Kinetics and mechanism of carbon-8 methylation of purine bases and nucleosides by methyl radical

Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides

Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.

Copper-catalyzed methylative difunctionalization of alkenes

Trifluoromethylative difunctionalization and hydrofunctionalization of unactivated alkenes have been developed into powerful synthetic methodologies. On the other hand, methylative difunctionalization of olefins remains an unexplored research field. We report in this paper the Cu-catalyzed alkoxy methylation, azido methylation of alkenes using dicumyl peroxide (DCP), and di-tert-butyl peroxide (DTBP) as methyl sources. Using functionalized alkenes bearing a tethered nucleophile (alcohol, carboxylic acid, and sulfonamide), methylative cycloetherification, lactonization, and cycloamination processes are subsequently developed for the construction of important heterocycles such as 2,2-disubstituted tetrahydrofurans, tetrahydropyrans, γ-lactones, and pyrrolidines with concurrent generation of a quaternary carbon center. The results of control experiments suggest that the 1,2-alkoxy methylation of alkenes goes through a radical-cation crossover mechanism, whereas the 1,2-azido methylation proceeds via a radical addition and Cu-mediated azide transfer process.

While the trifluoromethylative difunctionalization of unactivated alkenes has been largely explored, methylative difunctionalization remains underinvestigated. Here, the authors report copper-catalyzed alkoxy- and azido-methylation reactions of alkenes leading to important synthetic building blocks and valuable O- and N-heterocycles.

Late-stage functionalization of biologically active heterocycles through photoredox catalysis

The direct CH functionalization of heterocycles has become an increasingly valuable tool in modern drug discovery. However, the introduction of small alkyl groups, such as methyl, by this method has not been realized in the context of complex molecule synthesis since existing methods rely on the use of strong oxidants and elevated temperatures to generate the requisite radical species. Herein, we report the use of stable organic peroxides activated by visible-light photoredox catalysis to achieve the direct methyl-, ethyl-, and cyclopropylation of a variety of biologically active heterocycles. The simple protocol, mild reaction conditions, and unique tolerability of this method make it an important tool for drug discovery.

Fluoroquinolones as potential photochemotherapeutic agents: covalent addition to guanosine monophosphate

The triplet aryl cation photochemically generated from fluoroquinolones bearing a fluoro atom at position 8 attacks guanosine monophosphate (k(r) > 10(9) M(-1)s(-1)) and forms covalent adducts. The reaction is a model for the implementation of oxygen-independent photochemotherapy.

Methylation of 2'-deoxyguanosine by a free radical mechanism

The mechanistic aspects of the methylation of guanine in DNA initiated by methyl radicals that are derived from the metabolic oxidation of some chemical carcinogens remain poorly understood. In this work, we investigated the kinetics and the formation of methylated guanine products by two methods: (i) the combination of *CH3 radicals and guanine neutral radicals, G(-H)*, and (ii) the direct addition of *CH3 radicals to guanine bases. The simultaneous generation of *CH3 and dG(-H)* radicals was triggered by the competitive one-electron oxidation of dimethyl sulfoxide (DMSO) and 2'-deoxyguanosine (dG) by photochemically generated sulfate radicals in deoxygenated aqueous buffer solutions (pH 7.5). The photolysis of methylcob(III)alamin to form *CH3 radicals was used to investigate the direct addition of these radicals to guanine bases. The major end products of the radical combination reactions are the 8-methyl-dG and N2-methyl-dG products formed in a ratio of 1:0.7. In contrast, the methylation of dG by *CH3 radicals generates mostly the 8-methyl-dG adduct and only minor quantities of N2-methyl-dG (1:0.13 ratio). The methylation of the self-complementary 5'-d(AACGCGAATTCGCGTT) duplexes was achieved by the selective oxidation of the guanines with carbonate radical anions in the presence of DMSO as the precursor of *CH3 radicals. The methyl-G lesions formed were excised by the enzymatic digestion and identified by LC-MS/MS methods using uniformly 15N-labeled 8-methyl-dG and N2-methyl-dG adducts as internal standards. The ratios of 8-methyl-G/N2-methyl-G lesions derived from the combination of methyl radicals with G(-H)* radicals positioned in double-stranded DNA or that with the free nucleoside dG(-H)* radicals were found to be similar. Utilizing the photochemical method and dipropyl or dibutyl sulfoxides as sources of alkyl radicals, the corresponding 8-alkyl-dG and N2-alkyl-dG adducts were also generated in ratios similar to those obtained with DMSO.

Reactive Oxygen Species, Isotope Effect, Essential Nutrients, and Enhanced Longevity

A method is proposed that has the potential to lessen detrimental damages caused by reactive oxygen species (ROS) to proteins, nucleic acids, lipids, and other components in living cells. Typically, ROS oxidize substrates by a mechanism involving hydrogen abstraction in a rate-limiting step. The sites within these (bio)molecules susceptible to oxidation by ROS can thus be "protected " using heavier isotopes such as (2)H (D, deuterium) and (13)C (carbon-13). Ingestion of isotopically reinforced building blocks such as amino acids, lipids and components of nucleic acids and their subsequent incorporation into macromolecules would make these more stable to ROS courtesy of an isotope effect. The implications may include enhanced longevity and increased resistance to cancer and age-related diseases.

