Local Excitation of the 5-Bromouracil Chromophore in DNA. Computational and UV Spectroscopic Studies

Dual Intrareticular Oxidation of Mixed-Ligand Metal-Organic Frameworks for Stepwise Electrochemiluminescence

This work presents a mixed-ligand metal-organic framework (m-MOF) integrated with two ligands, one as a luminophore and the other as a coreactant, on one metal node for self-enhanced electrochemiluminescence (ECL). Both 9,10-di(p-carboxyphenyl)anthracene (DPA) and 1,4-diazabicyclo[2.2.2]octane (D-H₂) ligands can be oxidized, generating the cation radicals DPA^+• and D-H₂^+•, respectively. The latter can be deprotonated to form the neutral radical (D-H^•) and then react with DPA^+• to produce excited DPA* for ECL emission without exogenous coreactants. As a result of the incorporation into the MOF framework and the intrareticular charge transfer between the two ligands, the ECL intensity of the m-MOF was increased 26.5-fold compared with that of the mixture of DPA and D-H₂ in aqueous solution. Moreover, with the process of second oxidation of D-H₂, stepwise ECL emission was observed as a result of local excitation in the DPA unit, which was identified through density functional theory calculations. Overall, the implementation of the mixed-ligand approach, which combines the luminophore and coreactant as linkers in reticular materials, enriches the fundamentals and applications of ECL systems.

Photoinduced electron transfer in 5-bromouracil labeled DNA. A contrathermodynamic mechanism revisited by electron transfer theories

The understanding of the 5-bromouracil (BrU) based photosensitization mechanism of DNA damage is of large interest due to the potential applications in photodynamic therapy. Photoinduced electron transfer (ET) in BrU labeled duplexes comprising the 5'-GBrU or 5'-ABrU sequence showed that a much lower reactivity was found for the 5'-GBrU pattern. Since the ionization potential of G is lower than that of A, this sequence selectivity has been dubbed a contrathermodynamic one. In the current work, we employ the Marcus and Marcus-Levich-Jortner theory of ET in order to shed light on the observed effect. By using a combination of Density Functional Theory (DFT) and solvation continuum models, we calculated the electronic couplings, reorganization energies, and thermodynamic stimuli for electron transfer which enabled the rates of forward and back ET to be estimated for the two considered sequences. The calculated rates show that the photoreaction could not be efficient if the ET process proceeded within the considered dimers. Only after introducing additional adenines between G and BrU, which accelerates the forward and slows down the back ET, is a significant amount of photodamage expected.

UV-induced electron transfer between triethylamine and 5-bromo-2'-deoxyuridine. A puzzle concerning the photochemical debromination of labeled DNA

5-Bromo-2'-deoxyuridine (BrdU) photosensitizes DNA to strand break formation. However, this type of photodamage is completely quenched by the presence of triethylamine (TEA) which originates from RP-HPLC purification commonly employed by oligonucleotide providers. While the presence of TEA in oligonucleotide samples does not interfere with PCR or other molecular biology applications, the mechanism of photochemical reaction proceeding in the labeled DNA is dramatically changed due to the photoinduced electron transfer (PET) between the photoexcited BrdU and the ground state TEA. For the first time, we demonstrated that the latter process produces 2'-deoxyuridne2'-deoxyuridine (debromination) in the labeled DNA instead of the expected strand break. PET between TEA and BrdU was additionally confirmed by the UV irradiations of aqueous solutions containing both species. Indeed, the efficient formation of 2'-deoxyuridine was observed in the studied photolytes. Moreover, we showed the formation of an additional product in these binary mixtures, i.e. imidazole derivative, that is not formed in DNA and was reported in the literature in the context of dark rather than photochemical processes. Using mass spectrometry we demonstrated that the amount of TEA impurity in the commercial samples of oligos exceeds up to 3 orders of magnitude that of the purchased DNA.

