Electron induced single strand break and cyclization: a DFT study on the radiosensitization mechanism of the nucleotide of 8-bromoguanine

Dissociative electron attachment to halogenated nucleotides: a quest for better radiosensitizers

Tumor hypoxia hampers radiotherapy efficacy, necessitating radiosensitizers. Substituted nucleobases offer advantages as radiosensitizers. They can be incorporated into DNA with minimal gene-expression alteration, selectively targeting tumor cells and having lower toxicity to normal tissues. They possess higher electron affinity than native DNA, facilitating rapid electron attachment for cancer-cell damage. Despite advancements, exploration beyond uracil nucleobases remains limited. Herein, we investigated electron attachment to potential radiosensitizers, specifically 5-halo-2'-deoxycytidine-3'-monophosphates (5X-3'-dCMPH). Our findings indicate that 5X-3'-dCMPH nucleotides possess higher electron affinity than unsubstituted 3'-dCMPH, suggesting halogenated nucleotides are better electron acceptors. Moreover, the high vertical detachment energy (VDE) implies minimal auto-detachment, and the dissociative electron attachment (DEA) pathways suggest that dehalogenation is the favored process for halogenated systems, supported by low dissociation barriers. Notably, 5Br-3'-dCMPH and 5I-3'-dCMPH exhibit nearly barrier-free dissociation after electron attachment, and thus, they may preferentially act as superior radiosensitizers.

Newly Designed Quasi-intrinsic Photosensitizers for Fluorescence Image-Guided Two-Photon Photodynamic Therapy with Type I/II Photoreactions

In this work, a set of quasi-intrinsic photosensitizers are theoretically proposed based on the 2-amino-8-(1'-β-d-2'-deoxyribofuranosyl)-imidazo[1,2-α]-1,3,5-triazin-4(8H)-one (P), which could pair with the 6-amino-5-nitro-3-(1'-β-d-2'-deoxyribofuranosyl)-2(1H)-pyridone (Z) and keep the essential structural characters of nucleic acid. It is revealed that the ring expansion and electron-donating/electron-withdrawing substitution bring enhanced two-photon absorption and bright photoluminescence of these monomers, thereby facilitating the selective excitation and tumor localization through fluorescence imaging. However, instead of undergoing radiative transition (S1 → S0), the base pairing induced fluorescence quenching and rapid intersystem crossing (S1 → Tn) are observed and characterized by the reduced singlet-triplet energy gaps and large spin-orbit coupling values. To ensure the phototherapeutic properties of the considered base pairs in long-lived T1 state, we examined the vertical electron affinity as well as vertical ionization potential for production of superoxide anions via Type I photoreaction, and their required T1 energy (0.98 eV) to generate singlet oxygen 1O2 via Type II mechanism.

Nitro rotation tuned dissociative electron attachment upon targeted radiosensitizer 4-substituted Z bases

In this work, a set of new potential radiation sensitizers (4-substituted Z-bases: 4XZ, X = F, Cl, Br, and I) are designed based on the artificial 6-amino-5-nitro-3-(1'-β-D-2'-deoxyribofuranosyl)-2(1H)-pyridone (Z), which can selectively bind to breast cancer cells. The calculated electron affinities in water solution show that the halogenated Z-bases are efficient electron acceptors which possess significant electron-withdrawing characters following the order of 4XZ > Z ≫ U. To ensure the effective electron attachment induced dissociation, we constructed the energy profiles related to the X-C bond cleavage of neutral and anionic bases. The results show that the X-C bond becomes relatively weak after the electron attachment. In particular, the electron induced dehalogenations of (4BrZ)^- and (4IZ)^- are low-barrier and exothermic, which support a high radiosensitivity. Furthermore, we characterized the vibrational excitation effect on the dissociative electron attachment, which demonstrates that the charge distribution can be regulated by the rotation-induced structural distortion accompanied by the electron localization on the nitro group. Also examined is the influence of base pairing on the dehalogenation, which is not only conducive to the electron-driven dissociation but is also beneficial to the stabilization of related products. The current study suggests 4BrZ and 4IZ can be regarded as potential targeted radiosensitizers with possible applications in reducing the side effects in radiotherapy.

