Comparison of Transition Metal-Mediated Oxidation Reactions of Guanine in Nucleoside and Single-Stranded Oligodeoxynucleotide Contexts

Copper trafficking systems in cells: insights into coordination chemistry and toxicity

Transition metal ions, such as copper, are indispensable components in the biological system. Copper ions which primarily exist in two major oxidation states Cu(I) and Cu(II) play crucial roles in various cellular processes including antioxidant defense, biosynthesis of neurotransmitters, and energy metabolism, owing to their inherent redox activity. The disturbance in copper homeostasis can contribute to the development of copper metabolism disorders, cancer, and neurodegenerative diseases, highlighting the significance of understanding the copper trafficking system in cellular environments. This review aims to offer a comprehensive overview of copper homeostatic machinery, with an emphasis on the coordination chemistry of copper transporters and trafficking proteins. While copper chaperones and the corresponding metalloenzymes are thoroughly discussed, we also explore the potential existence of low-molecular-mass metal complexes within cellular systems. Furthermore, we summarize the toxicity mechanisms originating from copper deficiency or accumulation, which include the dysregulation of oxidative stress, signaling pathways, signal transduction, and amyloidosis. This perspective review delves into the current knowledge regarding the intricate aspects of the copper trafficking system, providing valuable insights into potential treatment strategies from the standpoint of bioinorganic chemistry.

Impact of organic chemistry conditions on DNA durability in the context of DNA-encoded library technology

High-power screening (HPS) technologies, such as DNA-encoded library (DEL) technology, could exponentially increase the dimensions of the chemical space accessible for drug discovery. The intrinsic fragile nature of DNA is associated with cumbersome limitations and DNA durability (e.g., depurination, loss of phosphate groups, adduct formation) is compromised in numerous organic chemistry conditions that require empirical testing. An atlas of reaction conditions (temperature, pH, solvent/buffer, ligands, oxidizing reagents, catalysts, scavengers in function of time) that have been systematically tested in multiple combinations, indicates precisely limits useful for DEL construction. More importantly, this approach could be used broadly to effectively evaluate DNA-compatibility of any novel on-DNA chemical reaction, and it is compatible with different molecular methodologies. This atlas and the general approach presented, by allowing novel reaction conditions to be performed in presence of DNA, should greatly help in expanding the DEL chemical space as well as any field involving DNA durability.

Identification of the Major Product of Guanine Oxidation in DNA by Ozone

Ozonolysis of guanosine formed the 5-carboxamido-5-formamido-2-iminohydantoin (2Ih) nucleoside along with trace spiroiminodihydantoin (Sp). On the basis of literature precedent, we propose an unconventional ozone mechanism involving incorporation of only one oxygen atom of O₃ to form 2Ih with evolution of singlet oxygen responsible for Sp formation. The increased yield of Sp in the buffered ¹O₂-stabilizing solvent D₂O, formation of 2Ih in a short oligodeoxynucleotide, and ¹⁸O-isotope labeling provided evidence to support this mechanism. The elusiveness and challenges of working with 2Ih are described in a series of studies on the significant context effects on the half-life of the 2Ih glycosidic bond.

Products of Oxidative Guanine Damage Form Base Pairs with Guanine

Among the natural bases, guanine is the most oxidizable base. The damage caused by oxidation of guanine, commonly referred to as oxidative guanine damage, results in the formation of several products, including 2,5-diamino-4H-imidazol-4-one (Iz), 2,2,4-triamino-5(2H)-oxazolone (Oz), guanidinoformimine (Gf), guanidinohydantoin/iminoallantoin (Gh/Ia), spiroiminodihydantoin (Sp), 5-carboxamido-5-formamido-2-iminohydantoin (2Ih), urea (Ua), 5-guanidino-4-nitroimidazole (NI), spirodi(iminohydantoin) (5-Si and 8-Si), triazine, the M+7 product, other products by peroxynitrite, alkylated guanines, and 8,5'-cyclo-2'-deoxyguanosine (cG). Herein, we summarize the present knowledge about base pairs containing the products of oxidative guanine damage and guanine. Of these products, Iz is involved in G-C transversions. Oz, Gh/Ia, and Sp form preferably Oz:G, Gh/Ia:G, and Sp:G base pairs in some cases. An involvement of Gf, 2Ih, Ua, 5-Si, 8-Si, triazine, the M+7 product, and 4-hydroxy-2,5-dioxo-imidazolidine-4-carboxylic acid (HICA) in G-C transversions requires further experiments. In addition, we describe base pairs that target the RNA-dependent RNA polymerase (RdRp) of RNA viruses and describe implications for the 2019 novel coronavirus (SARS-CoV-2): When products of oxidative guanine damage are adapted for the ribonucleoside analogs, mimics of oxidative guanine damages, which can form base pairs, may become antiviral agents for SARS-CoV-2.