Insights into the deactivation of 5-bromouracil after ultraviolet excitation

5-Bromouracil is a nucleobase analogue that can replace thymine in DNA strands and acts as a strong radiosensitizer, with potential applications in molecular biology and cancer therapy. Here, the deactivation of 5-bromouracil after ultraviolet irradiation is investigated in the singlet and triplet manifold by accurate quantum chemistry calculations and non-adiabatic dynamics simulations. It is found that, after irradiation to the bright ππ* state, three main relaxation pathways are, in principle, possible: relaxation back to the ground state, intersystem crossing (ISC) and C-Br photodissociation. Based on accurate MS-CASPT2 optimizations, we propose that ground-state relaxation should be the predominant deactivation pathway in the gas phase. We then employ different electronic structure methods to assess their suitability to carry out excited-state dynamics simulations. MRCIS (multi-reference configuration interaction including single excitations) was used in surface hopping simulations to compute the ultrafast ISC dynamics, which mostly involves the 1nOπ* and 3ππ* states.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

DNA Distortion Caused by Uracil-Containing Intrastrand Cross-Links

Four uracil-containing intrastrand cross-links have been detected in human cells upon UV irradiation of 5-bromouracil-containing DNA, namely 5'-G[8-5]U-3', 5'-U[5-8]G-3', 5'-A[8-5]U-3', and 5'-A[2-5]U-3'. These lesions feature unique composition and connectivity compared with other intrastrand cross-links reported in the literature. For the first time, structural information obtained using molecular dynamics (MD) simulations reveal that all four lesions distort the DNA helix, which can involve an extrahelical location of the cross-link, changes in the helical interactions of the complementary nucleotides, or disruption of hydrogen bonding in the flanking base pairs up to two positions from the cross-linked site; however, the degree of distortion varies between the cross-links, being affected by the sequence, nucleobase-nucleobase connectivity, and the purine involved. Most importantly, the relative distortion of the damaged DNA provides the first structural explanation for the observed abundances of the four uracil-containing cross-links. Furthermore, the highly distorted conformations suggest that these lesions will likely have severe implications for DNA replication and repair processes in cells.

Photoinduced single strand breaks and intrastrand cross-links in an oligonucleotide labeled with 5-bromouracil

5-Bromouracil (BrU) is photoreactive toward near UVB photons and can be introduced into genomic DNA during its biosynthesis in cells. However, PCR seems to be a simpler approach, which can be used to obtain labeled DNA similar to that synthesized within the cell. In the current work, PCR has been employed and optimized in order to substitute all thymines (besides those present in starters) with BrU in the dsDNA fragment of 80 base pairs (bp) in length. The modified oligonucleotide was irradiated with 300 nm photons in a buffered aqueous solution (pH = 7) and digested with a cocktail of enzymes specific to the phosphodiester bond cleavage. Initially, the extent of damage in the intact photolyte was measured with DHPLC. Then, the digested reaction mixture was subjected to HPLC and MS analyses and, in addition to the formation of 5-bromo-2'-deoxuyridine, which proves the occurrence of single strand breaks (SSBs) due to irradiation, U∧U and U∧C dimers were found, whose molecular structure was confirmed by MS/MS analysis. Although the abundance of such tandem lesions is lower than that of the SSB type, they pose a potent threat to genome integrity. Thus, our findings shed new light on the photosensitizing properties of BrU toward DNA.

Formation mechanism and structure of a guanine-uracil DNA intrastrand cross-link

The formation and structure of the 5'-G[8-5]U-3' intrastrand cross-link are studied using density functional theory and molecular dynamics simulations due to the potential role of this lesion in the activity of 5-halouracils in antitumor therapies. Upon UV irradiation of 5-halouracil-containing DNA, a guanine radical cation reacts with the uracil radical to form the cross-link, which involves phosphorescence or an intersystem crossing and a rate-determining step of bond formation. Following ionizing radiation, guanine and the uracil radical react, with a rate-limiting step involving hydrogen atom removal. Although cross-link formation from UV radiation is favored, comparison of calculated reaction thermokinetics with that for related experimentally observed purine-pyrimidine cross-links suggests this lesion is also likely to form from ionizing radiation. For the first time, the structure of 5'-G[8-5]U-3' within DNA is identified by molecular dynamics simulations. Furthermore, three conformations of cross-linked DNA are revealed, which differ in the configuration of the complementary bases. Distortions, such as unwinding, are localized to the cross-linked dinucleotide and complementary nucleotides, with minimal changes to the flanking bases. Global changes to the helix, such as bending and groove alterations, parallel cisplatin-induced distortions, which indicate 5'-G[8-5]U-3', may contribute to the cytotoxicity of halouracils in tumor cell DNA using similar mechanisms.