Independent Generation and Reactivity of 2‘-Deoxyurid-1‘-yl

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.

Targeted DNA oxidation and trajectory of radical DNA using DFT based QM/MM dynamics

Molecular insight into electronic rearrangements and structural trajectories arising from oxidative damages to DNA backbone is of crucial importance in understanding the effect of ionizing radiation, developing DNA biosensors and designing effective DNA cleaving molecules. Employing a Density Functional Theory based multi-scale Quantum-Mechanical-Molecular-Mechanical (QM/MM) simulation and a suitable partitioning of the Hamiltonian on solvated nucleotide, and single-, and double-stranded DNA, we mimic hydrogen transfer reactions from the backbone by OH radicals and report structural trajectories arising from on-the-fly electronic charge- and spin-density redistribution in these three different structural topologies of DNA. Trajectories reveal that H4′ abstraction can disrupt the deoxyribose moiety through the formation of C4′=O4′ ketone and a π-bond with base at C1′-N9 in a nucleotide versus only partial ketone formation in single- and double-stranded DNA, where the orientation of the base is topologically restrained. However, H5′ abstraction can lead DNA cleavage at 5′ end through the formation of C5′=O5′ ketone and breakage of P-O5′ bond. Results demonstrate that structural damages from oxidative reactions are restrained by base stacking and base-pair hydrogen bonding. The methodology can be suitably used to study targeted DNA and RNA damages from radicals and radiomimetic drugs to design DNA cleaving molecules for chemotherapy.

Reactivity of Nucleic Acid Radicals

Nucleic acid oxidation plays a vital role in the etiology and treatment of diseases, as well as aging. Reagents that oxidize nucleic acids are also useful probes of the biopolymers' structure and folding. Radiation scientists have contributed greatly to our understanding of nucleic acid oxidation using a variety of techniques. During the past two decades organic chemists have applied the tools of synthetic and mechanistic chemistry to independently generate and study the reactive intermediates produced by ionizing radiation and other nucleic acid damaging agents. This approach has facilitated resolving mechanistic controversies and lead to the discovery of new reactive processes.

In vivo detection and replication studies of α-anomeric lesions of 2'-deoxyribonucleosides

DNA damage, arising from endogenous metabolism or exposure to environmental agents, may perturb the transmission of genetic information by blocking DNA replication and/or inducing mutations, which contribute to the development of cancer and likely other human diseases. Hydroxyl radical attack on the C1′, C3′ and C4′ of 2-deoxyribose can give rise to epimeric 2-deoxyribose lesions, for which the in vivo occurrence and biological consequences remain largely unexplored. Through independent chemical syntheses of all three epimeric lesions of 2′-deoxyguanosine (dG) and liquid chromatography-tandem mass spectrometry analysis, we demonstrated unambiguously the presence of substantial levels of the α-anomer of dG (α-dG) in calf thymus DNA and in DNA isolated from mouse pancreatic tissues. We further assessed quantitatively the impact of all four α-dN lesions on DNA replication in Escherichia coli by employing a shuttle-vector method. We found that, without SOS induction, all α-dN lesions except α-dA strongly blocked DNA replication and, while replication across α-dA was error-free, replicative bypass of α-dC and α-dG yielded mainly C→A and G→A mutations. In addition, SOS induction could lead to markedly elevated bypass efficiencies for the four α-dN lesions, abolished the G→A mutation for α-dG, pronouncedly reduced the C→A mutation for α-dC and triggered T→A mutation for α-dT. The preferential misincorporation of dTMP opposite the α-dNs could be attributed to the unique base-pairing properties of the nucleobases elicited by the inversion of the configuration of the N-glycosidic linkage. Our results also revealed that Pol V played a major role in bypassing α-dC, α-dG and α-dT in vivo. The abundance of α-dG in mammalian tissue and the impact of the α-dNs on DNA replication demonstrate for the first time the biological significance of this family of DNA lesions.

