Oxidation of DNA: damage to nucleobases

The Influence of Oxidized Imino-Allantoin in the Presence of OXOG on Double Helix Charge Transfer: A Theoretical Approach

The genome is continuously exposed to a variety of harmful factors that result in a significant amount of DNA damage. This article examines the influence of a multi-damage site containing oxidized imino-allantoin (OXIa) and 7,8-dihydro-8-oxo-2'-deoxyguanosine (OXOdG) on the spatial geometry, electronic properties, and ds-DNA charge transfer. The ground stage of a d[A1OXIa2A3OXOG4A5]*d[T5C4T3C2T1] structure was obtained at the M06-2X/6-D95**//M06-2X/sto-3G level of theory in the condensed phase, with the energies obtained at the M06-2X/6-31++G** level. The non-equilibrated and equilibrated solvent-solute interactions were also considered. Theoretical studies reveal that the radical cation prefers to settle on the OXOG moiety, irrespective of the presence of OXIa in a ds-oligo. The lowest vertical and adiabatic ionization potential values were found for the OXOG:::C base pair (5.94 and 5.52 [eV], respectively). Conversely, the highest vertical and adiabatic electron affinity was assigned for OXIaC as follows: 3.15 and 3.49 [eV]. The charge transfers were analyzed according to Marcus' theory. The highest value of charge transfer rate constant for hole and excess electron migration was found for the process towards the OXOGC moiety. Surprisingly, the values obtained for the driving force and activation energy of electro-transfer towards OXIa2C4 located this process in the Marcus inverted region, which is thermodynamically unfavorable. Therefore, the presence of OXIa can slow down the recognition and removal processes of other DNA lesions. However, with regard to anticancer therapy (radio/chemo), the presence of OXIa in the structure of clustered DNA damage can result in improved cancer treatment outcomes.

Selective Tautomer Production and Cryogenic Ion Spectroscopy of Radical Cations: The Uracil and Thymine Cases

The vibrational and electronic spectroscopy of the radical cations of two nucleobases (NB) (uracil and thymine) was studied by cryogenic ion photodissociation spectroscopy. The radical cations have been generated from the photodissociation of NB-Ag+ complexes. A charge transfer process from the NB to Ag+ governs the deactivation mechanism, leading to the formation of the radical cation without further tautomerization. Single- and double-resonance spectroscopy allows for structural assignments of both the silver complexes and the radical cations by comparison with DFT-based calculations. Interestingly, a tautomer-dependent fragmentation is observed in the thymine enol form that involves the loss of NCO, a fragment which was never reported before for this NB. This selective photodissociation of silver complexes containing aromatic chromophore greatly expands the current technique to produce isomer-selected radical cations in the gas phase providing benchmark experimental data to assess calculations of open-shell species.

Effects of Hydrogen Peroxide on the Hydrogen Bonding Structure and Dynamics of Water and Its Influence on the Aqueous Solvation of the Insulin Monomer

The hydrogen bond structure and dynamics of water and hydrogen peroxide (H2O2) in their binary mixtures have been studied at 298 K by classical molecular dynamics simulations. Twelve different concentrations of aqueous-H2O2 solutions are considered for this study. We have analyzed the interactions between water and H2O2 by site-site pair correlation functions and observed that the probability of formation of OW···HP hydrogen bonds are higher compared to OP···HW. The second solvation shell of water is strongly affected by increasing H2O2 concentrations (XP > 0.50), which signifies the destruction of the tetrahedral network structure of water. The translational and rotational dynamics of water and H2O2 do not significantly change up to 25% of H2O2 in aqueous mixtures. The hydrogen bond lifetime of water-water, water-H2O2, and H2O2-H2O2 in the aqueous-H2O2 solutions shows a very minimal change with increasing H2O2 concentrations. In addition to this, we also investigated the effect of H2O2 on the insulin monomer and observed that higher concentrations of H2O2 (XP = 0.10) change the secondary structure. The influence of H2O2 is more on chain-B than that on chain-A in the insulin monomer. The H2O2 occupancy at the protein surface is higher for negatively charged (GLU) and polar (ASN and THR) amino acid residues compared with that for positively charged and neutral residues in the solutions.

DNA-Histone Cross-Link Formation via Hole Trapping in Nucleosome Core Particles

Radical cations (holes) produced in DNA by ionizing radiation and other oxidants yield DNA-protein cross-links (DPCs). Detailed studies of DPC formation in chromatin via this process are lacking. We describe here a comprehensive examination of DPC formation within nucleosome core particles (NCPs), which are the monomeric component of chromatin. DNA holes are introduced at defined sites within NCPs that are constructed from the bottom-up. DPCs form at DNA holes in yields comparable to those of alkali-labile DNA lesions that result from water trapping. DPC-forming efficiency and site preference within the NCP are dependent on translational and rotational positioning. Mass spectrometry and the use of mutant histones reveal that lysine residues in histone N-terminal tails and amino termini are responsible for the DPC formation. These studies are corroborated by computational simulation at the microsecond time scale, showing a wide range of interactions that can precede DPC formation. Three consecutive dGs, which are pervasive in the human genome, including G-quadruplex-forming sequences, are sufficient to produce DPCs that could impact gene expression.

8-oxoguanine riboswitches in bacteria detect and respond to oxidative DNA damage

Riboswitches rely on structured aptamer domains to selectively sense their target ligands and regulate gene expression. However, some riboswitch aptamers in bacteria carry mutations in their otherwise strictly conserved binding pockets that change ligand specificities. The aptamer domain of a riboswitch class originally found to selectively sense guanine forms a three-stem junction that has since been observed to exploit numerous alterations in its ligand-binding pocket. These rare variants have modified their ligand specificities to sense other purines or purine derivatives, including adenine, 2'-deoxyguanosine (three classes), and xanthine. Herein, we report the characteristics of a rare variant that is narrowly distributed in the Paenibacillaceae family of bacteria. Known representatives are always associated with genes encoding 8-oxoguanine deaminase. As predicted from this gene association, these variant riboswitches tightly bind 8-oxoguanine (8-oxoG), strongly discriminate against other purine derivatives, and function as genetic "ON" switches. Following exposure of cells to certain oxidative stresses, a representative 8-oxoG riboswitch activates gene expression, likely caused by the accumulation of 8-oxoG due to oxidative damage to G nucleobases in DNA, RNA, and the nucleotide pool. Furthermore, an engineered version of the variant aptamer was prepared that exhibits specificity for 8-oxoadenine, further demonstrating that RNA aptamers can acquire mutations that expand their ability to detect and respond to oxidative damage.

