Photochemical Formation of Cyclobutane Pyrimidine Dimers in DNA through Electron Transfer from a Flanking Base

High-Throughput Screening for Ultrafast Photochemical Reaction Discovery

High-repetition-rate lasers present an opportunity to extend ultrafast spectroscopy from a detailed probe of singular model photochemical systems to a routine analysis technique in training machine learning models to aid the design cycle of photochemical syntheses. We bring together innovations in line scan cameras and micro-electro-mechanical grating modulators with sample delivery via high-pressure liquid chromatography pumps to demonstrate a transient absorption spectrometer that can characterize photoreactions initiated with ultrashort ultraviolet pulses in a time scale of minutes. Furthermore, we demonstrate that the ability to rapidly screen an important class of photochemical system, pyrimidine nucleosides, can be used to explore the effect of conformational modification on the evolution of excited-state processes.

Tracking the Early Stage of Triplet-Induced Photodamage in a DNA Dimer and Oligomer Containing 5-Methylcytosine

Methylation at the C5 position of cytosine, a naturally occurring epigenetic modification on DNA, shows a high correlation with mutational hotspots in disease such as skin cancer. Due to its essential biological relevance, numerous studies were devoted to confirming that the methylated sites favor the formation of the cyclobutane pyrimidine dimer (CPD), a well-known UV-induced lesion. However, photophysical and photochemical properties of dinucleotides and polynucleotides containing 5-methylcytosine (5mC) remain elusive. Herein, a charge transfer (CT) triplet state, generated via intersystem crossing (ISC) from a CT singlet state that enhanced after methylation on cytosine, is directly observed by using femtosecond transient absorption (TA) and time-resolved mid-infrared (TRIR) spectroscopy together with quantum chemical calculations for the first time in the T5mC dimer. Such an ISC process is quenched due to limitations of the ground-state geometries in 5mC-containing single-strand oligomer d(T5mC)9. This mechanistic information is important for understanding the early stage of triplet state-induced CPD formation in 5mC containing DNA.

Remote Photodamaging of DNA by Photoinduced Energy Transport

Local DNA photodamaging by light is well-studied and leads to a number of structurally identified direct damage, in particular cyclobutane pyrimidine dimers, and indirect oxidatively generated damage, such as 8-oxo-7,8-hydroxyguanine. Similar damages have now been found at remote sites, at least more than 105 Å (30 base pairs) away from the site of photoexcitation. In contrast to the established mechanisms of local DNA photodamaging, the processes of remote photodamage are only partially understood. Known pathways include those to remote oxidatively generated DNA photodamages, which were elucidated by studying electron hole transport through the DNA about 20 years ago. Recent studies with DNA photosensitizers and mechanistic proposals on photoinduced DNA-mediated energy transport are summarized in this minireview. These new mechanisms to a new type of remote DNA photodamaging provide an important extension to our general understanding to light-induced DNA damage and their mutations.

Stabilization of the Triplet Biradical Intermediate of 5-Methylcytosine Enhances Cyclobutane Pyrimidine Dimer (CPD) Formation in DNA

Cyclobutane pyrimidine dimer (CPD) is a photoproduct formed by two stacked pyrimidine bases through a cycloaddition reaction upon irradiation. Owing to its close association with skin cancer, the mechanism of CPD formation has been studied thoroughly. Among many aspects of CPD, its formation involving 5-methylcytosine (5mC) has been of special interest because the CPD yield is known to increase with C5-methylation of cytosine. In this work, high-level quantum mechanics/molecular mechanics (QM/MM) calculations are used to examine a previously experimentally detected pathway for CPD formation in hetero (thymine-cytosine and thymine-5mC) dipyrimidines, which is facilitated through intersystem crossing in thymine and formation of a triplet biradical intermediate. A DNA duplex model system containing a core sequence TmCG or TCG is used. The stabilization of a radical center in the biradical intermediate by the methyl group of 5mC can lead to increased CPD yield in TmCG compared with its non-methylated counterpart, TCG, thereby suggesting the existence of a new pathway of CPD formation enhanced by 5mC.