Independent generation and reactivity of uridin-2'-yl radical

The uridin-2'-yl radical (1) has been proposed as an intermediate during RNA oxidation. However, its reactivity has not been thoroughly studied due to the complex conditions under which it is typically generated. The uridin-2'-yl radical was independently generated from a benzyl ketone (2a) via Norrish type I photocleavage upon irradiation at λmax = 350 nm. Dioxygen and β-mercaptoethanol are unable to compete with loss of uracil from 1 in phosphate buffer. Thiol trapping competes with uracil fragmentation in less polar solvent conditions. This is ascribed mostly to a reduction in the rate constant for uracil elimination in the less polar solvent. Hydrogen atom transfer to 1 from β-mercaptoethanol occurs exclusively from the α-face to produce arabinouridine. Mass balances range from 72 to 95%. Furthermore, the synthesis of 2a is amenable to formation of the requisite phosphoramidite for solid-phase oligonucleotide synthesis. This and the fidelity with which the urdin-2'-yl radical is generated from 2a suggest that this precursor should be useful for studying the radical's reactivity in synthetic oligonucleotides.

Epimeric 2-deoxyribose lesions: Products from the improper chemical repair of 2-deoxyribose radicals

Genomic integrity is constantly challenged by DNA damaging agents such as reactive oxygen species (ROS). Consequently, DNA damage can compromise the fidelity and efficiency of essential DNA metabolic processes, including replication and transcription, which may contribute significantly to the etiology of many human diseases. Here, we review one family of DNA lesions, the epimeric 2-deoxyribose lesions, which arise from the improper chemical repair of the 2-deoxyribose radicals. Unlike most other DNA lesions, the epimeric 2-deoxyribose lesions are indistinguishable from their corresponding unmodified nucleosides in both molecular mass and chemical reactivity. We placed our emphasis of discussion on the formation of these lesions, their impact on the structure and stability of duplex DNA, their biological consequences, their potential therapeutic relevance, and future research directions about these modified nucleosides.

Synthesis and analysis of oligonucleotides containing abasic site analogues

DNA damage results in the formation of abasic sites from the formal hydrolysis of the glycosidic bond (AP) and several oxidized abasic lesions. Previous studies on AP sites revealed that DNA polymerases preferentially incorporated dA opposite them in approximately 80% of the replication events in Escherichia coli. These results were consistent with the hypothesis that the AP sites are noninstructive lesions due to the absence of a Watson-Crick base whose bypass adheres to the "A-rule." Recent replication studies of the oxidized abasic lesion, 2-deoxyribonolactone (L), revealed that DNA polymerase(s) does not apply the A-rule when bypassing it and incorporates large amounts of dG opposite L. These studies suggested that abasic sites such as L do direct polymerases to selectively incorporate nucleotides opposite them. However, it was not possible to determine the structural basis for this molecular recognition from these experiments. A group of oligonucleotides containing analogues of the AP and L lesions were synthesized and characterized as probes to gain insight into the structural basis for the distinct effect of 2-deoxyribonolactone on replication. These molecules will be useful tools for studying replication in cells and in vitro.

DNA strand damage product analysis provides evidence that the tumor cell-specific cytotoxin tirapazamine produces hydroxyl radical and acts as a surrogate for O(2)