A loss-of-function mutation in human Oxidation Resistance 1 disrupts the spatial-temporal regulation of histone arginine methylation in neurodevelopment

BACKGROUND

Oxidation Resistance 1 (OXR1) gene is a highly conserved gene of the TLDc domain-containing family. OXR1 is involved in fundamental biological and cellular processes, including DNA damage response, antioxidant pathways, cell cycle, neuronal protection, and arginine methylation. In 2019, five patients from three families carrying four biallelic loss-of-function variants in OXR1 were reported to be associated with cerebellar atrophy. However, the impact of OXR1 on cellular functions and molecular mechanisms in the human brain is largely unknown. Notably, no human disease models are available to explore the pathological impact of OXR1 deficiency.

RESULTS

We report a novel loss-of-function mutation in the TLDc domain of the human OXR1 gene, resulting in early-onset epilepsy, developmental delay, cognitive disabilities, and cerebellar atrophy. Patient lymphoblasts show impaired cell survival, proliferation, and hypersensitivity to oxidative stress. These phenotypes are rescued by TLDc domain replacement. We generate patient-derived induced pluripotent stem cells (iPSCs) revealing impaired neural differentiation along with dysregulation of genes essential for neurodevelopment. We identify that OXR1 influences histone arginine methylation by activating protein arginine methyltransferases (PRMTs), suggesting OXR1-dependent mechanisms regulating gene expression during neurodevelopment. We model the function of OXR1 in early human brain development using patient-derived brain organoids revealing that OXR1 contributes to the spatial-temporal regulation of histone arginine methylation in specific brain regions.

CONCLUSIONS

This study provides new insights into pathological features and molecular underpinnings associated with OXR1 deficiency in patients.

DNA-Compatible Copper/TEMPO Oxidation for DNA-Encoded Libraries

Aldehydes are important synthons for DNA-encoded library (DEL) construction, but the development of a DNA-compatible method for the oxidation of alcohols to aldehydes remains a significant challenge in the field of DEL chemistry. We report that a copper/TEMPO catalyst system enables the solution-phase DNA-compatible oxidation of DNA-linked primary activated alcohols to aldehydes. The semiaqueous, room-temperature reaction conditions afford oxidation of benzylic, heterobenzylic, and allylic alcohols in high yield, with DNA compatibility verified by mass spectrometry, qPCR, Sanger sequencing, and ligation assays. Subsequent transformations of the resulting aldehydes demonstrate the potential of this method for robust library diversification.

Hydrogen Peroxide-Triggered Disassembly of Boronic Ester-Cross-Linked Brush-Arm Star Polymers

The concentrations of reactive oxygen species (ROS), e.g., H2O2, are often elevated in diseased tissue microenvironments. Therefore, the selective detection of ROS could enable new diagnostic methods or tools for chemical biology. Here, we report the synthesis of boronic ester-bis-norbornene core-cross-linked brush-arm star polymers (BASPs) with polyethylene glycol (PEG) or PEG-branch-spirocyclohexyl nitroxide (chex) shells. Size exclusion chromatography (SEC) and dynamic light scattering (DLS) showed that these BASPs have narrowly dispersed molar masses and average hydrodynamic diameters of 23 ± 2 nm, respectively. Moreover, due to their core-shell structures, these BASPs disassemble into bottlebrush fragments with improved selectivity for H2O2 over ROS such as peroxynitrite (ONOO-) and hypochlorite (-OCl). Finally, H2O2 induced disassembly of chex-containing BASPs induces a change in transverse magnetic relaxivity that can be detected via magnetic resonance imaging (MRI). Chex-BASPs may represent a valuable new diagnostic tool for H2O2 sensing.

Research progress on the role and mechanism of DNA damage repair in germ cell development

In the complex and dynamic processes of replication, transcription, and translation of DNA molecules, a large number of replication errors or damage can occur which lead to obstacles in the development process of germ cells and result in a decreased reproductive rate. DNA damage repair has attracted widespread attention due to its important role in the maintenance and regulation of germ cells. This study reports on a systematic review of the role and mechanism of DNA damage repair in germline development. First, the causes, detection methods, and repair methods of DNA damage, and the mechanism of DNA damage repair are summarized. Second, a summary of the causes of abnormal DNA damage repair in germ cells is introduced along with common examples, and the relevant effects of germ cell damage. Third, we introduce the application of drugs related to DNA damage repair in the treatment of reproductive diseases and related surgical treatment of abnormal DNA damage, and summarize various applications of DNA damage repair in germ cells. Finally, a summary and discussion is given of the current deficiencies in DNA damage repair during germ cell development and future research development. The purpose of this paper is to provide researchers engaged in relevant fields with a further systematic understanding of the relevant applications of DNA damage repair in germ cells and to gain inspiration from it to provide new research ideas for related fields.

Secondary Electron Attachment-Induced Radiation Damage to Genetic Materials

Reactions of radiation-produced secondary electrons (SEs) with biomacromolecules (e.g., DNA) are considered one of the primary causes of radiation-induced cell death. In this Review, we summarize the latest developments in the modeling of SE attachment-induced radiation damage. The initial attachment of electrons to genetic materials has traditionally been attributed to the temporary bound or resonance states. Recent studies have, however, indicated an alternative possibility with two steps. First, the dipole-bound states act as a doorway for electron capture. Subsequently, the electron gets transferred to the valence-bound state, in which the electron is localized on the nucleobase. The transfer from the dipole-bound to valence-bound state happens through a mixing of electronic and nuclear degrees of freedom. In the presence of aqueous media, the water-bound states act as the doorway state, which is similar to that of the presolvated electron. Electron transfer from the initial doorway state to the nucleobase-bound state in the presence of bulk aqueous media happens on an ultrafast time scale, and it can account for the decrease in DNA strand breaks in aqueous environments. Analyses of the theoretically obtained results along with experimental data have also been discussed.

The life and times of endogenous opioid peptides: Updated understanding of synthesis, spatiotemporal dynamics, and the clinical impact in alcohol use disorder

The opioid G-protein coupled receptors (GPCRs) strongly modulate many of the central nervous system structures that contribute to neurological and psychiatric disorders including pain, major depressive disorder, and substance use disorders. To better treat these and related diseases, it is essential to understand the signaling of their endogenous ligands. In this review, we focus on what is known and unknown about the regulation of the over two dozen endogenous peptides with high affinity for one or more of the opioid receptors. We briefly describe which peptides are produced, with a particular focus on the recently proposed possible synthesis pathways for the endomorphins. Next, we describe examples of endogenous opioid peptide expression organization in several neural circuits and how they appear to be released from specific neural compartments that vary across brain regions. We discuss current knowledge regarding the strength of neural activity required to drive endogenous opioid peptide release, clues about how far peptides diffuse from release sites, and their extracellular lifetime after release. Finally, as a translational example, we discuss the mechanisms of action of naltrexone (NTX), which is used clinically to treat alcohol use disorder. NTX is a synthetic morphine analog that non-specifically antagonizes the action of most endogenous opioid peptides developed in the 1960s and FDA approved in the 1980s. We review recent studies clarifying the precise endogenous activity that NTX prevents. Together, the works described here highlight the challenges and opportunities the complex opioid system presents as a therapeutic target.