Potent Oxidation of DNA by Haloquinoid Disinfection Byproducts to the More Mutagenic Imidazolone dIz via an Unprecedented Haloquinone-Enoxy Radical-Mediated Mechanism

Halogenated quinones are a class of carcinogenic intermediates and newly identified chlorination disinfection byproducts in drinking water. We found recently that halogenated quinones could enhance the decomposition of hydroperoxides independent of transition-metal ions and formation of the novel quinone enoxy/ketoxy radicals. Here, we show that the major oxidation product was 2-amino-5-[(2-deoxy-β-d-erythro-pentofuranosyl)amino]-4H-imidazol-4-one (dIz) when the nucleoside 2'-deoxyguanosine (dG) was treated with tetrachloro-1,4-benzoquinone (TCBQ) and t-butyl hydroperoxide (t-BuOOH). The formation of dIz was markedly inhibited by typical radical spin-trapping agents. Interestingly and unexpectedly, we found that the generated quinone enoxy radical played a critical role in dIz formation. Using [¹⁵N₅]-8-oxodG, dIz was found to be produced either directly from dG or through the transient formation of 8-oxodG. Based on these data, we proposed that the production of dIz might be through an unusual haloquinone-enoxy radical-mediated mechanism. Analogous results were observed in the oxidation of ctDNA by TCBQ/t-BuOOH and when t-BuOOH was substituted by the endogenously generated physiologically relevant hydroperoxide 13S-hydroperoxy-9Z,11E-octadecadienoic acid. This is the first report that halogenated quinoid carcinogens and hydroperoxides can induce potent oxidation of dG to the more mutagenic product dIz via an unprecedented quinone-enoxy radical-mediated mechanism, which may partly explain their potential carcinogenicity.

Computational Study of the Oxidation of Guanine To Form 5-Carboxyamido-5-formamido-2-iminohydantoin (2Ih)

Oxidative damage to DNA leads to a number of two-electron oxidation products of guanine such as 8-oxo-7,8-dihydroguanine (8oxoG). 5-Carboxyamido-5-formamido-2-iminohydantoin (2Ih) is another two-electron oxidation product that forms in competition with 8oxoG. The pathways for the formation of 2Ih have been studied by density functional theory using the ωB97XD functional with the 6-31+G(d,p) basis set and SMD implicit water solvation plus a small number of explicit water molecules positioned to help stabilize charged species and facilitate reaction steps. For oxidative conditions that produce hydroxyl radical, such as Fenton chemistry, hydroxy radical can add at C4, C5, or C8. Addition at C4 or C5 followed by loss of H₂O produces guanine radical. Guanine radical can also be produced directly by oxidation of guanine by reactive oxygen species (ROS). A C5-OH intermediate can be formed by addition of superoxide to C5 of guanine radical followed by reduction. Alternatively, the C5-OH intermediate can be formed by hydroxy radical addition at C5 and oxidation by ³O₂. The competition between oxidative and reductive pathways depends on the reaction conditions. Acyl migration of the C5-OH intermediate yields reduced spiroiminodihydantoin (Sp^red). Subsequent water addition at C8 of Sp^red and N7-C8 ring opening produces 2Ih. Hydroxy radical addition at C8 can lead to a number of products. Oxidation and tautomerization produces 8oxoG. Alternatively, addition of superoxide at C5 and reduction results in a C5, C8 dihydroxy intermediate. For this species, the low energy pathway to 2Ih is N7-C8 ring opening followed by acyl migration. Ring opening occurs more easily at C8-N9 but leads to a higher energy analogue of 2Ih. Thus, the dominant pathway for the production of 2Ih depends on the nature of the reactive oxygen species and on the presence or absence of reducing agents.