Singlet O2 Reactions with Radical Cations of 8-Bromoguanine and 8-Bromoguanosine: Guided-Ion Beam Mass Spectrometric Measurements and Theoretical Treatments

8-Bromoguanosine is generated in vivo as a biomarker for early inflammation. Its formation and secondary reactions lead to a variety of biological sequelae at inflammation sites, most of which are mutagenic and linked to cancer. Herein, we report the formation of radical cations of 8-bromoguanine (8BrG^•+) and 8-bromoguanosine (8BrGuo^•+) and their reactions toward the lowest excited singlet molecular oxygen (¹O₂)─a common reactive oxygen species generated in biological systems. This work aims to investigate synergistic, oxidatively generated damage of 8-brominated guanine and guanosine that may occur upon ionizing radiation, one-electron oxidation, and ¹O₂ oxidation. Capitalizing on measurements of reaction product ions and cross sections of 8BrG^•+ and 8BrGuo^•+ with ¹O₂ using guided-ion beam tandem mass spectrometry and augmented by computational modeling of the prototype reaction system, 8BrG^•+ + ¹O₂, using the approximately spin-projected ωB97XD/6-31+G(d,p) density functional theory, the coupled cluster DLPNO-CCSD(T)/aug-cc-pVTZ and the multireference CASPT2(21,15)/6-31G**, probable reaction products, and potential energy surfaces (PESs) were mapped out. 8BrG^•+ and 8BrGuo^•+ present similar exothermic oxidation products, and their reaction efficiencies with ¹O₂ increase with decreasing collision energy. Both single- and multireference theories predicted that the two most energetically favorable reaction pathways correspond to ¹O₂-addition to the C8 and C5-positions of 8BrG^•+, respectively. The CASPT2-calculated PES represents the best quantitative agreement with the experimental benchmark, in that the oxidation exothermicity is close to the water hydration energy of product ions and, thus, is able to eliminate a water ligand in the product ions.

Theoretical studies on the purine radical induced purine-purine type intrastrand cross-links

At the density functional theory (DFT) level, addition reactions between the guanine-8-yl radical and its 3'/5' neighboring purine deoxynucleosides forming the purine-purine type intrastrand cross-links were studied. It is found that addition of the guanine-8-yl radical to the C8 site of its 5' neighboring deoxyguanosine or deoxyadenosine is a two-step reaction consisting of a structurally relatively unfavourable conformational transformation step, while the corresponding 3' C8 addition is straightforward and kinetically more efficient. The 3' C8 preference of the guanine-8-yl radical additions indicates the existence of an obvious sequence effect, which is completely opposite to that observed in the formation of pyrimidine radicals induced DNA intrastrand cross-links. The detrimental effects from steric hindrance and stabilizing weak interactions make these addition reactions markedly suppressed in double stranded DNA. This work broadens our knowledge about the possible types of DNA intrastrand cross-links.

DNA intrastrand cross-links induced by the purine-type deoxyguanosine-8-yl radical: a DFT study

Currently, all known DNA intrastrand cross-links are found to be induced by pyrimidine-type radicals; however, whether or not purine-type radicals are able to cause DNA intrastrand cross-links remains unclear. In the present study, probable additions of the highly reactive deoxyguanosine-8-yl radical to its 3'/5' neighboring pyrimidine nucleotides in four model compounds, 5'-G˙T-3', 5'-TG˙-3', 5'-G˙C-3', and 5'-CG˙-3', were studied using density functional theory (DFT) methods. In single-stranded DNA, the deoxyguanosine-8-yl radical is preferred to efficiently attack the C5 site of its 3' neighboring deoxythymidine or deoxycytidine, forming the G[8-5]T or G[8-5]C intrastrand cross-link rather than the C6 site forming the G[8-6]T or G[8-6]C intrastrand cross-link. The four corresponding sequence isomers, namely T[5-8]G, T[6-8]G, C[5-8]G, and C[6-8]G, formed by additions of deoxyguanosine-8-yl radical to its 5' neighboring pyrimidine nucleotides are predicted to be formed inefficiently. In double-stranded DNA, considering the detrimental effects of stabilizing weak interactions on related structural adjustments required in each addition reaction path, relatively lower reaction yields are suggested for the G[8-5]T and G[8-5]C intrastrand cross-links, while the formation of the other six intrastrand cross-links becomes quite difficult. All calculations definitely demonstrate that, in addition to pyrimidine-type radicals, the purine-type deoxyguanosine-8-yl radical is able to attack its 3'/5' neighboring pyrimidine nucleotides forming several DNA intrastrand cross-links.