Oxidatively generated tandem DNA modifications by pyrimidinyl and 2-deoxyribosyl peroxyl radicals

Molecular oxygen sensitizes DNA to damage induced by ionizing radiation, Fenton-like reactions, and other free radical-mediated reactions. It rapidly converts carbon-centered radicals within DNA into peroxyl radicals, giving rise to a plethora of oxidized products consisting of nucleobase and 2-deoxyribose modifications, strand breaks and abasic sites. The mechanism of formation of single oxidation products has been extensively studied and reviewed. However, much evidence shows that reactive peroxyl radicals can propagate damage to vicinal components in DNA strands. These intramolecular reactions lead to the dual alteration of two adjacent nucleotides, designated as tandem or double lesions. Herein, current knowledge about the formation and biological implications of oxidatively generated DNA tandem lesions is reviewed. Thus far, most reported tandem lesions have been shown to arise from peroxyl radicals initially generated at pyrimidine bases, notably thymine, followed by reaction with 5'-flanking bases, especially guanine, although contiguous thymine lesions have also been characterized. Proper biomolecular processing is impaired by several tandem lesions making them refractory to base excision repair and potentially more mutagenic.

A Forward Vision for Chemodynamic Therapy: Issues and Opportunities

Since the insight to fuse Fenton chemistry and nanomedicine into cancer therapy, great signs of progress have been made in the field of chemodynamic therapy (CDT). However, the exact mechanism of CDT is obscured by the unique tumor chemical environment and inevitable nanoparticle-cell interactions, thus impeding further development. In this Scientific Perspective, the significance of CDT is clarified, the complex mechanism is deconstructed into primitive chemical and biological interactions, and the mechanism research directions based on the chemical kinetics and biological signaling pathways are discussed in detail. Moreover, beneficial outlooks are presented to enlighten the evolution of next-generation CDT. Hopefully, this Scientific Perspective can inspire new ideas and advances for CDT and provide a reference for breaking down the interdisciplinary barriers in the field of nanomedicine.

Transverse electronic transport properties of single DNA nucleobase pairs between different electrode materials

Detection of gene mutation through electronic transport properties measurements is an attractive research topic. For this purpose, we computed the current-voltage characteristics of adenine-thymine and guanine-cytosine nucleobase pairs, using a combination method of density-functional theory with non-equilibrium Green's function. Gene mutation was also simulated by structural change in nucleobase pairs by a double proton transfer mechanism. Four different metal electrodes were tested. Comparing the results, nucleobase pairs between platinum surfaces showed distinct electronic transport properties. Such as reverse rectifying direction and negative differential resistance behaviors. The discrepancy can be explained from series of electronic and structural analyses. All these results made identification of structural changes in individual DNA nucleobase pairs possible.

CuII-mediated stabilisation of DNA duplexes bearing consecutive ethenoadenine lesions and its application to a metal-responsive DNAzyme

Metal-mediated nucleobase pairing can play a central role in the expression of metal-responsive DNA functions. We report the Cu^II-mediated stabilisation of DNA duplexes bearing damaged nucleobases, 1,N⁶-ethenoadenine (εA), as metal-binding sites, which was utilised to construct a metal-responsive DNAzyme. Consecutive incorporation of three or more εA-εA mismatch pairs allowed for Cu^II-dependent significant duplex stabilisation through metal-mediated εA-Cu^II-εA base pairing. Subsequently, a split DNAzyme with three εA-Cu^II-εA base pairs was strategically designed. The activity of the εA-modified DNAzyme was enhanced by 5.3-fold upon addition of Cu^II ions. This study demonstrates the utility of εA lesions for building metal-responsive DNA architectures.

Mapping the diffusion pattern of 1O2 along DNA duplex by guanine photooxidation with an appended biphenyl photosensitizer

To realize nucleic acid-targeting photodynamic therapy, a photosensitizer should be attached at the optimal position on a complementary oligonucleotide, where a guanine photooxidation is maximized. Here we show the photooxidation of 22 DNA duplexes with varied lengths between a 1O2-generating biphenyl photosensitizer attached at a midchain thymine in a strand and the single guanine reactant in the other strand. The best photooxidation efficiencies are achieved at 9, 10, and 21 base intervals, which coincides with the pitch of 10.5 base pairs per turn in a DNA duplex. The low efficiencies for near and far guanines are due to quenching of the biphenyl by guanine and dilution of 1O2 by diffusion, respectively. The 1O2-diffusion mapping along DNA duplex provides clues to the development of efficient and selective photosensitizer agents for nucleic acid-targeting photodynamic therapy, as well as an experimental demonstration of diffusion of a particle along cylindrical surface in molecular level.

Functionalized electrodes embedded in nanopores: read-out enhancement?

In this review, functionalized nanogaps embedded in nanopores are discussed in view of their high biosensitivity in detecting biomolecules, their length, type, and sequence. Specific focus is given on nanoelectrodes functionalized with tiny nanometer-sized diamond-like particles offering vast functionalization possibilities for gold junction electrodes. This choice of the functionalization, in turn, offers nucleotide-specific binding possibilities improving the detection signals arising from such functionalized electrodes potentially embedded in a nanopore. The review sheds light onto the use and enhancement of the tunnelling recognition in functionalized nanogaps towards sensing DNA nucleotides and mutation detection, providing important input for a practical realization.

OGG1 in the Kidney: Beyond Base Excision Repair

8-Oxoguanine DNA glycosylase (OGG1) is a repair protein for 8-oxoguanine (8-oxoG) in eukaryotic atopic DNA. Through the initial base excision repair (BER) pathway, 8-oxoG is recognized and excised, and subsequently, other proteins are recruited to complete the repair. OGG1 is primarily located in the cytoplasm and can enter the nucleus and mitochondria to repair damaged DNA or to exert epigenetic regulation of gene transcription. OGG1 is involved in a wide range of physiological processes, such as DNA repair, oxidative stress, inflammation, fibrosis, and autophagy. In recent years, studies have found that OGG1 plays an important role in the progression of kidney diseases through repairing DNA, inducing inflammation, regulating autophagy and other transcriptional regulation, and governing protein interactions and functions during disease and injury. In particular, the epigenetic effects of OGG1 in kidney disease have gradually attracted widespread attention. This study reviews the structure and biological functions of OGG1 and the regulatory mechanism of OGG1 in kidney disease. In addition, the possibility of OGG1 as a potential therapeutic target in kidney disease is discussed.

Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations

Molecular dynamics simulations and geometry optimizations carried out at the quantum level as well as by quantum mechanical/molecular mechanics methods predict that short, single-stranded DNA oligonucleotides adopt conformations very similar to those observed in crystallographic double-stranded B-DNA, with rise coordinates close to ≈3.3 Å. In agreement with the experimental evidence, the computational results show that DNA single strands rich in adjacent purine nucleobases assume more regular arrangements than poly-thymine. The preliminary results suggest that single-stranded poly-cytosine DNA should also retain a substantial helical order in solution. A comparison of the structures of single and double helices confirms that the B-DNA motif is a favorable arrangement also for single strands. Indeed, the optimal geometry of the complementary single helices is changed to a very small extent in the formation of the duplex.

Modeling Charge Transfer Reactions by Hopping between Electronic Ground State Minima: Application to Hole Transfer between DNA Bases

In this paper, we extend the previously described general model for charge transfer reactions, introducing specific changes to treat the hopping between energy minima of the electronic ground state (i.e., transitions between the corresponding vibrational ground states). We applied the theoretical–computational model to the charge transfer reactions in DNA molecules which still represent a challenge for a rational full understanding of their mechanism. Results show that the presented model can provide a valid, relatively simple, approach to quantitatively study such reactions shedding light on several important aspects of the reaction mechanism.

Tracking of progressing human DNA polymerase δ holoenzymes reveals distributions of DNA lesion bypass activities

During DNA replication, DNA lesions in lagging strand templates are initially encountered by DNA polymerase δ (pol δ) holoenzymes comprised of pol δ and the PCNA processivity sliding clamp. These encounters are thought to stall replication of an afflicted template before the lesion, activating DNA damage tolerance (DDT) pathways that replicate the lesion and adjacent DNA sequence, allowing pol δ to resume. However, qualitative studies observed that human pol δ can replicate various DNA lesions, albeit with unknown proficiencies, which raises issues regarding the role of DDT in replicating DNA lesions. To address these issues, we re-constituted human lagging strand replication to quantitatively characterize initial encounters of pol δ holoenzymes with DNA lesions. The results indicate pol δ holoenzymes support dNTP incorporation opposite and beyond multiple lesions and the extent of these activities depends on the lesion and pol δ proofreading. Furthermore, after encountering a given DNA lesion, subsequent dissociation of pol δ is distributed around the lesion and a portion does not dissociate. The distributions of these events are dependent on the lesion and pol δ proofreading. Collectively, these results reveal complexity and heterogeneity in the replication of lagging strand DNA lesions, significantly advancing our understanding of human DDT.

Premature aging is associated with higher levels of 8-oxoguanine and increased DNA damage in the Polg mutator mouse

Mitochondrial dysfunction plays an important role in the aging process. However, the mechanism by which this dysfunction causes aging is not fully understood. The accumulation of mutations in the mitochondrial genome (or "mtDNA") has been proposed as a contributor. One compelling piece of evidence in support of this hypothesis comes from the Polg^D257A/D257A mutator mouse (Polg^mut/mut ). These mice express an error-prone mitochondrial DNA polymerase that results in the accumulation of mtDNA mutations, accelerated aging, and premature death. In this paper, we have used the Polg^mut/mut model to investigate whether the age-related biological effects observed in these mice are triggered by oxidative damage to the DNA that compromises the integrity of the genome. Our results show that mutator mouse has significantly higher levels of 8-oxoguanine (8-oxoGua) that are correlated with increased nuclear DNA (nDNA) strand breakage and oxidative nDNA damage, shorter average telomere length, and reduced mtDNA integrity. Based on these results, we propose a model whereby the increased level of reactive oxygen species (ROS) associated with the accumulation of mtDNA mutations in Polg^mut/mut mice results in higher levels of 8-oxoGua, which in turn lead to compromised DNA integrity and accelerated aging via increased DNA fragmentation and telomere shortening. These results suggest that mitochondrial play a central role in aging and may guide future research to develop potential therapeutics for mitigating aging process.

Capturing Protein-Nucleic Acid Interactions by High-Intensity Laser-Induced Covalent Crosslinking

Interactions of DNA with structural proteins such as histones, regulatory proteins, and enzymes play a crucial role in major cellular processes such as transcription, replication and repair. The in vivo mapping and characterization of the binding sites of the involved biomolecules are of primary importance for a better understanding of genomic deployment that is implicated in tissue and developmental stage-specific gene expression regulation. The most powerful and commonly used approach to date is immunoprecipitation of chemically cross-linked chromatin (XChIP) coupled with sequencing analysis (ChIP-seq). While the resolution and the sensitivity of the high-throughput sequencing techniques have been constantly improved little progress has been achieved in the crosslinking step. Because of its low efficiency the use of the conventional UVC lamps remains very limited while the formaldehyde method was established as the "gold standard" crosslinking agent. Efficient biphotonic crosslinking of directly interacting nucleic acid-protein complexes by a single short UV laser pulse has been introduced as an innovative technique for overcoming limitations of conventionally used chemical and photochemical approaches. In this survey, the main available methods including the laser approach are critically reviewed for their ability to generate DNA-protein crosslinks in vitro model systems and cells.

Enzymatic Synthesis and Antioxidant Activity of Mono- and Diacylated Epigallocatechin Gallate and Related By-Products

Ester derivatives of epigallocatechin gallate (EGCG) were enzymatically prepared by one-step transesterification with vinyl fatty acids consisting of varying acyl groups ranging from 2 to 18 carbon atoms (acetate, butyrate, caproate, caprylate, caprate, laurate, myristate, and stearate). The main acylation products were EGCG monoesters and diesters. However, due to the presence of trace amounts of water in the reaction medium, minor but noticeable hydrolysis of EGCG also occurred as a side reaction which required a prolonged purification process due to the formation of by-products such as gallic acid, epigallocatechin, and their esters. In this contribution, 8 EGCG monoesters, 7 EGCG diesters, and 7 gallic acid monoesters were isolated and purified, and the acylation positions were characterized. Meanwhile, several classical chemicals (DPPH, ABTS, FRAP, and Fe²⁺ chelation assays), food (β-carotene bleaching assay), and biological (LDL and DNA oxidation assays) models were conducted to evaluate and systematically compare their antioxidant efficacy. The lipophilicity of the EGCG derivatives increased with the increasing chain length of the acyl group and led to the fluctuation of their antioxidant efficacies. Three main factors, namely, the reduction potential, the partition coefficient of solute in the solvent system, and the steric hindrance of antioxidant agent and related substrates were considered to help explain the biased antioxidant performance of EGCG derivatives upon acylation modification. The results strongly suggest that the acylated EGCGs have great potential as lipophilic alternatives to the water-soluble EGCG in lipid-based matrices.

