and the derivatives. The results provide a unifying experimental characterization at an improved level of detail about the photophysics of Cyt and its analogues under biologically relevant conditions and may help in understanding the photostability as well as photo-damages of the bases and related DNAs.

Direct Visualization of Excited-State Symmetry Breaking Using Ultrafast Time-Resolved Infrared Spectroscopy

Most symmetric quadrupolar molecules designed for two-photon absorption behave as dipolar molecules in the S1 electronic excited state. This is usually explained by a breakup of the symmetry in the excited state. However, the origin of this process and its dynamics are still not fully understood. Here, excited-state symmetry breaking in a quadrupolar molecule with a D-π-A-π-D motif, where D and A are electron donating and accepting units, is observed in real time using ultrafast transient infrared absorption spectroscopy. The nature of the relaxed S1 state was found to strongly depend on the solvent polarity: (1) in nonpolar solvents, it is symmetric and quadrupolar; (2) in weakly polar media, the quadrupolar state observed directly after excitation transforms to a symmetry broken S1 state with one arm bearing more excitation than the other; and (3) in highly polar solvents, the excited state evolves further to a purely dipolar S1 state with the excitation localized entirely on one arm. The time scales associated with the transitions between these states coincide with those of solvation dynamics, indicating that symmetry breaking is governed by solvent fluctuations.

Long-Lived Excited-State Dynamics of i-Motif Structures Probed by Time-Resolved Infrared Spectroscopy

UV-generated excited states of cytosine (C) nucleobases are precursors to mutagenic photoproduct formation. The i-motif formed from C-rich sequences is known to exhibit high yields of long-lived excited states following UV absorption. Here the excited states of several i-motif structures have been characterized following 267 nm laser excitation using time-resolved infrared spectroscopy (TRIR). All structures possess a long-lived excited state of ∼300 ps and notably in some cases decays greater than 1 ns are observed. These unusually long-lived lifetimes are attributed to the interdigitated DNA structure which prevents direct base stacking overlap.

Electronic and structural elements that regulate the excited-state dynamics in purine nucleobase derivatives

The excited-state dynamics of the purine free base and 9-methylpurine are investigated using experimental and theoretical methods. Femtosecond broadband transient absorption experiments reveal that excitation of these purine derivatives in aqueous solution at 266 nm results primarily in ultrafast conversion of the S2(ππ*) state to the vibrationally excited (1)nπ* state. Following vibrational and conformational relaxation, the (1)nπ* state acts as a doorway state in the efficient population of the triplet manifold with an intersystem crossing lifetime of hundreds of picoseconds. Experiments show an almost 2-fold increase in the intersystem crossing rate on going from polar aprotic to nonpolar solvents, suggesting that a solvent-dependent energy barrier must be surmounted to access the singlet-to-triplet crossing region. Ab initio static and surface-hopping dynamics simulations lend strong support to the proposed relaxation mechanism. Collectively, the experimental and computational results demonstrate that the accessibility of the nπ* states and the topology of the potential energy surfaces in the vicinity of conical intersections are key elements in controlling the excited-state dynamics of the purine derivatives. From a structural perspective, it is shown that the purine chromophore is not responsible for the ultrafast internal conversion in the adenine and guanine monomers. Instead, C6 functionalization plays an important role in regulating the rates of radiative and nonradiative relaxation. C6 functionalization inhibits access to the (1)nπ* state while simultaneously facilitating access to the (1)ππ*(La)/S0 conical intersection, such that population of the (1)nπ* state cannot compete with the relaxation pathways to the ground state involving ring puckering at the C2 position.

Excited-state hydrogen atom abstraction initiates the photochemistry of β-2'-deoxycytidine

Understanding the effects of ultraviolet radiation on nucleotides in solution is an important step towards a comprehensive description of the photochemistry of nucleic acids and their constituents. Apart from having implications for mutagenesis and DNA photoprotection mechanisms, the photochemistry of cytidines is a central element in UV-assisted syntheses of pyrimidine nucleotides under prebiotically plausible conditions. In this contribution, we present UV-irradiation experiments of β-2'-deoxycytidine in aqueous solution involving H-D exchange followed by NMR spectroscopic analysis of the photoproducts. We further elucidate the outcome of these experiments by means of high-level quantum chemical calculations. In particular, we show that prolonged UV-irradiation of cytidine may lead to H-C1' hydrogen atom abstraction by the carbonyl oxygen atom of cytosine. This process may enable photoanomerisation and nucleobase loss, two previously unexplained photoreactions observed in pyrimidine nucleotides.