SSRP1 Cooperates with PARP and XRCC1 to Facilitate Single-Strand DNA Break Repair by Chromatin Priming

DNA single-strand breaks (SSB) are the most common form of DNA damage, requiring repair processes that to initiate must overcome chromatin barriers. The FACT complex comprised of the SSRP1 and SPT16 proteins is important for maintaining chromatin integrity, with SSRP1 acting as an histone H2A/H2B chaperone in chromatin disassembly during DNA transcription, replication, and repair. In this study, we show that SSRP1, but not SPT16, is critical for cell survival after ionizing radiation or methyl methanesulfonate-induced single-strand DNA damage. SSRP1 is recruited to SSB in a PARP-dependent manner and retained at DNA damage sites by N-terminal interactions with the DNA repair protein XRCC1. Mutational analyses showed how SSRP1 function is essential for chromatin decondensation and histone H2B exchange at sites of DNA strand breaks, which are both critical to prime chromatin for efficient SSB repair and cell survival. By establishing how SSRP1 facilitates SSB repair, our findings provide a mechanistic rationale to target SSRP1 as a general approach to selectively attack cancer cells. Cancer Res; 77(10); 2674-85. ©2017 AACR.

Mechanisms Responsible for High Energy Radiation Induced Damage to Single-Stranded DNA Modified by Radiosensitizing 5-Halogenated Deoxyuridines

Experimental studies showed that high energy radiation induced base release and DNA backbone breaks mainly occur at the neighboring 5' nucleotide when a single-stranded DNA is modified by radiosensitizing 5-halogenated deoxyuridines. However, no mechanism can be used to interpret these experimental observations. To better understand the radiosensitivity of 5-halogenated deoxyuridines, mechanisms involving hydrogen abstraction by the uracil-5-yl radical from the C2' and C3' positions of an adjacent nucleotide separately followed by the C3'-O3' or N-glycosidic bond rupture and the P-O3' bond breakage are investigated in the DNA sequence 5'-TU(•)-3' employing density functional theory calculations in the present study. It is found that hydrogen abstractions from both positions are comparable with the one from the C2' site slightly more favorable. The N-glycosidic bond cleavage in the neighboring 5' nucleotide following the internucleotide C2'-Ha abstraction is estimated to have the lowest activation free energies, indicating that the adjacent 5' base release dominates electron induced damage to single-stranded DNA incorporated by 5-halogenated deoxyuridines. Relative to the P-O3' bond breakage after the internucleotide C3'-H abstraction, the C3'-O3' bond rupture in the neighboring 5' nucleotide following the internucleotide C2'-Ha abstraction is predicted to have a lower activation free energy, implying that single-stranded DNA backbone breaks are prone to occur at the C3'-O3' bond site. The 5'-TU(•)-3' species has substantial electron affinity and can even capture a hydrated electron, forming the 5'-TU(-)-3' anion. However, the electron induced C3'-O3' bond rupture in 5'-TU(-)-3' anion via a pathway of internucleotide proton abstraction is only minor in both the gas phase and aqueous solution. The present theoretical predictions can interpret rationally experimental observations, thereby demonstrating that the mechanisms proposed here are responsible for high energy radiation induced damage to single-stranded DNA incorporated by radiosensitizing 5-halogenated deoxyuridines. By comparing with previous results, our work proves that the radiosensitizing action of 5-bromo-2-deoxyuridine is not weaker but stronger than its isomer 6-bromo-2-deoxyuridine on the basis of the available data.

Two-photon-absorption DNA sensitization via solvated electron production: unraveling photochemical pathways by molecular modeling and simulation

Infrared optical properties and photochemistry of a potential therapeutic dye interacting with DNA: a multiscale computational approach.