Robust silver-mediated imidazolo-dC base pairs in metal DNA: dinuclear silver bridges with exceptional stability in double helices with parallel and antiparallel strand orientation

A new unprecedented metal-mediated base pair was designed that stabilizes reverse Watson-Crick DNA (parallel strand orientation, ps) as well as canonical Watson-Crick DNA (antiparallel strand orientation, aps). This base pair contains two imidazolo-dC units decorated with furan residues. Tm measurements and spectroscopic studies reveal that each silver-mediated furano-imidazolo-dC forms exceptionally stable duplexes with ps and aps chain orientation. This stability increase by a silver-mediated base pair is the highest reported so far for ps and aps DNA helices.

Guanine oxidation product 5-carboxamido-5-formamido-2-iminohydantoin induces mutations when bypassed by DNA polymerases and is a substrate for base excision repair

Guanine (G) is a target for oxidation by reactive oxygen species in DNA, RNA, and the nucleotide pool. Damage to DNA yields products with alternative properties toward DNA processing enzymes compared to those of the parent nucleotide. A new lesion, 5-carboxamido-5-formamido-2-iminohydantoin (2Ih), bearing a stereocenter in the base was recently identified from the oxidation of G. DNA polymerase and base excision repair processing of this new lesion has now been evaluated. Single nucleotide insertion opposite (S)-2Ih and (R)-2Ih in the template strand catalyzed by the DNA polymerases Klenow fragment exo(-), DPO4, and Hemo KlenTaq demonstrates these lesions to cause point mutations. Specifically, they promote 3-fold more G·C → C·G transversion mutations than G·C → T·A, and (S)-2Ih was 2-fold more blocking for polymerase bypass than (R)-2Ih. Both diastereomer lesions were found to be substrates for the DNA glycosylases NEIL1 and Fpg, and poorly excised by endonuclease III (Nth). The activity was independent of the base pair partner. Thermal melting, CD spectroscopy, and density functional theory geometric optimization calculations were conducted to provide insight into these polymerase and DNA glycosylase studies. These results identify that formation of the 2Ih lesions in a cell would be mutagenic in the event that they were not properly repaired.

5-Carboxamido-5-formamido-2-iminohydantoin, in Addition to 8-oxo-7,8-Dihydroguanine, Is the Major Product of the Iron-Fenton or X-ray Radiation-Induced Oxidation of Guanine under Aerobic Reducing Conditions in Nucleoside and DNA Contexts

Exogenously and endogenously produced reactive oxygen species attack the base and sugar moieties of DNA showing a preference for reaction at 2'-deoxyguanosine (dG) sites. In the present work, dG was oxidized by HO(•) via the Fe(II)-Fenton reaction or by X-ray radiolysis of water. The oxidized lesions observed include the 2'-deoxynucleosides of 8-oxo-7,8-dihydroguanine (dOG), spiroiminodihydantoin (dSp), 5-guanidinohydantoin (dGh), oxazolone (dZ), 5-carboxamido-5-formamido-2-iminohydantoin (d2Ih), 5',8-cyclo-2'-deoxyguanosine (cyclo-dG), and the free base guanine (Gua). Reactions conducted with ascorbate or N-acetylcysteine as a reductant under aerobic conditions identified d2Ih as the major lesion formed. Studies were conducted to identify the role of O2 and the reductant in product formation. From these studies, mechanisms are proposed to support d2Ih as a major oxidation product detected under aerobic conditions in the presence of the reductant. These nucleoside observations were then validated in oxidations of oligodeoxynucleotide and λ-DNA contexts that demonstrated high yields of d2Ih in tandem with dOG, dSp, and dGh. These results identify dG oxidation to d2Ih to occur in high yields leading to a hypothesis that d2Ih could be found from in cells stressed with HO(•). Further, the distorted ring structure of d2Ih likely causes this lesion to be highly mutagenic.