Discrimination between Different DNA Lesions by Monitoring Single-Molecule Polymerase Stalling Kinetics during Nanopore Sequencing

O⁶-Carboxymethylguanosine (O⁶-CMG), O⁶-methylguanosine (O⁶-MeG), and abasic site (AP site) are DNA lesions induced by alkylating agents. Identification of these lesions in DNA may aid in understanding their relevance to carcinogenesis and may be used for diagnosis. Nanopore sequencing (NPS) may directly report nucleotide modifications solely from the nanopore readout. However, the conventional NPS strategy still suffers from interferences from neighboring sequences. Instead, by observation of the enzymatic stalling kinetics caused by the O⁶-CMG, O⁶-MeG, or AP site, discrimination between different DNA lesions is directly achieved. This strategy is not interfered with by the sequence context around the lesion. The lesion, which retards the movement of the DNA through the pore, efficiently prohibits misreading of the DNA lesion. These results suggest a new strategy in the identification of DNA lesions or DNA modifications. It also provides a high-resolution biophysical tool to investigate enzymatic kinetics caused by DNA lesions and the corresponding enzymes.

A mitochondria-targeted rhodol fluorescent probe for imaging of hydrogen peroxide in living cells

Hydrogen peroxide (H₂O₂) is a main member of reactive oxygen species (ROS) in cells that has a significant impact on various physiological and pathological processes of organisms. Here, we designed and synthesized a new type of fluorescent probe Rhodol-OAc for the specific detection of H₂O₂. The probe had good water solubility, high selectivity and sensitivity to H₂O₂, low cytotoxicity, excellent mitochondrial targeting ability, etc. It was successfully applied in the imaging of exogenous and endogenous H₂O₂ in living cells. In addition, theoretical calculations were carried out to clarify the luminescence mechanism of the probe. More importantly, we successfully applied the probe to indirectly detect xanthine and glucose, the metabolism of which generates H₂O₂, and achieved satisfactory results.

Chemical Proteomics of the Tumor Suppressor Fhit Covalently Bound to the Cofactor Ap3A Elucidates Its Inhibitory Action on Translation

The tumor suppressor protein fragile histidine triad (Fhit) is known to be associated with genomic instability and apoptosis. The tumor-suppressive function of Fhit depends on the interaction with the alarmone diadenosine triphosphate (Ap₃A), a noncanonical nucleotide whose concentration increases upon cellular stress. How the Fhit-Ap₃A complex exerts its signaling function is unknown. Here, guided by a chemical proteomics approach employing a synthetic stable Fhit-Ap₃A complex, we found that the Fhit-Ap₃A complex, but not Fhit or Ap₃A alone, impedes translation. Our findings provide a mechanistic model in which Fhit translocates from the nucleolus into the cytosol upon stress to form an Fhit-Ap₃A complex. The Fhit-Ap₃A complex impedes translation both in vitro and in vivo, resulting in reduced cell viability. Overall, our findings provide a mechanistic model by which the tumor suppressor Fhit collaborates with the alarmone Ap₃A to regulate cellular proliferation.

A Dynamic Model for Estimating the Interaction of ROS–PUFA–Antioxidants in Rabbit

Defining optimal nutrition in animals and humans remains a main scientific challenge. The objective of the work was to develop a dynamic model of reactive oxygen species (ROS)–polyunsaturated fatty acid (PUFA)–antioxidant homeostasis using the rabbit as a model. The problem entity was to evaluate the main metabolites generated from interactions between traits included in the conceptual model and identified by three main sub–models: (i) ROS generation, (ii) PUFA oxidation and (iii) antioxidant defence. A mathematical model (VENSIM software) that consisted of molecular stocks (INPUTs, OUTPUTs), exchange flows (intermediate OUTPUTs) and process rates was developed. The calibration was performed by using standard experimental data (Experiment 1), whereas the validation was carried out in Experiments 2 and 3 by using supra–nutritional dietary inputs (VIT E+ and PUFA+). The accuracy of the models was measured using 95% confidence intervals. Analytical OUTPUTs (ROS, PUFA, Vit E, Ascorbic acid, Iso–/NeuroProstanes, Aldehydes) were well described by the standard model. There was also good accuracy for the VIT E+ scenario, whereas some compensatory rates (Kc1–Kc4) were added to assess body compensation when high levels of dietary PUFA were administered (Experiment 3). In conclusion, the model can be very useful for predicting the effects of dietary treatments on the redox homeostasis of rabbits.

Naked-Eye Detection of Hydrogen Peroxide on Photoluminescent Paper Discs

We have developed a turn-on photoluminescence protocol to detect hydrogen peroxide (H₂O₂) utilizing a supramolecular hydrogel as a sensing platform. Hydrogen peroxide is widely used in formulations, starting from healthcare products to explosives. It is also known to induce deleterious health effects at its irregular physiological concentration and considered as a biomarker in various disease conditions. We designed molecule 2, which releases the Tb³⁺ sensitizer biphenyl-4-carboxylic acid (1) upon unmasking by hydrogen peroxide. This chemistry led us to develop a sensitive photoluminescence assay for H₂O₂ through the 1-induced photoluminescence of terbium (Tb³⁺) in a hydrogel matrix. Paper discs (0.45 cm) were coated with the soft hydrogel to make the sensing process simple and cost-effective. The green luminescence from the paper discs, observed under a UV lamp, allowed naked-eye detection of H₂O₂ in the micromolar level without any sophisticated instrumentation. Image processing software or a plate reader can be used for the accurate quantification of the analyte in micromolar and nanomolar ranges. Several commercial hand sanitizers containing hydrogen peroxide were tested by this method. The results indicated that this low-cost system could be practically adopted, especially in resource-limited areas, to quantify/detect H₂O₂ for quality control purposes or other applications.

Auxiliary Therapeutic Role of Cholinergic Agents: Mechanistic Insights into the Antioxidant Behavior of Alzheimer's Disease Drugs

Repurposing of existing drugs toward new therapeutic use(s) has become an emergent area of research in current times. In this context, the antioxidant behavior of eight cholinergic drugs used in the treatment of Alzheimer's disease (AD) was investigated theoretically. The low bond dissociation enthalpy values in all of the compounds advocated for the hydrogen atom transfer mechanism toward the observed antioxidant behavior. The kinetic study for the reaction of the drugs with hydroperoxyl radicals indicated an indirect reaction path owing to the presence of pre- and postreaction complexes. In some cases, the rate constant for the H-abstraction reaction (k = 2.8 × 10³ L mol^-1 s^-1) is found to be close to that of a well-known non-phenolic antioxidant, α-terpinene (k = 4.3 × 10³ L mol^-1 s^-1). Quantification of charge transfer character among the drugs with DNA bases and molecular docking calculations confirmed the groove binding model and predicted the drugs to be safe from DNA damage. A theoretical evaluation of the mechanistic details governing the antioxidant property along with the proven stress reversal ability of these AD drugs provided new insights to design and develop more efficient drugs with dual therapeutic potential.