Mechanisms of Damage to DNA Labeled with Electrophilic Nucleobases Induced by Ionizing or UV Radiation

Hypoxia--a hallmark of solid tumors--makes hypoxic cells radioresistant. On the other hand, DNA, the main target of anticancer therapy, is not sensitive to the near UV photons and hydrated electrons, one of the major products of water radiolysis under hypoxic conditions. A possible way to overcome these obstacles to the efficient radio- and photodynamic therapy of cancer is to sensitize the cellular DNA to electrons and/or ultraviolet radiation. While incorporated into genomic DNA, modified nucleosides, 5-bromo-2'-deoxyuridine in particular, sensitize cells to both near-ultraviolet photons and γ rays. It is believed that, in both sensitization modes, the reactive nucleobase radical is formed as a primary product which swiftly stabilizes, leading to serious DNA damage, like strand breaks or cross-links. However, despite the apparent similarity, such radio- and photosensitization of DNA seems to be ruled by fundamentally different mechanisms. In this review, we demonstrate that the most important factors deciding on radiodamage to the labeled DNA are (i) the electron affinity (EA) of modified nucleoside (mNZ), (ii) the local surroundings of the label that significantly influences the EA of mNZ, and (iii) the strength of the chemical bond holding together the substituent and a nucleobase. On the other hand, we show that the UV damage to sensitized DNA is governed by long-range photoinduced electron transfer, the efficiency of which is controlled by local DNA sequences. A critical review of the literature mechanisms concerning both types of damage to the labeled biopolymer is presented. Ultimately, the perspectives of studies on DNA sensitization in the context of cancer therapy are discussed.

The radiosensitivity of 5- and 6-bromocytidine derivatives--electron induced DNA degradation

Halogenated nucleotides belong to the group of radiosensitizers that sensitize solid tumors when incorporated into genomic DNA. Here, we consider the propensity of two isomeric bromocytidine derivatives, 3',5'-diphosphates of 5-bromo-2'-deoxycytidine (5BrdCDP) and 6-bromo-2'-deoxycytidine (6BrdCDP), to be damaged by electrons - one of the most abundant products formed during radiotherapy. An intranucleotide degradation mechanism leading to phosphodiester bond breakage (a model of single strand breakage in labeled DNA) and a ketone derivative formation was found for 6BrdCDP, while for 5BrdCDP a similar mechanism is sterically hindered. 5BrdCDP is, therefore, suggested to undergo electron induced degradation involving hydrogen transfer from a neighboring nucleotide or environment.

Anion states and fragmentation of 2-chloroadenine upon low-energy electron collisions

We report on a joint theoretical and experimental investigation into the electron-induced fragmentation of 2-chloroadenine, for electrons up to 12 eV. Our results suggest that 2-chloroadenine can be considered as potential radiosensitiser.

Sequence dependence of electron-induced DNA strand breakage revealed by DNA nanoarrays

The electronic structure of DNA is determined by its nucleotide sequence, which is for instance exploited in molecular electronics. Here we demonstrate that also the DNA strand breakage induced by low-energy electrons (18 eV) depends on the nucleotide sequence. To determine the absolute cross sections for electron induced single strand breaks in specific 13 mer oligonucleotides we used atomic force microscopy analysis of DNA origami based DNA nanoarrays. We investigated the DNA sequences 5′-TT(XYX)₃TT with X = A, G, C and Y = T, BrU 5-bromouracil and found absolute strand break cross sections between 2.66 · 10⁻¹⁴ cm² and 7.06 · 10⁻¹⁴ cm². The highest cross section was found for 5′-TT(ATA)₃TT and 5′-TT(ABrUA)₃TT, respectively. BrU is a radiosensitizer, which was discussed to be used in cancer radiation therapy. The replacement of T by BrU into the investigated DNA sequences leads to a slight increase of the absolute strand break cross sections resulting in sequence-dependent enhancement factors between 1.14 and 1.66. Nevertheless, the variation of strand break cross sections due to the specific nucleotide sequence is considerably higher. Thus, the present results suggest the development of targeted radiosensitizers for cancer radiation therapy.