Computational studies of electronic circular dichroism spectra predict absolute configuration assignments for the guanine oxidation product 5-carboxamido-5-formamido-2-iminohydantoin

Oxidation of the guanine heterocycle by two electrons can yield the chiral product 5-carboxamido-5-formamido-2-iminohydantoin (2Ih). The 2Ih free base enantiomers were synthesized from 2'-deoxyguanosine oxidized with a Cu(II)/H₂O₂ oxidant system followed by hydrolysis of the N-glycosidic bond. These isomers were each studied by electronic circular dichroism spectroscopy for determination of their absolute configurations. Time-dependent density functional theory calculations of the expected spectra were completed in both the gas phase and with solvent modeling in order to interpret the experimental spectra and provide the absolute configuration assignments.

Rates of chemical cleavage of DNA and RNA oligomers containing guanine oxidation products

The nucleobase guanine in DNA (dG) and RNA (rG) has the lowest standard reduction potential of the bases, rendering it a major site of oxidative damage in these polymers. Mapping the sites at which oxidation occurs in an oligomer via chemical reagents utilizes hot piperidine for cleaving oxidized DNA and aniline (pH 4.5) for cleaving oxidized RNA. In the present studies, a series of time-dependent cleavages of DNA and RNA strands containing various guanine lesions were examined to determine the strand scission rate constants. The guanine base lesions 8-oxo-7,8-dihydroguanine (OG), spiroiminodihydantoin (Sp), 5-guanidinohydantoin (Gh), 2,2,4-triamino-2H-oxazol-5-one (Z), and 5-carboxamido-5-formamido-2-iminohydantoin (2Ih) were evaluated in piperidine-treated DNA and aniline-treated RNA. These data identified wide variability in the chemical lability of the lesions studied in both DNA and RNA. Further, the rate constants for cleaving lesions in RNA were generally found to be significantly smaller than for lesions in DNA. The OG nucleotides were poorly cleaved in DNA and RNA; Sp nucleotides were slowly cleaved in DNA and did not cleave significantly in RNA; Gh and Z nucleotides cleaved in both DNA and RNA at intermediate rates; and 2Ih oligonucleotides cleaved relatively quickly in both DNA and RNA. The data are compared and contrasted with respect to future experimental design.

Specific recognition of guanines in non-duplex regions of nucleic acids with potassium tungstate and hydrogen peroxide

Structural features of nucleic acids have become an integral part of current biomedical research. Highly selective and readily performed methods with little toxicity that target guanosines in non-duplex nucleic acids are needed, which led us to search for an effective agent for guanosine sequencing. Treatment of DNA or RNA with potassium tungstate and hydrogen peroxide produced damaged guanosines in DNA or RNA sequences. The damaged guanosines in non-duplex DNA could be cleaved by hot piperidine. Similarly, damaged guanosines in non-duplex RNA could be cleaved by aniline acetate. We could identify structural features of nucleic acid using this strategy instead of dimethyl sulphate and Ribonuclease T1.

Endonuclease and Exonuclease Activities on Oligodeoxynucleotides Containing Spiroiminodihydantoin Depend on the Sequence Context and the Lesion Stereochemistry

