Unified Description of Ultrafast Excited State Decay Processes in Epigenetic Deoxycytidine Derivatives

Quantum Mechanics/Molecular Mechanics Studies on the Excited-State Relaxation Mechanisms of Cytidine Analogues: 2'-Deoxy-5-Methylcytidine and 2'-Deoxy-5-Hydroxymethylcytidine in Aqueous Solution

We have used the high-level QM(CASPT2//CASSCF)/MM method to investigate the excited-state properties and decay pathways of two important cytidine analogues, i.e., 2'-deoxy-5-methylcytidine (5mdCyd) and 2'-deoxy-5-hydroxymethylcytidine (5hmdCyd), in aqueous solution. In view of the computed minimum-energy structures, conical intersections, and crossing points, and the relevant excited-state decay paths including the different internal conversion (IC) and intersystem crossing (ISC) routes in and between the S1, T1, T2, and S0 states, we finally provided the feasible excited-state relaxation mechanisms of these two important epigenetic DNA nucleosides. Upon 285 nm photoexcitation, the lowest spectroscopically bright S1(ππ*) state is initially populated in the Franck-Condon (FC) region in both solvated systems and then mainly occurs direct IC to the ground state through the nearby accessible S1/S0 conical intersection, with the QM(CASPT2)/MM computed energy barriers of 9.5 and 1.6 kcal/mol for 5mdCyd and 5hmdCyd, respectively. In addition, the S1(ππ*) state can partially hop to the T1(ππ*) state directly or is mediated by the T2(ππ*) state. In comparison to the favorable singlet-mediated IC channel, the minor S1→T1 and S1→T2→T1 ISCs would take place slowly. Subsequently, the T1 state will further approach the nearby T1/S0 crossing point to slowly deactivate to the S0 state. Due to the T1/S0 crossing point above the T1-MIN as well with the small T1/S0 SOC, i.e., 9.8 kcal/mol and 0.3 cm-1 in 5mdCyd and 8.7 kcal/mol and 1.9 cm-1 in 5hmdCyd, the slow ISC would trap the system in the T1 state for a long time. The present work rationalizes the excited-state dynamics of 5mdCyd and 5hmdCyd in aqueous solution and could provide mechanistic insights into understanding the photophysics and photochemistry of similar epigenetic DNA nucleosides and their derivatives.

Quantum mechanics/molecular mechanics studies on mechanistic photophysics of epigenetic C5-halogenated DNA nucleosides: 2'-deoxy-5-chlorocytidine and 2'-deoxy-5-bromocytidine in aqueous solution

In this work, we have employed the high-level QM(CASPT2//CASSCF)/MM method to study the photophysical mechanisms of two important metabolized DNA/RNA nucleoside byproducts, i.e., 2'-deoxy-5-chlorocytidine (5CldCyd) and 2'-deoxy-5-bromocytidine (5BrdCyd), in aqueous solution. On the basis of our optimized minimum-energy structures, conical intersections, and crossing points, as well as the computed associated excited-state relaxation pathways involving the different internal conversion (IC) and intersystem crossing (ISC) processes in and between the S1, T1, T2, and S0 states, we have suggested the feasible excited-state relaxation mechanisms of these two important epigenetic halogenated DNA nucleosides. The initially populated spectroscopic bright 1ππ* state in the Franck-Condon (FC) region is the S1 state both for 5CldCyd and 5BrdCyd under 295 nm irradiation. The excited S1 state first evolves into its minimum S1-MIN and rapidly undergoes efficient IC to the S0 state via the nearby low-lying S1/S0 conical intersection. The corresponding energy barrier of the S1 → S0 IC path in 5CldCyd is estimated to be 4.6 kcal mol-1 at the QM(CASPT2)/MM level, while it is found to be an almost barrierless process in 5BrdCyd. In addition to this very efficient IC, the S1 state can partially slowly undergo ISC to transfer to the T1 state. Because the small spin-orbit couplings (SOCs) of S1/T1 and S1/T2 are estimated to be less than 5.0 cm-1 at the QM(CASPT2)/MM level, the ISC involved T1 formation is not so efficient. The resulting T1 state from the minor S1 → T1 and S1 → T2 → T1 ISCs will first relax to its minimum T1-MIN and continue to approach the nearby accessible T1/S0 crossing point, followed by further T1 → S0 ISC to the S0 state. Relatively, the T1 → S0 ISC of 5BrdCyd is significantly enhanced by a large T1/S0 SOC of 32.9 cm-1 at the T1/S0 crossing point. The present work rationalizes the excited-state dynamics of 5CldCyd and 5BrdCyd in aqueous solution and could provide mechanistic insights into understanding the photophysics of similar halogenated DNA nucleosides and their derivatives.

Structure-Photophysical Property Relationships in Noncanonical and Synthetic Nucleobases

This review provides focused coverage of the photophysical properties of noncanonical and synthetic nucleobases reported over the past decade. It emphasizes key research findings and physical insights gathered for prebiotic and fluorescent nucleobase analogs, sulfur- and selenium-substituted nucleobases, aza-substituted nucleobases, epigenetic nucleobases and their oxidation products, and nucleobases utilized for expanding DNA/RNA to reveal central structure-photophysical property relationships. Further research and development in this emerging field, coupled with machine learning methods, will enable the effective harnessing of nucleobases' modifications for applications in biotechnology, biomedicine, therapeutics, and even the creation of live semisynthetic organisms.