Modulation of the Directionality of Hole Transfer between the Base and the Sugar-Phosphate Backbone in DNA with the Number of Sulfur Atoms in the Phosphate Group

This work shows that S atom substitution in phosphate controls the directionality of hole transfer processes between the base and sugar-phosphate backbone in DNA systems. The investigation combines synthesis, electron spin resonance (ESR) studies in supercooled homogeneous solution, pulse radiolysis in aqueous solution at ambient temperature, and density functional theory (DFT) calculations of in-house synthesized model compound dimethylphosphorothioate (DMTP(O^-)═S) and nucleotide (5'-O-methoxyphosphorothioyl-2'-deoxyguanosine (G-P(O^-)═S)). ESR investigations show that DMTP(O^-)═S reacts with Cl₂^•- to form the σ²σ*¹ adduct radical -P-S[Formula: see text]Cl, which subsequently reacts with DMTP(O^-)═S to produce [-P-S[Formula: see text]S-P-]^-. -P-S[Formula: see text]Cl in G-P(O^-)═S undergoes hole transfer to Gua, forming the cation radical (G^•+) via thermally activated hopping. However, pulse radiolysis measurements show that DMTP(O^-)═S forms the thiyl radical (-P-S^•) by one-electron oxidation, which did not produce [-P-S[Formula: see text]S-P-]^-. Gua in G-P(O^-)═S is oxidized unimolecularly by the -P-S^• intermediate in the sub-picosecond range. DFT thermochemical calculations explain the differences in ESR and pulse radiolysis results obtained at different temperatures.

Cryogenic IR and UV spectroscopy of isomer-selected cytosine radical cation

The UV photodissociation of cryogenic-cooled isomer-selected cytosine–silver complex leads to the production of cytosine radical cation without isomerization.

Epitranscriptomics of cardiovascular diseases (Review)

RNA modifications have recently become the focus of attention due to their extensive regulatory effects in a vast array of cellular networks and signaling pathways. Just as epigenetics is responsible for the imprinting of environmental conditions on a genetic level, epitranscriptomics follows the same principle at the RNA level, but in a more dynamic and sensitive manner. Nevertheless, its impact in the field of cardiovascular disease (CVD) remains largely unexplored. CVD and its associated pathologies remain the leading cause of death in Western populations due to the limited regenerative capacity of the heart. As such, maintenance of cardiac homeostasis is paramount for its physiological function and its capacity to respond to environmental stimuli. In this context, epitranscriptomic modifications offer a novel and promising therapeutic avenue, based on the fine‑tuning of regulatory cascades, necessary for cardiac function. This review aimed to provide an overview of the most recent findings of key epitranscriptomic modifications in both coding and non‑coding RNAs. Additionally, the methods used for their detection and important associations with genetic variations in the context of CVD were summarized. Current knowledge on cardiac epitranscriptomics, albeit limited still, indicates that the impact of epitranscriptomic editing in the heart, in both physiological and pathological conditions, holds untapped potential for the development of novel targeted therapeutic approaches in a dynamic manner.

Electron Holes in G-Quadruplexes: The Role of Adenine Ending Groups

The study deals with four-stranded DNA structures (G-Quadruplexes), known to undergo ionization upon direct absorption of low-energy UV photons. Combining quantum chemistry calculations and time-resolved absorption spectroscopy with 266 nm excitation, it focuses on the electron holes generated in tetramolecular systems with adenine groups at the ends. Our computations show that the electron hole is placed in a single guanine site, whose location depends on the position of the adenines at the 3' or 5' ends. This position also affects significantly the electronic absorption spectrum of (G⁺)^● radical cations. Their decay is highly anisotropic, composed of a fast process (<2 µs), followed by a slower one occurring in ~20 µs. On the one hand, they undergo deprotonation to (G-H2)^● radicals and, on the other, they give rise to a reaction product absorbing in the 300-500 nm spectral domain.

Genotoxic C8-Arylamino-2'-deoxyadenosines Act as Latent Alkylating Agents to Induce DNA Interstrand Cross-Links

DNA interstrand cross-links (ICLs) are extremely deleterious and structurally diverse, driving the evolution of ICL repair pathways. Discovering ICL-inducing agents is, thus, crucial for the characterization of ICL repair pathways and Fanconi anemia, a genetic disease caused by mutations in ICL repair genes. Although several studies point to oxidative stress as a cause of ICLs, oxidative stress-induced cross-linking events remain poorly characterized. Also, polycyclic aromatic amines, potent environmental carcinogens, have been implicated in producing ICLs, but their identities and sequences are unknown. To close this knowledge gap, we tested whether ICLs arise by the oxidation of 8-arylamino-2'-deoxyadenosine (ArNHdA) lesions, adducts produced by arylamino carcinogens. Herein, we report that ArNHdA acts as a latent cross-linking agent to generate ICLs under oxidative conditions. The formation of an ICL from 8-aminoadenine, but not from 8-aminoguanine, highlights the specificity of 8-aminopurine-mediated ICL production. Under the influence of the reactive oxygen species (ROS) nitrosoperoxycarbonate, ArNHdA (Ar = biphenyl, fluorenyl) lesions were selectively oxidized to generate ICLs. The cross-linking reaction may occur between the C2-ArNHdA and N2-dG, presumably via oxidation of ArNHdA into a reactive diiminoadenine intermediate followed by the nucleophilic attack of the N2-dG on the diiminoadenine. Overall, ArNHdA-mediated ICLs represent rare examples of ROS-induced ICLs and polycyclic aromatic amine-mediated ICLs. These results reveal novel cross-linking chemistry and the genotoxic effects of arylamino carcinogens and support the hypothesis that C8-modified adenines with low redox potential can cause ICLs in oxidative stress.

Research progress of azido-containing Pt(IV) antitumor compounds

Cancer is a long-known incurable disease, and the medical use of cisplatin has been a significant discovery. However, the side-effects of cisplatin necessitate the development of new and improved drug. Therefore, in this study, we focused on the photoactivatable Pt(IV) compounds Pt[(X₁)(X₂)(Y₁)(Y₂)(N₃)₂], which have a completely novel mechanism of action. Pt(IV) can efficiently overcome the side-effects of cisplatin and other drugs. Here, we have demonstrated, summarized and discussed the effects and mechanism of these compounds. Compared to the relevant articles in the literature, we have provided a more detailed introduction and a made comprehensive classification of these compounds. We believe that our results can effectively provide a reference for the development of these drugs.

