Electronic Spectra of the H and OH Adducts of Cytosine

The multi-channel reaction of the OH radical with 5-hydroxymethylcytosine: a computational study

The hydroxyl radical may attack the new cytosine derivative 5-hydroxymethylcytosine (5-hmCyt), causing DNA oxidative damage. Two distinct mechanisms have been explored and our results provide some evidence between 5-hmCyt and tumor development.

Looking for Waldo: a potential thermodynamic signature to DNA damage

DNA in its simplest form is an ensemble of nucleic acids, water, and ions, and the conformation of DNA is dependent on the relative proportions of all three components. When DNA is covalently damaged by endogenous or exogenous reactive species, including those produced by some anticancer drugs, the ensemble undergoes localized changes that affect nucleic acid structure, thermodynamic stability, and the qualitative and quantative arrangement of associated cations and water molecules. Fortunately, the biological effects of low levels of DNA damage are successfully mitigated by a large number of proteins that efficiently recognize and repair DNA damage in the midst of a vast excess of canonical DNA.

In this Account, we explore the impact of DNA modifications on the high resolution and dynamic structure of DNA, DNA stability, and the uptake of ions and water and explore how these changes may be sensed by proteins whose function is to initially locate DNA lesions. We discuss modifications on the nucleobases that are located in the major and minor grooves of DNA and include lesions that are observed in vivo, including oxidized bases, as well as some synthetic nucleobases that allow us to probe how the location and nature of different substituents affect the thermodynamics and structure of the DNA ensemble. It is demonstrated that disruption of a cation binding site in the major groove by modification of the N7-position on the purines, which is the major site for DNA alkylation, is enthalpically destabilizing. Accordingly, tethering a cationic charge in the major groove is enthalpically stabilizing.

The combined structural and thermodynamic studies provide a detailed picture of how different DNA lesions affect the dynamics of DNA and how modified bases interact with their environment. Our work supports the hypothesis that there is a “thermodynamic signature” to DNA lesions that can be exploited in the initial search that requires differentiation between canonical DNA and DNA with a lesion. The differentiation between a lesion and a cognate lesion that is a substrate for a particular enzyme involves another layer of thermodynamic and kinetic factors.

Thermodynamic signature of DNA damage: characterization of DNA with a 5-hydroxy-2'-deoxycytidine·2'-deoxyguanosine base pair

Oxidation of DNA due to exposure to reactive oxygen species is a major source of DNA damage. One of the oxidation lesions formed, 5-hydroxy-2'-deoxycytidine, has been shown to miscode by some replicative DNA polymerases but not by error prone polymerases capable of translesion synthesis. The 5-hydroxy-2'-deoxycytidine lesion is repaired by DNA glycosylases that require the 5-hydroxycytidine base to be extrahelical so it can enter into the enzyme's active site where it is excised off the DNA backbone to afford an abasic site. The thermodynamic and nuclear magnetic resonance results presented here describe the effect of a 5-hydroxy-2'-deoxycytidine·2'-deoxyguanosine base pair on the stability of two different DNA duplexes. The results demonstrate that the lesion is highly destabilizing and that the energy barrier for the unstacking of 5-hydroxy-2'-deoxycytidine from the DNA duplex may be low. This could provide a thermodynamic mode of adduct identification by DNA glycosylases that requires the lesion to be extrahelical.

Repair Reactions of Pyrimidine-Derived Radicals by Aliphatic Thiols

Pyrimidinyl radicals of various structures (Pyr*) were generated in aqueous and alcohol-containing solutions by means of pulse radiolysis to determine the rate constants of their repair reactions by different thiols (RSH = cysteamine, 2-mercaptoethanol, cysteine, and penicillamine): Pyr* + RSH --> PyrH + RS*. C5-OH and C6-OH adduct radicals of the pyrimidines react with thiols with k9 = (1.2-10.0) x 10(6) dm3 mol(-1) s(-1). Similar repair rate constants were found for uracil- and thymine-derived N1-centered radicals, k31 = (1.5-6.1) x 10(6) dm3 mol(-1) s(-1). However, pyrimidine radical anions protonated at their C6 position and C6-uracilyl radicals, with carbonyl groups at their C5 position, react with thiols faster, with k24 = (0.5-7.6) x 10(7) dm3 mol(-1) s(-1) and k14 = (1.4-4.8) x 10(7) dm3 mol(-1) s(-1), respectively. Quantum chemical calculations, at the B3LYP/6-31G(d,p) and self-consistent reaction field polarizable continuum model level point to the combined effects of the energy gap between interacting molecular orbitals, charge distribution within different pyrimidine-derived radicals, and the coefficients of the atomic orbitals as the possible reasons for the differences in the rate constants of repair.

Thiyl Radical Interaction with Pyrimidine C5−C6 Double Bond

Addition and elimination interaction of thiyl radicals with the C5-C6 double bond in pyrimidines was studied by the pulse radiolysis technique in aqueous solution with the use of different monitoring systems. For this purpose, p-thiocresol, cysteamine hydrochloride, and mercaptoethanol were used. The rate constants of addition and elimination of thiyl radicals were determined by applying the modified version of ACUCHEM (computer program for modeling complex reaction systems). Aliphatic thiyl radicals add to the pyrimidine C5-C6 double bond with k = 1.0-3.0 x 10(7) dm3 mol(-1) s(-1), whereas elimination takes place with k = 0.7-2.0 x 10(5) s(-1). Quantum chemical calculations at the B3LYP/6-31G(d)/PCM level show that the addition should occur at the C6 position of the pyrimidine ring and that the energy of interaction between thiyl radicals and the pyrimidine double bond C5-C6 is low.