The compound 3-amino-1,2,4-benzotriazine 1,4-dioxide (tirapazamine, TPZ) is a clinically promising anticancer agent that selectively kills the oxygen-poor (hypoxic) cells found in solid tumors. It has long been known that, under hypoxic conditions, TPZ causes DNA strand damage that is initiated by the abstraction of hydrogen atoms from the deoxyribose phosphate backbone of duplex DNA, but exact chemical mechanisms underlying this process remain unclear. Here we describe detailed characterization of sugar-derived products arising from TPZ-mediated strand damage. We find that the action of TPZ on duplex DNA under hypoxic conditions generates 5-methylene-2-furanone (6), oligonucleotide 3'-phosphoglycolates (7), malondialdehyde equivalents (8 or 9), and furfural (10). These results provide evidence that TPZ-mediated strand damage arises via hydrogen atom abstraction from both the most hindered (C1') and least hindered (C4' and C5') positions of the deoxyribose sugars in the double helix. The products observed are identical to those produced by hydroxyl radical. Additional experiments were conducted to better understand the chemical pathways by which TPZ generates the observed DNA-damage products. Consistent with previous work showing that TPZ can substitute for molecular oxygen in DNA damage reactions, it is found that, under anaerobic conditions, reaction of TPZ with a discrete, photogenerated C1'-radical in a DNA 2'-oligodeoxynucleotide cleanly generates the 2-deoxyribonolactone lesion (5) that serves as the precursor to 5-methylene-2-furanone (6). Overall, the results provide insight regarding the chemical structure of the DNA lesions that confront cellular repair, transcription, and replication machinery following exposure to TPZ and offer new information relevant to the chemical mechanisms underlying TPZ-mediated strand cleavage.

Elucidating DNA damage and repair processes by independently generating reactive and metastable intermediates

DNA damage is a double-edged sword. The modifications produced in the biopolymer are associated with aging, and give rise to a variety of diseases, including cancer. DNA is also the target of anti-tumor agents and the most generally used nonsurgical treatment of cancer, ionizing radiation. Agents that damage DNA produce a variety of radicals. Elucidating the chemistry of individual DNA radicals is challenging due to the availability of multiple reactive pathways and complexities inherent with carrying out mechanistic studies on a heterogeneous polymer. The ability to independently generate radicals and their metastable products at defined sites in DNA has greatly facilitated understanding this biologically important chemistry.

Automated synthesis, characterization, and structural analysis of oligonucleotide C-3'-radical precursors

C-3'-Acyl-3'-xylothymidine-containing oligonucleotides have been designed and synthesized for their use as radical precursors in the study of oxidative DNA damage initiated by a C-3'-radical. These oligomers were efficiently obtained using automated DNA synthesis techniques based on H-phosphonate chemistry. CD spectra and melting curves of the synthesized oligonucleotides were compared to those of their unmodified and xylomodified counterparts. The conformational analysis and hybridization studies indicate that the combination of the photolabile acyl group and the inversion of configuration at the sugar has no profound effect on the overall conformation of C-3'-acyl-2'-deoxy-3'-xylonucleotides as compared to their natural analogues. These systems should provide excellent tools for the elucidation of DNA damage processes.

Independent generation of the 5-hydroxy-5,6-dihydrothymidin-6-yl radical and its reactivity in dinucleoside monophosphates

Hydroxyl radical is a major reactive oxygen species produced by gamma-radiolysis of water or Fenton reaction. It attacks pyrimidine bases and gives the 5-hydroxy-5,6-dihydropyrimidin-6-yl radical as the major product. Here we report the synthesis of all four stereoisomers of 5-hydroxy-6-phenylthio-5,6-dihydrothymidine (T*), which, upon 254 nm UV irradiation, give rise to the 5-hydroxy-5,6-dihydrothymidin-6-yl radical (I). We also incorporated the photolabile radical precursors into dinucleoside monophosphates d(GT*) and d(TT*) and characterized major products resulting from the 254-nm irradiation of these dinucleoside monophosphates. Our results showed that, under anaerobic conditions, the most abundant product emanating from the 254-nm irradiation of d(GT*) and d(TT*) is an abasic site lesion. Products with the thymine portion being modified to thymine glycol and 5-hydroxy-5,6-dihydrothymine were also observed. In addition, we demonstrated that radical I can attack the C8 carbon atom of its 5' neighboring guanine and give rise to a novel cross-link lesion. Moreover, LC-MS/MS results showed that gamma-radiation of d(GT) under anaerobic condition yielded the same type of cross-link lesions.