Deprotonation Dynamics of Guanine Radical Cations†

This review is dedicated to guanine radical cations (G⁺ )^· that are precursors to oxidatively generated damage to DNA. (G⁺ )^· are unstable in neutral aqueous solution and tend to lose a proton. The deprotonation process has been studied by time-resolved absorption experiments in which (G⁺ )^· radicals are produced either by an electron abstraction reaction, using an external oxidant, or by low-energy/low-intensity photoionization of DNA. Both the position of the released proton and the dynamics of the process depend on the secondary DNA structure. While deprotonation in duplex DNA leads to (G-H1)^· radicals, in guanine quadruplexes the (G-H2)^· analogs are observed. Deprotonation in monomeric guanosine proceeds with a time constant of ˜60 ns; in genomic DNA, it is completed within 2 µs; and in guanine quadruplexes, it spans from at least 30 ns to over 50 µs. Such a deprotonation dynamics in four-stranded structures, extended over more than three decades of times, is correlated with the anisotropic structure of DNA and the mobility of its hydration shell. In this case, commonly used second-order reaction models are inappropriate for its description.

Biomimetic Iron Complex Achieves TET Enzyme Reactivity*

The epigenetic marker 5-methyl-2'-deoxycytidine (5mdC) is the most prevalent modification to DNA. It is removed inter alia via an active demethylation pathway: oxidation by Ten-Eleven Translocation 5-methyl cytosine dioxygenase (TET) and subsequent removal via base excision repair or direct demodification. Recently, we have shown that the synthetic iron(IV)-oxo complex [FeIV (O)(Py5 Me2 H)]2+ (1) can serve as a biomimetic model for TET by oxidizing the nucleobase 5-methyl cytosine (5mC) to its natural metabolites. In this work, we demonstrate that nucleosides and even short oligonucleotide strands can also serve as substrates, using a range of HPLC and MS techniques. We found that the 5-position of 5mC is oxidized preferably by 1, with side reactions occurring only at the strand ends of the used oligonucleotides. A detailed study of the reactivity of 1 towards nucleosides confirms our results; that oxidation of the anomeric center (1') is the most common side reaction.

Human Hazard Assessment Using Drosophila Wing Spot Test as an Alternative In Vivo Model for Genotoxicity Testing-A Review

Genomic instability, one of cancer's hallmarks, is induced by genotoxins from endogenous and exogenous sources, including reactive oxygen species (ROS), diet, and environmental pollutants. A sensitive in vivo genotoxicity test is required for the identification of human hazards to reduce the potential health risk. The somatic mutation and recombination test (SMART) or wing spot test is a genotoxicity assay involving Drosophila melanogaster (fruit fly) as a classical, alternative human model. This review describes the principle of the SMART assay in conjunction with its advantages and disadvantages and discusses applications of the assay covering all segments of health-related industries, including food, dietary supplements, drug industries, pesticides, and herbicides, as well as nanoparticles. Chemopreventive strategies are outlined as a global health trend for the anti-genotoxicity of interesting herbal extract compounds determined by SMART assay. The successful application of Drosophila for high-throughput screening of mutagens is also discussed as a future perspective.

The Time Scale of Electronic Resonance in Oxidized DNA as Modulated by Solvent Response: An MD/QM-MM Study

The time needed to establish electronic resonant conditions for charge transfer in oxidized DNA has been evaluated by molecular dynamics simulations followed by QM/MM computations which include counterions and a realistic solvation shell. The solvent response is predicted to take ca. 800–1000 ps to bring two guanine sites into resonance, a range of values in reasonable agreement with the estimate previously obtained by a kinetic model able to correctly reproduce the observed yield ratios of oxidative damage for several sequences of oxidized DNA.

Antioxidant Barrier and Oxidative Damage to Proteins, Lipids, and DNA/RNA in Adrenal Tumor Patients

This study is the first to assess redox balance, glutathione metabolism, and oxidative damage to RNA/DNA, proteins, and lipids in the plasma/serum and urine of patients with adrenal masses. The study included 70 patients with adrenal tumors divided into three subgroups: incidentaloma (n = 30), pheochromocytoma (n = 20), and Cushing's/Conn's adenoma (n = 20), as well as 60 healthy controls. Blood and urine samples were collected before elective endoscopic adrenalectomy. Antioxidant defense capacity was significantly decreased (serum/plasma: superoxide dismutase (SOD), catalase (CAT) and reduced glutathione (GSH), uric acid (UA); urine: SOD, GSH, UA) in patients with adrenal masses. The oxidative damage to proteins (advanced glycation end products (AGE), advanced oxidation protein products (AOPP)) and lipids (lipid hydroperoxides (LOOH), and malondialdehyde (MDA)) was higher in the plasma and urine of these patients. Plasma MDA and DNA/RNA oxidation products, with high sensitivity and specificity, can help to diagnose pheochromocytoma. This biomarker differentiates patients with pheochromocytoma from Cushing's/Conn's adenoma as well as from heathy controls. Plasma RNA/DNA oxidation was also positively correlated with urine metanephrine. Oxidative stress can play a crucial role in adrenal tumors. However, further studies are required to clarify the role of redox signaling in adrenal masses.

The genomes of ancient date palms germinated from 2,000 y old seeds

Resurrection genomics is an alternative to ancient DNA approaches in studying the genetics and evolution of past and possibly extinct populations. By reviving biological material such as germinating ancient seeds from archaeological and paleontological sites, or historical collections, one can study genomes of lost populations. We applied this approach by sequencing the genomes of seven Judean date palms (Phoenix dactylifera) that were germinated from ∼2,000 y old seeds recovered in the Southern Levant. Using this genomic data, we were able to document that introgressive hybridization of the wild Cretan palm Phoenix theophrasti into date palms had occurred in the Eastern Mediterranean by ∼2,200 y ago and examine the evolution of date palm populations in this pivotal region two millennia ago.

Seven date palm seeds (Phoenix dactylifera L.), radiocarbon dated from the fourth century BCE to the second century CE, were recovered from archaeological sites in the Southern Levant and germinated to yield viable plants. We conducted whole-genome sequencing of these germinated ancient samples and used single-nucleotide polymorphism data to examine the genetics of these previously extinct Judean date palms. We find that the oldest seeds from the fourth to first century BCE are related to modern West Asian date varieties, but later material from the second century BCE to second century CE showed increasing genetic affinities to present-day North African date palms. Population genomic analysis reveals that by ∼2,400 to 2,000 y ago, the P. dactylifera gene pool in the Eastern Mediterranean already contained introgressed segments from the Cretan palm Phoenix theophrasti, a crucial genetic feature of the modern North African date palm populations. The P. theophrasti introgression fraction content is generally higher in the later samples, while introgression tracts are longer in these ancient germinated date palms compared to modern North African varieties. These results provide insights into crop evolution arising from an analysis of plants originating from ancient germinated seeds and demonstrate what can be accomplished with the application of a resurrection genomics approach.