The solvent effect and identification of a weakly emissive state in nonradiative dynamics of guanine nucleosides and nucleotides--a combined femtosecond broadband time-resolved fluorescence and transient absorption study

A combined method of femtosecond broadband time-resolved fluorescence (fs-TRF) and transient absorption (fs-TA) was employed to investigate the excited state dynamics of 2'-deoxyguanosine (dG) and 2'-deoxyguanosine 5'-monophosphate (dGMP). Comparative fs-TRF and fs-TA measurements were conducted on dG and dGMP in neutral water, deuterated water, and methanol with excitation wavelengths of 245, 267 and 285 nm. Very similar results were observed with dG and dGMP. The data provide compelling evidence for the co-existence of two nonradiative pathways. One is the generally recognized Laππ* mediated channel, the other involves an unprecedented weakly emissive state which plays a significant role in the overall deactivation processes. The Laππ* channel features biphasic dynamics with time constants (τ1/τ2) of ~0.2/0.8 ps in water and ~0.25/1.0 ps in methanol. The biphasic decay arises due to a partial transfer with τ1 of the Laππ* population to the newly identified state followed by conversion in τ2 of the remaining Laππ* molecules into the electronic ground state. The channel mediated by the weakly emissive species shows solvent-dependent dynamics with time constants (τ3) of ~2.0 ps in water, ~2.3 ps in deuterated water, and ~4.1 ps in methanol. The species features absorption at UV wavelengths (~300-400 nm) and exhibits deeply red-shifted fluorescence (λmax ~ 520 nm) with polarization direction varied markedly from that of the Laππ* but close to the Lbππ*. This species acts as an effective quenching state to the radiative decay of the brightly emissive Laππ* and Lbππ*. It sets in promptly (<~50 fs) after the photoexcitation and is further populated through nonadiabatic coupling with the Laππ*. The overall involvement of this state is facilitated with excitation at high energy and is favoured in methanol over water. According to the spectral character and the solvent effect in particular the kinetic isotope effect, the species is tentatively associated to the πσ* state with charge transfer (CT) character which is considered to be preferentially stabilized by hydrogen-bonding between the guanine amino and surrounding solvent molecules. The result of this study leads to a dramatically different picture of guanine deactivation. It demonstrates a crucial role of the solvent in shaping the nonradiative dynamics of guanine nucleosides and nucleotides. The data presented are important for understanding the detailed photophysics of not only the monomeric guanine but also DNA assemblies that contain guanine in base pairs or have a guanine tetrad as the structural motif.

Fingerprinting DNA oxidation processes: IR characterization of the 5-methyl-2'-deoxycytidine radical cation

Methylated cytidine plays an important role as an epigenetic signal in gene regulation. Its oxidation products are assumed to be involved in active demethylation processes but also in damaging DNA. Here, we report the photochemical production of the 5-methyl-2'-deoxycytidine radical cation via a two-photon ionization process. The radical cation is detected by time-resolved IR spectroscopy and identified by band assignment using density functional theory calculations. Two final oxidation products are characterized with liquid chromatography coupled to mass spectrometry.

Broadband infrared and Raman probes of excited-state vibrational molecular dynamics: simulation protocols based on loop diagrams

Vibrational motions in electronically excited states can be observed either by time and frequency resolved infrared absorption or by off resonant stimulated Raman techniques. Multipoint correlation function expressions are derived for both signals. Three representations which suggest different simulation protocols for the signals are developed. These are based on the forward and the backward propagation of the wavefunction, sum over state expansion using an effective vibrational Hamiltonian or a semiclassical treatment of a bath. We show that the effective temporal (Δt) and spectral (Δω) resolution of the techniques is not controlled solely by experimental knobs but also depends on the system dynamics being probed. The Fourier uncertainty ΔωΔt > 1 is never violated.

Ultrafast IR spectroscopy of polymeric cytosine nucleic acids reveal the long-lived species is due to a localised state

The decay pathways of UV-excited cytosine polymers are investigated using picosecond time-resolved infrared spectroscopy. Similar yields of a non-emissive (1)nπ* state are found in the single-stranded dC(30) polymer as in the dCMP monomer, but with a longer lifetime in the polymer (80 ps vs. 39 ps). A longer lifetime is also found in the d(CpC) dinucleotide. No evidence of excimer states is observed, suggesting that localised (1)nπ* excited states are the most significant intermediates present on the picosecond timescale.