Inhibition of DNA polymerase activity by thymine hydrates

A Plausible Mechanism of Uracil Photohydration Involves an Unusual Intermediate

It is well-known that photolysis of pyrimidine nucleobases, such as uracil, in an aqueous environment results in the formation of hydrate as one of the main products. Although several hypotheses regarding photohydration have been proposed in the past, e.g., the zwitterionic and "hot" ground-state mechanisms, its detailed mechanism remains elusive. Here, theoretical nonadiabatic simulations of the uracil photodynamics reveal the formation of a highly energetic but kinetically stable intermediate that features a half-chair puckered pyrimidine ring and a strongly twisted intracyclic double bond. The existence and the kinetic stability of the intermediate are confirmed by a variety of computational chemistry methods. According to the simulations, the unusual intermediate is mainly formed almost immediately (∼50-200 fs) upon photoabsorption and survives long enough to engage in a hydration reaction with a neighboring water. A plausible mechanism of uracil photohydration is proposed on the basis of the modeling of nucleophilic insertion of water into the twisted double bond of the intermediate.

Mechanistic insights into photoinduced damage of DNA and RNA nucleobases in the gas phase and in bulk solution

The mechanistic details of well-known photohydrate lesions are explored using state-of-the-art computational methods.

Incipient intraepidermal cutaneous squamous cell carcinoma: a proposal for reclassifying and grading solar (actinic) keratoses

Actinic keratoses (AKs) are primarily induced by ultraviolet (UV) radiation and are often identified as premalignant lesions. In our opinion, AKs are proliferations of transformed, neoplastic keratinocytes confined to the epidermis that may eventually extend into the dermis, at which point they are termed squamous cell carcinoma (SCC). In contrast to AKs, SCCs have the potential to metastasize and kill. This process is analogous to that of evolving carcinoma of the uterine cervix that has been termed cervical intraepithelial neoplasia (CIN), a time-tested and reliable classification that provides clinicians with accurate information on which to base treatment decisions regarding cervical neoplasms following biopsy testing. A similar classification scheme could provide guidance to clinicians for the diagnosis and treatment of evolving SCC of the skin and as such, we propose a similar classification using the terminology keratinocytic intraepidermal neoplasia (KIN). This system is more reflective of the histology and natural history of SCC and eliminates ambiguity in the terminology of lesions currently referred to as AKs. The KIN classification defines features by which individual specimens can be objectively graded and specific treatment recommendations are made based on the grade of the lesion. We propose that the term keratinocytic intraepidermal neoplasia (KIN) be used to define and describe evolving SCC of the skin and that the term actinic (solar) keratosis be eliminated.

5-Methylcytosine attack by hydroxyl free radicals and during carbon tetrachloride promoted liver microsomal lipid peroxidation: structure of reaction products

We recently reported that trichloromethyl and trichloromethylperoxyl radicals attack 5-methylcytosine (5MC) to give several products derived from hydroxylation, deamination or halogenation reactions. Hydroxyl radicals and lipid peroxidation (LP) are more frequently involved in deleterious pathological or toxicological processes than those CCl4 derived radicals and thus we considered it of interest to test whether they also alter 5MC. We observed that OH radicals generated by 0.1 mM Fe2+/2.5 mM H202 at 25 degrees C for 1 h led to the production of 5-hydroxymethylcytosine (5MHC). When OH generation was performed with UV light (254 nm, 3400 muWatt/cm2) and 2mM H202 during 4 min at 25 degrees C the following products were observed: 5-hydroxy-5-methylhydantoin, 5-hydroxyhydantoin, 5MHC, thymine glycol (two isomers) and 5-hydroxymethyl-6-hydroxycytosine. When 5MC was exposed to liver microsomal suspensions in the presence of NADPH generating system and carbon tetrachloride during 1 h at 37 degrees C and under air, the formation of only 5HMC was observed. Detection and identification of all reaction products was done by GC/MS analysis of trimethylsilyl derivatives of the bases. If similar reactions occurred in DNA, these results might be of relevance to gene control, differentiation and carcinogenesis.

The effects of the ring fragmentation product of thymidine C5-hydrate on phosphodiesterases and klenow (exo-) fragment

N-(2-Deoxy-beta-D-erythro-pentofuranosyl)-N-3-(2R-hydroxyisobutyric acid)urea (alpha-R-hydroxy-beta-ureidoisobutyric acid, 8) was site specifically incorporated into a series of oligonucleotides via the ammonolysis of biopolymers containing 5R-thymidine C5-hydrate (3). alpha-R-hydroxy-beta-ureidoisobutyric acid (8) inhibits snake venom phosphodiesterase, lambda exonuclease and Klenow (exo-) fragment. Kinetic measurements for insertion of nucleotides opposite 8 by Klenow (exo-) fragment indicate that this lesion is instructive.