Endothelial Endothelin Receptor A Expression Is Associated With Podocyte Injury and Oxidative Stress in Patients With Focal Segmental Glomerulosclerosis

Introduction

The podocyte is thought to be the mainly affected cell type in focal segmental glomerulosclerosis (FSGS). However, recent studies have also indicated a role for glomerular endothelial cells and podocyte−endothelial crosstalk in FSGS development. An experimental model for podocyte injury showed that increased endothelin-1 (ET-1) signaling between podocytes and endothelial cells induces endothelial oxidative stress and subsequent podocyte loss. In the current study, we investigated endothelial endothelin receptor A (ET_AR) expression in patients with FSGS and its association with podocyte injury and glomerular oxidative stress.

Methods

We selected 39 biopsy samples of patients with FSGS and 8 healthy control subjects, and stained them for ET_AR, nephrin and 8-oxo-guanine, a DNA lesion caused by oxidative damage. Glomeruli with ET_AR-positive endothelium and with nephrin loss were scored, and the 8-oxo-guanine−positive glomerular area was measured.

Results

The mean percentage of glomeruli with ET_AR-positive endothelial cells in patients with FSGS was higher compared to that in healthy control subjects (52% vs. 7%; P < 0.001). The presence of glomerular ET_AR-positive endothelium was strongly associated with nephrin loss both on the biopsy level (rho = 0.47; P < 0.01), as on the level of individual glomeruli (odds ratio = 2.0; P < 0.001). Moreover, glomeruli with ET_AR-positive endothelium showed more 8-oxo-guanine−positive staining (1.9% vs. 2.4%; P = 0.037). Finally, 8-oxo-guanine positivity in glomeruli was associated with increased levels of proteinuria.

Conclusion

Taking together our findings, we show that ET_AR is increased in glomerular endothelial cells of patients with FSGS and associated with podocyte damage and glomerular oxidative stress. These findings support the hypothesis that ET-1 signaling in glomerular endothelial cells contributes to disease development in patients with FSGS.

A pH-sensitive drug delivery system based on hyaluronic acid co-deliver doxorubicin and aminoferrocene for the combined application of chemotherapy and chemodynamic therapy

Doxorubicin is a broad-spectrum antineoplastic drug used in tumor therapy, its clinical application is limited by side effects on normal tissues. In this article, a pH-responsive drug delivery system (NPs(DOX/AFc)) with co-delivers doxorubicin (DOX) and aminoferrocene (AFc) was prepared by a two-step synthesis method including the oxidation of hyaluronic acid and Schiff base reaction. NPs(DOX/AFc) can be used in combination therapy of chemodynamic therapy (CDT) and chemotherapy (CT), thus the dosage of the chemotherapeutic drug DOX was reduced. The drug release behavior of NPs(DOX/AFc) in vitro showed that acid-responsive drug releases under the endosomal/lysosomal environment were 56.5 % of DOX and 61.8 % of AFc. In vitro toxicity experiments showed that DOX and AFc had synergistic effects (CI = 0.878). The results of intracellular ROS measurement and the mitochondrial membrane potential analysis showed that in tumor cells NPs(DOX₄/AFc) induced more production of reactive oxygen species and more loss of the mitochondrial membrane potential. In short, this co-delivery system based on polymer prodrugs provides a new idea for the combined application of CT and CDT.

19-(Benzyloxy)-19-oxojolkinolide B (19-BJB), an ent-abietane diterpene diepoxide, inhibits the growth of bladder cancer T24 cells through DNA damage

Diterpenoids jolkinolide A and B, were first isolated from Euphorbia fischeriana. In our previous research, 19-(Benzyloxy)-19-oxojolkinolide B (19-BJB), a derivative of jolkinolides, was synthesized as a novel ent -abietane diterpene diepoxide. In this study, 19-BJB showed strong in vitro activity against bladder cancer cell lines. DNA damage which was observed through the interaction of 19-BJB with nucleotide chains and affected DNA repair resulted in the activation of checkpoint kinase 1 (Chk1) and checkpoint kinase 2 (Chk2) in bladder cancer cell lines. In vivo testing in nude mice also proved that 19-BJB revealed a potential inhibitory effect on tumor growth. Additionally, the 3D-QSAR models of jolkinolides were established. Briefly, we proved that 19-BJB could potentially be used as a drug to inhibit the growth of bladder tumor.

Tackling a Curious Case: Generation of Charge-Tagged Guanosine Radicals by Gas-Phase Electron Transfer and Their Characterization by UV-vis Photodissociation Action Spectroscopy and Theory

We report the generation of gas-phase riboguanosine radicals that were tagged at ribose with a fixed-charge 6-(trimethylammonium)hexane-1-aminocarbonyl group. The radical generation relied on electron transfer from fluoranthene anion to noncovalent dibenzocrown-ether dication complexes which formed nucleoside cation radicals upon one-electron reduction and crown-ether ligand loss. The cation radicals were characterized by collision-induced dissociation (CID), photodissociation (UVPD), and UV-vis action spectroscopy. Identification of charge-tagged guanosine radicals was challenging because of spontaneous dissociations by loss of a hydrogen atom and guanine that occurred upon storing the ions in the ion trap without further excitation. The loss of H proceeded from an exchangeable position on N-7 in guanine that was established by deuterium labeling and was the lowest energy dissociation of the guanosine radicals according to transition-state energy calculations. Rate constant measurements revealed an inverse isotope effect on the loss of either hydrogen or deuterium with rate constants k_H = 0.25-0.26 s^-1 and k_D = 0.39-0.54 s^-1. We used time-dependent density functional theory calculations, including thermal vibronic effects, to predict the absorption spectra of several protomeric radical isomers. The calculated spectra of low-energy N-7-H guanine-radical tautomers closely matched the action spectra. Transition-state-theory calculations of the rate constants for the loss of H-7 and guanine agreed with the experimental rate constants for a narrow range of ion effective temperatures. Our calculations suggest that the observed inverse isotope effect does not arise from the isotope-dependent differences in the transition-state energies. Instead, it may be caused by the dynamics of post-transition-state complexes preceding the product separation.

Effect of DNA Glycosylases OGG1 and Neil1 on Oxidized G-Rich Motif in the KRAS Promoter

The promoter of the Kirsten ras (KRAS) proto-oncogene contains, upstream of the transcription start site, a quadruplex-forming motif called 32R with regulatory functions. As guanine under oxidative stress can be oxidized to 8-oxoguanine (8OG), we investigated the capacity of glycosylases 8-oxoguanine glycosylase (OGG1) and endonuclease VIII-like 1 (Neil1) to excise 8OG from 32R, either in duplex or G-quadruplex (G4) conformation. We found that OGG1 efficiently excised 8OG from oxidized 32R in duplex but not in G4 conformation. By contrast, glycosylase Neil1 showed more activity on the G4 than the duplex conformation. We also found that the excising activity of Neil1 on folded 32R depended on G4 topology. Our data suggest that Neil1, besides being involved in base excision repair pathway (BER), could play a role on KRAS transcription.