Generation of a C-3'-thymidinyl radical in single-stranded oligonucleotides under anaerobic conditions

[reaction: see text] A C-3'-thymidinyl radical has been photochemically generated site-specifically in DNA oligonucleotides. A nucleoside H-phosphonate bearing a C-3' acetyl group was incorporated into DNA oligomers using a hand-coupling technique. When nucleotides containing the modified monomer were photolyzed (> or =320 nm) in the presence of a hydrogen atom donor, reduction products were detected by RP-HPLC and MALDI-ToF MS analysis.

Independent generation and characterization of a C2'-oxidized abasic site in chemically synthesized oligonucleotides

Abasic lesions, which are formed endogenously and as a consequence of exogenous agents, are lethal and mutagenic. Hydrogen atom abstraction from C2' in DNA under aerobic conditions produces an oxidized abasic lesion (C2-AP), along with other forms of DNA damage. The effects of C2-AP on DNA structure and function are not well understood. A method for the solid-phase synthesis of oligonucleotides containing C2-AP lesions is reported. The lesion is released via periodate oxidation of a triol containing a vicinal diol. The triol is introduced via a phosphoramidite that is compatible with standard oligonucleotide synthesis and deprotection conditions. UV-melting studies indicate that the C2-AP lesion has a comparable effect on the thermal stability of duplex DNA as other abasic lesions. The C2-AP lesion is rapidly cleaved by piperidine at 90 degrees C. However, cleavage by NaOH (0.1 M, 37 degrees C) shows that C2-AP is considerably less labile (t(1/2) = 3.3 +/- 0.2 h) than other abasic lesions.

Repair of oxidized abasic sites by exonuclease III, endonuclease IV, and endonuclease III

2-Deoxyribonolactone (L) and the C4'-oxidized abasic site (C4-AP) are produced by a variety of DNA-damaging agents. If not repaired, these lesions can be mutagenic. Exonuclease III and endonuclease IV are the major enzymes in E. coli responsible for 5'-incision of abasic sites (APs), the first steps in AP repair. Endonuclease III efficiently excises AP lesions via intermediate Schiff-base formation. Incision of L and C4-AP lesions by exonuclease III and endonuclease IV was determined under steady-state conditions using oligonucleotide duplexes containing the lesions at defined sites. An abasic lesion (AP) in an otherwise identical DNA sequence was incised by exonuclease III or endonuclease IV approximately 6-fold more efficiently than either of the oxidized abasic sites (L, C4-AP). Endonuclease IV incision efficiency of 2-deoxyribonolactone or C4-AP was independent of whether the lesion was opposite dA or dG. 2-Deoxyribonolactone is known to cross-link to endonuclease III (Hashimoto, M. (2001) J. Am. Chem. Soc. 123, 3161.). However, the C4-AP lesion is efficiently excised by endonuclease III. Oxidized abasic site repair by endonuclease IV and endonuclease III (C4-AP only) is approximately 100-fold less efficient than repair by exonuclease III. These results suggest that the first step of C4-AP and L oxidized abasic site repair will be the same as that of regular AP lesions in E. coli.

Mutagenic effects of 2-deoxyribonolactone in Escherichia coli. An abasic lesion that disobeys the A-rule

Abasic sites are often referred to as noninstructive lesions. The C1'-oxidized abasic site (2-deoxyribonolactone, L) is produced by several DNA damaging agents, including gamma-radiolysis and the neocarzinostatin chromophore (NCS). The effects of a C1'-oxidized abasic site incorporated at a defined site in single-stranded plasmid were examined in SOS polymerase-proficient and -deficient Escherichia coli. For comparison, experiments utilizing plasmids containing an abasic site (AP) were carried out side by side. In contrast to plasmid containing AP, dA and dG were incorporated most often when plasmid containing L was replicated. The ratio of dG:dA incorporation depended upon local sequence and varied from 0.9 to 2.2. High levels of translesion incorporation of dA are consistent with previous observations that treatment of DNA with the neocarzinostatin chromophore resulted in large amounts of G.C --> A.T transitions [Povirk and Goldberg (1986) Nucleic Acids Res. 14, 1417] and support the proposal that L is the source of these mutations. Both abasic lesions were 100% lethal in triple knockout cells lacking pol II, pol IV, and pol V. Analysis of translesion synthesis in repair-deficient cells revealed that pol V played a significant role in replication of L and AP. Significant levels of -1 frameshifts were formed in 5'-d(CL) sequences in the presence of pol V and were the exclusive product in pol V-deficient cells. Frameshift products were not formed when the nucleotide on the 5'-side of L was either dT or dG. Deleting pol II or pol IV had only modest effects on replication of L-containing plasmid but significantly decreased the amount of -1 frameshift product formed from an AP lesion. Experiments carried out side by side using otherwise identical plasmids containing an AP site illustrate the distinct properties of these two abasic lesions and that neither should be thought of as noninstructive.