Molecular dynamics simulations of the effects of ring-saturated thymine lesions on DNA structure

The effect of thymine lesions produced by radiation or oxidative damage on DNA structure was studied by molecular dynamics simulations of native and damaged DNA. Thymine in position 7 of native dodecamer d(CGCGAATTCGCG)2 was replaced by one of the four thymine lesions 5-hydroxy-5,6-dihydrothymine, 6-hydroxy-5,6-dihydrothymine (thymine photohydrate), 5,6-dihydroxy-5,6-dihydro-thymine (thymine glycol), and 5,6-dihydrothymine. Simulations were performed with Assisted Model Building with Energy Refinement force field. Solvent was represented by a rectangular box of water with periodic boundary conditions applied. A constant temperature and constant volume protocol was used. The observed level of distortions of DNA structure depends on the specific nature of the lesion. The 5,6-dihydrothymine does not cause distinguishable perturbations to DNA. Other lesions produce a dramatic increase in the rise parameter between the lesion and the 5' adjacent adenine. These changes are accompanied by weakening of Watson-Crick hydrogen bonds in the A6-T19 base pair on the 5' side of the lesion. The lesioned bases also show negative values of inclination relative to the helical axis. No changes in the pattern of backbone torsional angles are observed with any of the lesions incorporated into DNA. The structural distortions in DNA correlate well with known biological effects of 5,6-dihydrothymine and thymine glycol on such processes as polymerase action or recognition by repair enzymes.

5-methylcytosine attack by free radicals arising from bromotrichloromethane in a model system: structures of reaction products

The interaction between free radicals derived from the catalytic decomposition of bromotrichloromethane and 5-methylcytosine (5MC) under different conditions were studied. The structures of the reaction products formed was established by the GC/MS analysis of their trimethylsilyl derivatives. Under anaerobic conditions, the formation of the following products was found: (1) thymine; (2) 5-hydroxymethyl uracil. Under aerobic conditions, the following reaction products were identified: (1) The same two products formed under anerobic conditions. (2) Monohydroxylated thymine. Precise location of the hydroxyl group was not established but probably corresponds to the six position isomer. (3) Two monochloro monohydroxy thymines. It is suggested that they are cis-trans isomers whose substituents are located at the 5-methyl and six positions of the base. (4) The trimethylsilyl derivative of thymine glycol. (5) Two monobromo monohydroxy adducts of thymine. One of them was detected as its underivatized form in the hydroxyl group position. (6) A partially silylated dihydroxythymine. When benzoyl peroxide was omitted from aerobic incubation mixtures, the compounds formed changed. No longer observable were: thymine; the two monochloro monohydroxy derivatives of thymine; thymine glycol, and one monohydroxythymine. On the other hand, two new reaction products were formed instead: a partially silylated monochloro-monohydroxy thymine and 5-hydroxymethyl-cytosine. If similar or equivalent reaction products were formed in DNA during CBrCl3 or CCl4 poisoning, results might be of relevance, because the 5MC content in DNA from eukaryotes is related to differentiation, gene control, and to carcinogenesis.

Energetic basis for structural preferences in 5/6-hydroxy-5,6-dihydropyrimidines: products of ionizing and ultraviolet radiation action on DNA bases

The structures of all diastereoisomers of 5/6-hydroxy-5,6-dihydropyrimidines have been optimized with ab initio quantum chemical calculations using a 6-31G basis set. The energies of the optimized structures were calculated at the MP2/6-31G* level. The hydroxyl group prefers an equatorial over an axial orientation at the C(5) position of pyrimidines by 3-4 kcal/mol. At the C(6) position, the axial orientation of hydroxyl is preferred by 3-4 kcal/mol. The factors responsible for the different preferences result from dipolar intramolecular interactions between the hydroxyl and C(4) = O(4) on the one hand, and the N(1)-H(1) on the other hand. As a consequence of these structural preferences, the pseudo axial positions at C(5) and C(6), which are perpendicular to the molecular plane, can be occupied by different substituents. These pseudo axial groups are expected to be a major source of distortions to DNA structure with more bulky groups having a greater effect. This may constitute a structural basis for interpretation of experimental results on the biological consequences of pyrimidine lesions. The conclusions drawn from the calculations correlate well with experimental observations on the biological activities of thymine lesions.

Structure-function studies of DNA damage using ab initio quantum mechanics and molecular dynamics simulation

Studies of ring-saturated pyrimidine base lesions are used to illustrate an integrated modeling approach that combines quantum-chemical calculations with molecular dynamics simulation. Electronic structure calculations on the lesions in isolation reveal strong conformational preferences due to interactions between equatorial substituents to the pyrimidine ring. Large distortions of DNA should result when these interactions force the methyl group of thymine to assume an axial orientation, as is the case for thymine glycol but not for dihydrothymine. Molecular dynamics simulations of the dodecamer d(CGCGAATTCGCG)2 with and without a ring-saturated thymine lesion at position T7 support this conclusion. Implications of these studies for recognition of thymine lesions by endonuclease III are also discussed.

Alkali-labile photolesions mapping to purine sites in ultraviolet-irradiated DNA

Gel sequencing experiments with the 5'- and 3'-end-labeled oligonucleotides d(A3GA4GA5GA6GA3G) and d(AT)10 have demonstrated that dimeric adenine photoproducts and thymine-adenine photoadducts constitute alkali-labile lesions in UV-irradiated DNA. On treatment with hot piperidine, DNA strand breakage occurs predominantly at the sites of 5'-adenines in the dimeric photoproducts and of 3'-adenines in the thymine-adenine photoadducts. With 5'-end-labeled oligonucleotides of mixed sequence, major UV-induced loci for alkaline cleavage map to purine bases flanked on their 5'-side by two pyrimidines. This behavior does not arise from enhanced photoreactivity of purines in this sequence context as has been inferred from photofootprinting studies. Instead, as shown by 3'-labeling and selective substitution with 5-methylcytosine, it results from the anomalous electrophoretic mobility of 5'-end-labeled fragments produced by alkaline cleavage of DNA at adjacent pyrimidine (6-4) pyrimidone photoproducts.