Potentiality of Nucleoside as Antioxidant by Analysis on Oxidative Susceptibility, Drug Discovery, and Synthesis

Nucleosides are sensitive sites towards oxidations caused by endogenous and exogenous oxidative resources, and a large number of the produced DNA lesions behave as pathogenesis eventually. We herein analyze oxidative modes of nucleosides and structure- activity relationships of some clinical nucleoside drugs. Together with our previous findings on the inhibitory effects of nucleoside derivatives against DNA oxidation, all these results imply a possibility for nucleoside to be a new member in the family of antioxidants. Then, some novel synthetic routines of nucleoside analogs are collected to reveal the applicability in the construction of nucleoside antioxidants. Therefore, it is reasonable to envision that the nucleoside antioxidant will be a novel topic in the research of both nucleosides and antioxidants.

The Excited State Dynamics of a Mutagenic Guanosine Etheno Adduct Investigated by Femtosecond Fluorescence Spectroscopy and Quantum Mechanical Calculations

Femtosecond fluorescence upconversion experiments were combined with CASPT2 and time dependent DFT calculations to characterize the excited state dynamics of the mutagenic etheno adduct 1,N2-etheno-2'-deoxyguanosine (ϵdG). This endogenously formed lesion is attracting great interest because of its ubiquity in human tissues and its highly mutagenic properties. The ϵdG fluorescence is strongly modified with respect to that of the canonical nucleoside dG, notably by an about 6-fold increase in fluorescence lifetime and quantum yield at neutral pH. In addition, femtosecond fluorescence upconversion experiments reveal the presence of two emission bands with maxima at 335 nm for the shorter-lived and 425 nm for the longer-lived. Quantum mechanical calculations rationalize these findings and provide absorption and fluorescence spectral shapes similar to the experimental ones. Two different bright minima are located on the potential energy surface of the lowest energy singlet excited state. One planar minimum, slightly more stable, is associated with the emission at 335 nm, whereas the other one, with a bent etheno ring, is associated with the red-shifted emission.

Natural Epigenetic DNA Modifications Cause Remote DNA Photodamage

5-Formyl-2'-deoxycytidine, an intermediate during the erasure of epigenetic marker 5-methyl-2'-deoxycytidine, and 5-formyl-2'-deoxyuridine, an oxidative lesion of thymidine, are naturally occurring DNA modifications. The carbonyl groups of these DNA modifications are the smallest possible photosensitizers and have the potential to generate cyclobutane pyrimidine dimers upon irradiation with UV light. To evidence this damaging potential, ternary DNA architectures were used, in which the photosensitizer and the damage site were located at well-defined positions in the sequences. The quantitative and time-dependent analysis revealed not only the high photodamaging potential of both natural DNA modifications but also the mechanisms for this new pathway to photodamage. 5-Formyl-2'-deoxycytidine is more efficiently generating cyclobutane pyrimidine dimers than 5-formyl-2'-deoxyuridine because the latter is also photochemically converted to 5-carboxy-2'-deoxyuridine. This demonstrates for the first time that epigenetic DNA modifications regulating gene expression interact with sunlight and can induce DNA photodamages.

Reconciling TD-DFT and CASPT2 electronic structure methods for describing the photophysics of DNA

Time-dependent density functional theory (TD-DFT) and multiconfigurational second-order perturbation theory (CASPT2) are two of the most widely used methods to investigate photoinduced dynamics in DNA-based systems. These methods sometimes give diverse dynamics in physiological environments usually modeled by quantum mechanics/molecular mechanics (QM/MM) protocol. In this work, we demonstrate for the uridine test case that the underlying topology of the potential energy surfaces of electronic states involved in photoinduced relaxation is similar in both electronic structure methods. This is verified by analyzing surface-hopping dynamics performed at the QM/MM level on aqueous solvated uridine at TD-DFT and CASPT2 levels. By constraining the dynamics to remain onπ π * state we observe similar fluctuations in energy and relaxation lifetimes in surface-hopping dynamics in both TD-DFT and experimentally validated CASPT2 methods. This finding calls for a systematic comparison of the ES potential energy surfaces of DNA and RNA nucleosides at the single- and multi-reference levels of theory. The anomalous long excited state lifetime at the TD-DFT level is explained byn π * trapping due to the tendency of TD-DFT in QM/MM schemes with electrostatic embedding to underestimate the energy of theπ π * state leading to a wrongπ π * / n π * energetic order. A study of the FC energetics suggests that improving the description of the surrounding environment through polarizable embedding or by the expansion of QM layer with hydrogen-bonded waters helps restore the correct state order at TD-DFT level. Thus by combining TDDFT with an accurate modeling of the environment, TD-DFT is positioned as the standout protocol to model photoinduced dynamics in DNA-based aggregates and multimers.

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.

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.

Ultrafast Electronic Relaxation in 6-Methyluracil and 5-Fluorouracil in Isolated and Aqueous Conditions: Substituent and Solvent Effects

We report ultrafast extreme ultraviolet photoelectron spectroscopy of 6-methyluracil (6mUra) and 5-fluorouracil (5FUra) in the gas phase and 6mUra and 5-fluorouridine in an aqueous environment. In the gas phase, internal conversion (IC) occurs from ¹ππ* to ¹nπ* states in tens of femtoseconds, followed by intersystem crossing to the ³ππ* state in several picoseconds. In an aqueous solution, 6mUra undergoes IC almost exclusively to the ground state (S₀) in about 100 fs, which is essentially the same process as that for unsubstituted uracil, but much faster than that for thymine (5-methyluracil). The different dynamics for C5 and C6 methylation suggest that IC from ¹ππ* to S₀ is facilitated by out-of-plane (OOP) motion of the C5 substituent. The slow IC for C5-substituted molecules in an aqueous environment is ascribed to the solvent reorganization that is required for this OOP motion to occur. The slow rate for 5FUrd may arise in part from an increased barrier height due to C5 fluorination.