Modeling deoxyribose radicals by neutralization-reionization mass spectrometry. Part 2. Preparation, dissociations, and energetics of 3-hydroxyoxolan-3-yl radical and cation

The title radical (1) is generated in the gas-phase by collisional neutralization of carbonyl-protonated oxolan-3-one. A 1.5% fraction of 1 does not dissociate and is detected following reionization as survivor ions. The major dissociation of 1 (approximately 56%) occurs as loss of the hydroxyl H atom forming oxolan-3-one (2). The competing ring cleavages by O[bond]C-2 and C-4[bond]C-5 bond dissociations combined account for approximately 42% of dissociation and result in the formation of formaldehyde and 2-hydroxyallyl radical. Additional ring-cleavage dissociations of 1 resulting in the formation of C(2)H(3)O and C(2)H(4)O cannot be explained as occurring competitively on the doublet ground (X) electronic state of 1, but are energetically accessible from the A and higher electronic states accessed by vertical electron transfer. Exothermic protonation of 2 also produces 3-oxo-(1H)-oxolanium cation (3(+)) which upon collisional neutralization gives hypervalent 3-oxo-(1H)-oxolanium radical (3). The latter dissociates spontaneously by ring opening and expulsion of hydroxy radical. Experiment and calculations suggest that carbohydrate radicals incorporating the 3-hydroxyoxolan-3-yl motif will prefer ring-cleavage dissociations at low internal energies or upon photoexcitation by absorbing light at approximately 590 and approximately 400 nm.

In vitro effects of a C4'-oxidized abasic site on DNA polymerases

Oxidative damage to DNA produces abasic sites resulting from the formal hydrolysis of the nucleotides' glycosidic bonds, along with a variety of oxidized abasic sites. The C4'-oxidized abasic site (C4-AP) is produced by several DNA-damaging agents. This lesion accounts for approximately 40% of the DNA damage produced by bleomycin. The effect of a C4'-oxidized abasic site incorporated at a defined site in a template was examined on Klenow fragments with and without 3' --> 5' exonuclease activity. Both enzymes preferentially incorporated dA > dG >> dC, T opposite C4-AP. Neither enzyme is able to extend the primer past the lesion. Experiments with regular AP sites in an otherwise identical template indicate that Klenow does not differentiate between these two disparate abasic sites. Extension of the primer by alternative polymerases pol II, pol II exo(-), pol IV, and pol V was examined. Pol II exo(-) was most efficient. Qualitative translesion synthesis experiments showed that pol II exo(-) preferentially incorporates T opposite C4-AP, followed in order by dG, dA, and dC. Thymidine incorporation opposite C4'-AP is distinct from the pol II exonuclease interaction with a regular AP site in an otherwise identical template. These in vitro experiments suggest that bypass polymerases may play a crucial role in survival of cells in which C4-AP is produced, and unlike a typical AP site, the C4-AP lesion may not follow the "A-rule". The interaction between bypass polymerases and a C4-AP lesion could explain the high levels of G:C --> T:A transversions in cells treated with bleomycin.

