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.

Probing of DNA Photochemistry with C-Nucleosides of Xanthones and Triphenylene as Photosensitizers To Study the Formation of Cyclobutane Pyrimidine Dimers

The direct and sequence-dependent investigation of photochemical processes in DNA on the way to cyclobutane pyrimidine dimers (CPDs) as DNA damage requires the probing by photochemically different photosensitizers. The C-nucleosides of xanthone, thioxanthone, 3-methoxyxanthone, and triphenylene as photosensitizers were synthesized by Heck couplings and incorporated into ternary photoactive DNA architectures. This structural approach allows the site-selective excitation of the DNA by UV light. Together with a single defined site for T-T dimerization, not only the direct CPD formation but also the distance-dependent CPD formation in DNA as well as the possibility for energy transport processes could be investigated. Direct CPD formation was observed with xanthone, 3-methoxyxanthone, and triphenylene as sensitizers but not with thioxanthone. Only xanthone was able to induce CPDs remotely by a triplet energy transfer over up to six intervening A-T base pairs. Taken together, more precise information on the sequence dependence of the DNA triplet photochemistry was obtained.

Molecular Wires for Efficient Long-Distance Triplet Energy Transfer

We propose design rules for building organic molecular bridges that enable coherent long-distance triplet-exciton transfer. Using these rules, we describe example polychromophoric structures with low inner-sphere exciton reorganization energies, low static and dynamic disorder, and enhanced π-stacking interactions between nearest-neighbor chromophores. These features lead to triplet-exciton eigenstates that are delocalized over several units at room temperature. The use of such bridges in donor-bridge-acceptor assemblies enables fast triplet-exciton transport over very long distances that is rate-limited by the donor-bridge injection and bridge-acceptor trapping rates.

Topology and Excited State Multiplicity as Controlling Factors in the Carbazole-Photosensitized CPD Formation and Repair

Photosensitized thymine<>thymine (Thy<>Thy) formation and repair can be mediated by carbazole (Cbz). The former occurs from the Cbz triplet excited state via energy transfer, while the latter takes place from the singlet excited state via electron transfer. Here, fundamental insight is provided into the role of the topology and excited state multiplicity, as factors governing the balance between both processes. This has been achieved upon designing and synthesizing different isomers of trifunctional systems containing one Cbz and two Thy units covalently linked to the rigid skeleton of the natural deoxycholic acid. The results shown here prove that the Cbz photosensitized dimerization is not counterbalanced by repair when the latter, instead of operating through-space, has to proceed through-bond.

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.

The Behavior of Triplet Thymine in a Model B-DNA Strand. Energetics and Spin Density Localization Revealed by ab initio Molecular Dynamics Simulations†

Among the naturally occurring nucleobases, thymine presents the lowest triplet state, hence it represents a hotspot for energy transfer and photosensitization. In turn, the population of the triplet state may lead to thymine dimerization and hence to the production of toxic DNA lesions and has been the subject of intensive theoretical and experimental investigations. Relying on QM/MM molecular dynamics simulations, we have sought to situate the energy of the lowest triplet state of thymine embedded in a B-DNA environment. The energy gap varies between 305 and 329 kJ mol^-1 when a single thymine is treated at the quantum chemistry level, depending on its position in the model double-stranded 16-bp oligonucleotide. The energy of triplet state decreases up to 300 kJ mol^-1 , due to polarization effects, when we consider coupled stacked nucleobases up to the inclusion of four nucleobases. Our value lies in good agreement with the energy inferred experimentally by Miranda and coworkers (270 kJ mol^-1 ), and our theoretical exploration opens the door to investigations toward other more complex and biologically relevant environments, such as thymines embedded in nucleosome core particles. Our investigations also provide a reference for further studies using semi-empirical approaches such as density functional-based tight-binding, allowing to further rationalize sequence effects.

Clustered DNA Damage: Electronic Properties and Their Influence on Charge Transfer. 7,8-Dihydro-8-Oxo-2'-Deoxyguaosine Versus 5',8-Cyclo-2'-Deoxyadenosines: A Theoretical Approach

Approximately 3 × 10¹⁷ DNA damage events take place per hour in the human body. Within clustered DNA lesions, they pose a serious problem for repair proteins, especially for iron–sulfur glycosylases (MutyH), which can recognize them by the electron-transfer process. It has been found that the presence of both 5′,8-cyclo-2′-deoxyadenosine (cdA) diastereomers in the ds-DNA structure, as part of a clustered lesion, can influence vertical radical cation distribution within the proximal part of the double helix, i.e., d[~oxoGcAoxoG~] (7,8-dihydro-8-oxo-2′-deoxyguaosine - ^oxodG). Here, the influence of cdA, “the simplest tandem lesion”, on the charge transfer through ds-DNA was taken into theoretical consideration at the M062x/6-31+G** level of theory in the aqueous phase. It was shown that the presence of (5′S)- or (5′R)-cdA leads to a slowdown in the hole transfer by one order of magnitude between the neighboring dG→^oxodG in comparison to “native” ds-DNA. Therefore, it can be concluded that such clustered lesions can lead to defective damage recognition with a subsequent slowing down of the DNA repair process, giving rise to an increase in mutations. As a result, the unrepaired, ^oxodG: dA base pair prior to genetic information replication can finally result in GC → TA or AT→CG transversion. This type of mutation is commonly observed in human cancer cells. Moreover, because local multiple damage sites (LMSD) are effectively produced as a result of ionization factors, the presented data in this article might be useful in developing a new scheme of radiotherapy treatment against the background of DNA repair efficiency.

Generation of the Thymine Triplet State by Through-Bond Energy Transfer

Benzophenone (BP) and drugs containing the BP chromophore, such as the non-steroidal anti-inflammatory drug ketoprofen, have been widely reported as DNA photosensitizers through triplet-triplet energy transfer (TTET). In the present work, a direct spectroscopic fingerprint for the formation of the thymine triplet (³ Thy*) by through-bond (TB) TTET from ³ BP* has been uncovered. This has been achieved in two new systems that have been designed and synthesized with one BP and one thymine (Thy) covalently linked to the two ends of the rigid skeleton of the natural bile acids cholic and lithocholic acid. The results shown here prove that it is possible to achieve triplet energy transfer to a Thy unit even when the photosensitizer is at a long (nonbonding) distance.

Machine Learning Prediction of DNA Charge Transport

First-principles calculations of charge transfer in DNA molecules are computationally expensive given that conducting charge carriers interact with intra- and intermolecular atomic motion. Screening sequences, for example, to identify excellent electrical conductors, is challenging even when adopting coarse-grained models and effective computational schemes that do not explicitly describe atomic dynamics. We present a machine learning (ML) model that allows the inexpensive prediction of the electrical conductance of millions of long double-stranded DNA (dsDNA) sequences, reducing computational costs by orders of magnitude. The algorithm is trained on short DNA nanojunctions with n = 3-7 base pairs. The electrical conductance of the training set is computed with a quantum scattering method, which captures charge-nuclei scattering processes. We demonstrate that the ML method accurately predicts the electrical conductance of varied dsDNA junctions tracing different transport mechanisms: coherent (short-range) quantum tunneling, on-resonance (ballistic) transport, and incoherent site-to-site hopping. Furthermore, the ML approach supports physical observations that clusters of nucleotides regulate DNA transport behavior. The input features tested in this work could be used in other ML studies of charge transport in complex polymers in the search for promising electronic and thermoelectric materials.