8-Oxo-7,8-dihydro-2'-deoxyguanosine (dOG), a well-studied oxidation product of 2'-deoxyguanosine (dG), is prone to facile further oxidation forming spiroiminodihydantoin 2'-deoxyribonucleoside (dSp) in the nucleotide pool and in single-stranded oligodeoxynucleotides (ODNs). Many methods for quantification of damaged lesions in the genome rely on digestion of DNA with exonucleases or endonucleases and dephosphorylation followed by LC-MS analysis of the resulting nucleosides. In this study, enzymatic hydrolysis of dSp-containing ODNs was investigated with snake venom phosphodiesterase (SVPD), spleen phosphodiesterase (SPD) and nuclease P1. SVPD led to formation of a dinucleotide, 5'-d(Np[Sp])-3' (N = any nucleotide) that included the undamaged nucleotide on the 5' side of dSp as the final product. This dinucleotide was a substrate for both SPD and nuclease P1. A kinetic study of the activity of SPD and nuclease P1 showed a sequence dependence on the nucleotide 5' to the lesion with rates in the order dG>dA>dT>dC. In addition, the two diastereomers of dSp underwent digestion at significantly different rates with dSp1>dSp2; nuclease P1 hydrolyzed the 5'-d(Np[Sp1])-3' dinucleotide two- to six-fold faster than the corresponding 5'-d(Np[Sp2])-3', while for SPD the difference was two-fold. These rates are chemically reasoned based on dSp diastereomer differences in the syn vs. anti glycosidic bond orientation. A method for the complete digestion of dSp-containing ODNs is also outlined based on treatment with nuclease P1 and SVPD. These findings have significant impact on the development of methods to detect dSp levels in cellular DNA.

G-quadruplex folds of the human telomere sequence alter the site reactivity and reaction pathway of guanine oxidation compared to duplex DNA

Telomere shortening occurs during oxidative and inflammatory stress with guanine (G) as the major site of damage. In this work, a comprehensive profile of the sites of oxidation and structures of products observed from G-quadruplex and duplex structures of the human telomere sequence was studied in the G-quadruplex folds (hybrid (K(+)), basket (Na(+)), and propeller (K(+) + 50% CH3CN)) resulting from the sequence 5'-(TAGGGT)4T-3' and in an appropriate duplex containing one telomere repeat. Oxidations with four oxidant systems consisting of riboflavin photosensitization, carbonate radical generation, singlet oxygen, and the copper Fenton-like reaction were analyzed under conditions of low product conversion to determine relative reactivity. The one-electron oxidants damaged the 5'-G in G-quadruplexes leading to spiroiminodihydantoin (Sp) and 2,2,4-triamino-2H-oxazol-5-one (Z) as major products as well as 8-oxo-7,8-dihydroguanine (OG) and 5-guanidinohydantoin (Gh) in low relative yields, while oxidation in the duplex context produced damage at the 5'- and middle-Gs of GGG sequences and resulted in Gh being the major product. Addition of the reductant N-acetylcysteine (NAC) to the reaction did not alter the riboflavin-mediated damage sites but decreased Z by 2-fold and increased OG by 5-fold, while not altering the hydantoin ratio. However, NAC completely quenched the CO3(•-) reactions. Singlet oxygen oxidations of the G-quadruplex showed reactivity at all Gs on the exterior faces of G-quartets and furnished the product Sp, while no oxidation was observed in the duplex context under these conditions, and addition of NAC had no effect. Because a long telomere sequence would have higher-order structures of G-quadruplexes, studies were also conducted with 5'-(TAGGGT)8-T-3', and it provided oxidation profiles similar to those of the single G-quadruplex. Lastly, Cu(II)/H2O2-mediated oxidations were found to be indiscriminate in the damage patterns, and 5-carboxamido-5-formamido-2-iminohydantoin (2Ih) was found to be a major duplex product, while nearly equal yields of 2Ih and Sp were observed in G-quadruplex contexts. These findings indicate that the nature of the secondary structure of folded DNA greatly alters both the reactivity of G toward oxidative stress as well as the product outcome and suggest that recognition of damage in telomeric sequences by repair enzymes may be profoundly different from that of B-form duplex DNA.

A single nuclease-resistant linkage in DNA as a versatile tool for the characterization of DNA lesions: application to the guanine oxidative lesion "G+34" generated by metalloporphyrin/KHSO(5) reagent

The oxidation of an oligonucleotide containing a single nuclease-resistant phosphodiester link, a stereoisomerically pure methylphosphonate, by manganese (Mn-TMPyP) or iron (Fe-TMPyP) porphyrin associated to KHSO(5) allowed the isolation and characterization of a guanine lesion corresponding to an increase of mass of 34 amu as compared to guanine ("G+34"), namely, 5-carboxamido-5-formamido-2-iminohydantoin. Enzymatic digestion of the damaged oligonucleotide afforded, apart from the undamaged nucleotide monomer pool, a unique dinucleotide doubly modified with a methylphosphonate and an oxidized guanine base that is suitable for NMR analysis. The method can be applied to the study of any DNA lesion. More importantly, the method can be extended to the analysis of DNA damage in a sequence context. Any preselected residue in a DNA sequence may be individually analyzed by the easy introduction of a single nuclease-resistant link at the 3'- or 5'-position.