Nucleophilic addition of benzenethiol to 1',2'-unsaturated nucleosides: 1'-C-phenylthio-2'-deoxynucleosides as anomeric radical precursors

The addition reaction of benzenethiol to the glycal portion of 1',2'-unsaturated uridine proceeds efficiently in the presence of Et(3)N. The mechanism involves nucleophilic attack of thiolate at the anomeric position in the rate-determining step, wherein conjugation between the nucleobase and the glycal portion is crucial. The derivative having a methyl group either at the 2'- or 6-position did not undergo this addition reaction, due to their sterically prohibited coplanarity. The 1',2'-unsaturated derivatives of thymine and adenine can also be used as substrates for this addition reaction. It was also shown that the resulting 1'-C-phenylthio-2'-deoxynucleosides serve as precursors for radical-mediated C-C bond formation at the anomeric position.

Chemistry of the 2-deoxyribonolactone lesion in oligonucleotides: cleavage kinetics and products analysis

Deoxyribonolactone in DNA is an oxidized abasic site damage that is produced by a variety of physical and chemical agents such as gamma-irradiation and ene-diyne antibiotics. The extent and biological significance of the lesion are poorly documented due to the high lability of the damaged DNA. The chemistry of degradation of deoxyribonolactone-containing DNA was investigated using oligonucleotides of different length (5-, 11-, 23-, 34-mers) in which the lactone was photochemically generated, as already reported, from oligonucleotide precursors containing a photoactive nitroindole residue. The procedure was successfully extended to double-strand synthesis by irradiation of the preformed duplex in which one strand contained the nitroindole residue. The degradation kinetics were investigated as a function of pH, temperature, length, and ionic strength. The cleavage fragments resulting from beta- and delta-eliminations were isolated and identified by (1)H NMR. It was found that the lesion is extremely sensitive to pH and temperature while slightly dependent upon ionic strength, length, and sequence. The cleavage rates for the beta- and delta-elimination steps are of the same order of magnitude. The deoxyribonolactone site leads to greater instability of DNA than the "regular" deoxyribose abasic site.

Site-specific generation of deoxyribonolactone lesions in DNA oligonucleotides

[reaction: see text] An efficient method for the site-specific generation of 2-deoxyribonolactone oxidative DNA damage lesions from a "photocaged" nucleoside analogue was developed. A nucleoside phosphoramidite bearing a C-1' nitrobenzyl cyanohydrin was prepared and incorporated into DNA oligonucleotides using automated DNA synthesis. The caged analogue, which was stable in aqueous solution, was converted to the 2-deoxyribonolactone lesion by UV irradiation. DNA containing the caged analogue and the deoxyribonolactone site were characterized by electrospray mass spectrometry (ES-MS).

Oxygen-dependent DNA damage amplification involving 5,6-dihydrothymidin-5-yl in a structurally minimal system

5,6-Dihydrothymidin-5-yl (1) was independently generated in a dinucleotide from a phenyl selenide precursor (4). Under free radical chain propagation conditions, the products resulting from hydrogen atom donation and radical-pair reaction are the major observed products in the absence of O(2). The stereoselectivity of the trapping process is dependent on the structure of the hydrogen atom donor. No evidence for internucleotidyl hydrogen atom abstraction by 1 was detected. The tandem lesion (17) resulting from hydrogen atom abstraction from the C1' position of the adjacent 2'-deoxyuridine by the peroxyl radical derived from 1 (3) is observed under aerobic conditions. The structure of this product is confirmed by independent synthesis and its transformation into a second independently synthesized product (24). Internucleotidyl hydrogen atom abstraction is effected selectively by the 5S-diastereomer of the peroxyl radical. The formation of dinucleotide 17 provides further support for the novel O(2)-dependent DNA damage amplification mechanism involving 1 reported previously (Greenberg, M. M.; et al. J. Am. Chem. Soc. 1997, 119, 1828).