Photoinduced DNA Lesions in Dormant Bacteria: The Peculiar Route Leading to Spore Photoproducts Characterized by Multiscale Molecular Dynamics*

Some bacterial species enter a dormant state in the form of spores to resist to unfavorable external conditions. Spores are resistant to a wide series of stress agents, including UV radiation, and can last for tens to hundreds of years. Due to the suspension of biological functions, such as DNA repair, they accumulate DNA damage upon exposure to UV radiation. Differently from active organisms, the most common DNA photoproducts in spores are not cyclobutane pyrimidine dimers, but rather the so-called spore photoproducts. This noncanonical photochemistry results from the dry state of DNA and its binding to small, acid-soluble proteins that drastically modify the structure and photoreactivity of the nucleic acid. Herein, multiscale molecular dynamics simulations, including extended classical molecular dynamics and quantum mechanics/molecular mechanics based dynamics, are used to elucidate the coupling of electronic and structural factors that lead to this photochemical outcome. In particular, the well-described impact of the peculiar DNA environment found in spores on the favored formation of the spore photoproduct, given the small free energy barrier found for this path, is rationalized. Meanwhile, the specific organization of spore DNA precludes the photochemical path that leads to cyclobutane pyrimidine dimer formation.

How Far Does Energy Migrate in DNA and Cause Damage? Evidence for Long-Range Photodamage to DNA

A new DNA architecture addresses the question, how far energy migrates in DNA and forms cyclobutane pyrimidine dimers (CPDs) as photodamages causing skin cancer. The 3-methoxyxanthone nucleoside allows site-selective photoenergy injection into DNA. The designated CPD site lacks the phosphodiester bond and can be placed in defined distances. The CPD formation links two oligonucleotides together and allows probing by gel electrophoresis. We obtained a sigmoidal distance dependence with R0 of 25±3 Å. Below R0 , short-range energy migration occurs with high CPD yields and shallow distance dependence, characteristic for a coherent process. 5-methyl-C as epigenetic modification on the 3'-side facilitates CPD formation. Above R0 , long-range incoherent energy migration occurs over 30 A-T pairs (105.4 Å). The evidence of long-range CPD formation is fundamental for our understanding of DNA photodamaging. Open access funding enabled and organized by Projekt DEAL.

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.

Role of charge transfer states into the formation of cyclobutane pyrimidine dimers in DNA

Photoinduced charge transfer between neighboring bases plays an important role in DNA. One of its important effects is shown in its ability to affect the photochemical yields of the formation of cyclobutane pyrimidine dimer (CPD) products between adjacent pyrimidine bases. In this work we examine how the energies of charge transfer states depend on the sequences of oligonucleotides using a hybrid quantum and molecular mechanics (QM/MM) methodology combined with the algebraic diagrammatic construction through a second order electronic structure method for excited states. Specifically, we examine 10 sequences with guanine being on the 5' or 3' position of two pyrimidine bases. The results show that the energies of charge transfer states are affected by the nature of the donor acceptor pair, by the distance between them, and by other electrostatic effects created by the surrounding environment.

Folding of cytosine-based nucleolipid monolayer by guanine recognition at the air-water interface

Monolayers of a cytosine-based nucleolipid (1,2-dipalmitoyl-sn-glycero-3-(cytidine diphosphate) (ammonium salt), CDP-DG) at basic subphase have been prepared at the air-water interface both in absence and presence of guanine. The formation of the complementary base pairing is demonstrated by combining surface experimental techniques, i.e., surface pressure (π)-area (A), Brewster angle microscopy (BAM), infrared spectroscopy (PM-IRRAS) and computer simulations. A folding of the cytosine-based nucleolipid molecules forming monolayer at the air-water interface occurs during the guanine recognition as absorbate host and is kept during several compression-expansion processes under set experimental conditions. The specificity between nitrogenous bases has been also registered. Finally, mixed monolayers of CDP-DG and a phospholipid (1,2-dimyristoyl-sn-glycero-3-phosphate (sodium salt), DMPA) has been studied and a molecular segregation of the DMPA molecules has been inferred by the additivity rule.