Lifetimes and reaction pathways of guanine radical cations and neutral guanine radicals in an oligonucleotide in aqueous solutions

The exposure of guanine in the oligonucleotide 5'-d(TCGCT) to one-electron oxidants leads initially to the formation of the guanine radical cation G(•+), its deptotonation product G(-H)(•), and, ultimately, various two- and four-electron oxidation products via pathways that depend on the oxidants and reaction conditions. We utilized single or successive multiple laser pulses (308 nm, 1 Hz rate) to generate the oxidants CO(3)(•-) and SO(4)(•-) (via the photolysis of S(2)O(8)(2-) in aqueous solutions in the presence and absence of bicarbonate, respectively) at concentrations/pulse that were ∼20-fold lower than the concentration of 5'-d(TCGCT). Time-resolved absorption spectroscopy measurements following single-pulse excitation show that the G(•+) radical (pK(a) = 3.9) can be observed only at low pH and is hydrated within 3 ms at pH 2.5, thus forming the two-electron oxidation product 8-oxo-7,8-dihydroguanosine (8-oxoG). At neutral pH, and single pulse excitation, the principal reactive intermediate is G(-H)(•), which, at best, reacts only slowly with H(2)O and lives for ∼70 ms in the absence of oxidants/other radicals to form base sequence-dependent intrastrand cross-links via the nucleophilic addition of N3-thymidine to C8-guanine (5'-G*CT* and 5'-T*CG*). Alternatively, G(-H)(•) can be oxidized further by reaction with CO(3)(•-), generating the two-electron oxidation products 8-oxoG (C8 addition) and 5-carboxamido-5-formamido-2-iminohydantoin (2Ih, by C5 addition). The four-electron oxidation products, guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp), appear only after a second (or more) laser pulse. The levels of all products, except 8-oxoG, which remains at a low constant value, increase with the number of laser pulses.

Oxidative DNA damage mediated by transition metal ions and their complexes

DNA damage by redox-active metal complexes depends on the interaction of the metal complex with DNA together with the mechanism of oxygen activation. Weak interaction, tight binding, and direct involvement of DNA in the coordination sphere of the metal are described. Metal complexes acting through the production of diffusing radicals and metal complexes oxidizing DNA by metal-centered active species are compared. Metal complexes able to form high-valent metal-oxo species in close contact with DNA and perform DNA oxidation in a way reminiscent of enzymatic chemistry are the most elegant systems.

Characterization of 2'-deoxyguanosine oxidation products observed in the Fenton-like system Cu(II)/H2O2/reductant in nucleoside and oligodeoxynucleotide contexts

Reactive oxygen species attack both base and sugar moieties in DNA with a preference among the bases for reaction at guanine. In the present study, 2'-deoxyguanosine (dG) was oxidized by a copper-mediated Fenton reaction with the reductants ascorbate or N-acetyl-cysteine, yielding oxidation on both the base and the sugar. The primary oxidized lesions observed in these studies include the 2'-deoxyribonucleosides of 8-oxo-7,8-dihydroguanosine (dOG), spiroiminodihydantoin (dSp), guanidinohydantoin (dGh), oxazolone (dZ), and 5-carboxamido-5-formamido-2-iminohydantoin (d2Ih), as well as the free base guanine. d2Ih was the major product observed in the nucleoside, single- and double-stranded oligodeoxynucleotide contexts and is proposed to arise from oxidation at C5 of guanine. Product distribution studies provide insight into the role of the reductant in partitioning of dG base oxidation along the C5 and C8 pathways.