Chemical and photochemical generated carbon-centered radical intermediate and its reaction with desoxyribonucleic acid

The possible action of carbon-centered radicals in promoting damage to DNA is explored by generation of the 2-phenylethyl radical. The radical is generated during oxidation of phenelzine (2-phenylethyl hydrazine) by ferricyanide, as well as optically from phenylpropionic acid. Covalent binding of the 2-phenylethyl radical to DNA is suggested by studies with the plasmid pBR 322 DNA. Other sensitive techniques used to study DNA damage were the interaction with formaldehyde at 60 degrees C and the fluorescence of DNA-Tb(III) and DNA-DAPI complexes. Theoretical MNDO calculations indicated a preferential attack at position 8 of the guanine residues. This study shows that the 2-phenylethyl radical is able to induce primary effects on nucleic acid structure, leading to alkylated products, especially at purine rings.

Alkylation and cleavage of DNA by carbon-centered radical metabolites

Although carbon-centered radicals are formed during the metabolism of several genotoxic compounds, they have received little attention as DNA damaging agents. Carbon-centered radicals, however, can both cleave the DNA backbone and alkylate DNA bases, as has been demonstrated to occur in chemical and biochemical systems. Also, in vivo DNA alkylation by methyl radicals has been evidenced by isolation of C8-methylguanine in hydrolysates of DNA from rats administered 1,2-dimethylhydrazine. While most of the studies related to DNA damage by free radicals have been focused on oxyradicals, further studies on DNA alterations promoted by carbon-centered radicals may be necessary to elucidate the mechanisms of action of chemical mutagens and carcinogens.

Chemical oxidation and metabolism of N-methyl-N-formylhydrazine. Evidence for diazenium and radical intermediates

N-Methyl N-formlhydrazine (1), a component of the mushroom Gyromitra esculenta, is a carcinogen. Its mode of action, however, is poorly understood. To determine the intermediates that may form during the metabolism of 1, we examined its oxidative chemistry, identified the products and inferred the intermediates on the basis of these products. The incubation of 1 with rat liver microsomes was also studied and the metabolites determined and quantified. Both the chemical and the microsome-mediated oxidation of 1 yielded formaldehyde and acetaldehyde. The formation of acetaldehyde requires (i) the oxidation of 1 to a diazenium ion (I) or diazene (II) and (ii) fragmentation of I/II to formyl and methyl radicals. It is suggested that these radical intermediates may be important in understanding and elucidating carcinogenesis by 1.

DNA alterations induced by the carbon-centered radical derived from the oxidation of 2-phenylethylhydrazine

The possible significance of carbon-centered radicals in hydrazine-induced carcinogenesis is explored by studies of the interaction between the 2-phenylethyl radical and DNA. The radical is efficiently generated during oxidation of phenelzine (2-phenylethylhydrazine) promoted by oxyhemoglobin or ferricyanide, as demonstrated by spin-trapping experiments and analysis of the reaction products. In the ferricyanide promoted oxidation, ethylbenzene formation accounts for about 40% of the initial drug concentration, from 5 to 100 mM phenelzine. By contrast, product formation in the presence of oxyhemoglobin depends on the enzyme concentration due to the fact that the prosthetic heme is destroyed during catalytic turnover. Covalent binding of the 2-phenylethyl radical to oxyhemoglobin is demonstrated by experiments with 2-[3H]phenelzine, where tritium incorporation to the protein is inhibited by the spin-trap, alpha-(4-pyridyl-1-oxide)-N-tert-butylnitrone. The 2-phenylethyl radical is also able to alkylate DNA as suggested by electrophoretic studies with plasmid DNA, and proved by experiments with 2-[3H]-phenelzine. The carbon-centered radical has a preference for attacking guanine residues as demonstrated by the use of sequencing techniques with 32P-DNA probes. The results indicate that the 2-phenylethyl radical is an important product of phenelzine oxidation and that this species can directly damage protein and DNA.

Why is the hydroxyl radical the only radical that commonly adds to DNA? Hypothesis: it has a rare combination of high electrophilicity, high thermochemical reactivity, and a mode of production that can occur near DNA

Free radicals do not commonly add to nucleotides in DNA, despite the fact that radicals are produced in all aerobically metabolizing cells. Why is this? For oxy-radicals, the ratio of the rate constant for addition to double bonds divided by that for H-abstraction from good H-donors parallels the electrophilicity of the radical, and among oxy-radicals the hydroxyl radical is the most electrophilic, with an unusually high ratio of Kad/kH. The hydroxyl radical also is very reactive in H-atom abstraction reactions, with a large absolute value of kH. However, the hydroxyl radical's high reactivity makes it unselective and relatively nondiscriminating between H-abstraction from a sugar moiety in DNA and penetration to, and reaction with, a base. Oxy-radicals such as alkoxyl and peroxyl radicals do not have as high electrophilicity or as high reactivity. Interestingly, carbon-centered radicals (such as the methyl radical) also can both add to double bonds and abstract H-atoms, but carbon-centered radicals are not commonly observed to add to DNA bases. However, they cannot be generated near DNA in vivo. In contrast, hydroxyl radical generating systems appear to complex with DNA and produce the hydroxyl radical in the immediate vicinity of the DNA, producing a type of DNA damage that is called site specific. Thus, addition of a radical to a DNA base may require all three features possessed by the hydroxyl radical: high electrophilicity, high thermokinetic reactivity, and a mechanism for production near DNA.