The 7-nitroindole nucleoside as a photochemical precursor of 2'-deoxyribonolactone: access to DNA fragments containing this oxidative abasic lesion

On the basis of molecular modeling studies, the 7-nitroindole nucleoside 1 was selected as a suitable photochemical precursor for photochemical generation of the C1' deoxyribosyl radical under irradiation, which led to 2'-deoxyribonolactone. The nitro-indole nucleoside derivatives 1a and 1b were prepared and their conformation was determined by X-ray crystallography and NMR spectroscopy. The photoreaction of these nucleosides gave the corresponding deoxyribonolactone derivatives efficiently, with release of 7-nitrosoindole. This reaction was successfully applied to synthesis of oligonucleotides containing the deoxyribonolactone lesion.

Independent generation and reactivity of 2-deoxy-5-methyleneuridin-5-yl, a significant reactive intermediate produced from thymidine as a result of oxidative stress

2'-Deoxy-5-methyleneuridin-5-yl (1) is produced in a variety of DNA damage processes and is believed to result in the formation of lesions that are mutagenic and refractory to enzymatic repair. 2'-Deoxy-5-methyleneuridin-5-yl (1) was independently generated under anaerobic conditions via Norrish Type I photocleavage during Pyrex filtered photolysis of the benzyl ketone 7. The radical (1) exhibits behavior consistent with that of a resonance-stabilized radical. The KIE for hydrogen atom transfer from t-BuSH was found to be 7.3 +/- 1.7. Competition studies between radical recombination and hydrogen atom donors (2,5-dimethyltetrahydrofuran, kTrap = 46.1 +/- 15.4 M(-1) s(-1); propan-2-ol, kTrap = 13.6 +/- 3.5 M(-1) s(-1)) chosen to mimic the carbohydrate components of 2'-deoxyribonucleotides suggest that 2'-deoxy-5-methyleneuridin-5-yl (1) may be able to transfer damage from the nucleobase to the deoxyribose of an adjacent nucleotide in DNA under hypoxic conditions.

Direct evidence for bimodal DNA damage induced by tirapazamine

The ability of tirapazamine (1, 3-amino-1,2,4-benzotriazine 1, 4-dioxide, SR4233) to fix DNA radical lesions is demonstrated by studying the reaction between the antitumor drug and an oligonucleotide radical that is independently produced at a defined site within a biopolymer. Using beta-mercaptoethanol as a competitor, it was determined that tirapazamine traps a C1'-nucleotide radical with a rate constant of approximately 2 x 10(8) M-1 s-1. Product and isotopic labeling studies suggest that tirapazamine reacts with the radical via covalent adduct formation, resulting primarily from reaction at the N-oxide oxygen. Intermediate covalent adducts could not be observed, but are postulated to decompose to the alkaline labile 2'-deoxyribonolactone lesion. These experiments affirm recent proposals suggesting that tirapazamine can serve as a surrogate for O2 in converting DNA radicals into toxic strand damage events.

Peroxy radical oxidation of thymidine

The peroxy radical (ROO) is unique among reactive oxygen species implicated in the production of DNA damage in that it possesses an extremely long half-life (order of seconds) and is predicted to have a relatively greater chemical selectivity in its reactions relative to other radical intermediates. Yet no product studies of the reactions of ROO with bases, nucleosides, or DNA have appeared, and thus no meaningful predictions can be made regarding its potential involvement in the production of DNA base damage and the mutagenic process. We report here on the reaction products formed by peroxy radical with thymidine, major target of oxidative base damage. ROO reacts with thymine to yield predominantly 5-Me oxidation products. The highly mutagenic 5-(hydroperoxymethyl)-2'-deoxyuridine, 5-formyl-2'-deoxyuridine, and 5-(hydroxymethyl)-2'-deoxyuridine are produced by peroxy radical oxidation. In contrast, 5Me oxidation products are minor products of thymidine oxidation by OH, which yields predominantly saturated derivatives via addition to the 5,6 double bound. A plausible mechanistic scheme for the formation of the base oxidation products of thymidine by peroxy radicals is presented. Attach at the deoxyribose moiety resulting in oxidative depyrimidination is also found to occur, as indicated by free base release. Phosphodiester backbone cleavage resulting in single and double strand breaks is also catalyzed by peroxy radical, as demonstrated using a plasmid nicking assay.