The photochemistry of 5-methylcytosine and 5-methyl-2'-deoxycytidine in aqueous solution

Ring-opening photoreactions of 5-methylcytosine with 3-mercaptopropionic acid and other thiols

The photoproducts from reaction of thymine with cysteine, an amino acid containing a sulfhydryl group, have been studied in detail, whereas results of less extensive studies have been reported for the uracil-cysteine system. However, products arising from corresponding reactions of cytosine and related compounds with compounds containing a sulfhydryl group have not been similarly studied. We report here the results of our study of the photoreaction of 5-methylcytosine (5MeCyt), a minor base occurring in mammalian DNA, with 3-mercaptopropionic acid (3MP), a model compound for cysteine. We found that this reaction proceeds at pH 7 to yield N-(N'-(2'-carboxyethyl)thiocarbamoyl)-3-amino-2-methylacrylamidine (Ia) as a primary photoproduct. A secondary thermal product, identified as 3-(2'-carboxyethylthio)-2-methylacrylamidine (IIa), appears if photoreacted solution is allowed to stand for appreciable times prior to workup; this latter compound is formed via an intermediate product. Heating of purified Ia at 100°C or standing at lower temperatures produces 3-amino-2-methylacrylamidine (IId); similarly, irradiation of Ia with UVB light in aqueous solution converts it into IId. Results from exploratory studies suggest that 5MeCyt similarly reacts with other thiols (2-mercaptoethanol, 2-mercaptoacetic acid) to form analogs of Ia and IIa. Other preliminary results suggest that 5-methyl-2'-deoxycytidine and 1,5-dimethylcytosine photoreact with 3MP to form compounds similar to Ia.

The photochemistry of thymidylyl-(3'-5')-5-methyl-2'-deoxycytidine in aqueous solution

The photochemistry of the dinucleoside monophosphate thymidylyl-(3'-5')-5-methyl-2'-deoxycytidine (Tpm5dC) has been studied in aqueous solution using both 254 nm and UV-B radiation. A variety of dinucleotide photoproducts containing 5-methylcytosine (m5C) have been isolated and characterized. These include two cyclobutane dimers (CBD) (the cis-syn [c,s]and trans-syn forms), a (6-4) adduct and its related Dewar isomer, and two isomers of a product in which the m5C moiety was converted into an acrylamidine. Small amounts of thymidylyl-(3'-5')-thymidine (TpT) were also formed, presumably as a secondary photoreaction product. In addition, a photoproduct was characterized in which the m5C moiety was lost, thus generating 3'-thymidylic acid esterified with 2'-deoxyribose at the 5-hydroxyl on the sugar moiety. The c,s CBD of Tpm5dC readily undergoes deamination to form the corresponding CBD of TpT. The kinetics of this deamination process has been studied; the corresponding enthalpy and entropy of activation for the reaction have been evaluated at pH 7.4 as being, respectively, 73.4 kJ/mol and -103.5 J/K mol. Deamination was not observed for the other characterized photoproducts of Tpm5dC.

Human DNA-demethylating activity: a glycosylase associated with RNA and PCNA

We have partially purified and characterized the 5-methylcytosine removing activity (5-meC-DNA Glycosylase) from HeLa cells with 700-fold enrichment. This activity cleaves DNA specifically at fully methylated CpG sites. The mechanism of 5-meC removal is base excision from fully methylated CpG loci on DNA, producing abasic sites. Hemi-methylated DNA is not a substrate. A prominent 52 KDa protein is present in all partially purified fractions. This activity is tightly associated with other nuclear factors and proteins, which resulted in differential fractionation of this activity on ion exchange columns. One nuclear factor associated with this activity is identified as RNA. Another nuclear protein, proliferating cell nuclear antigen (PCNA) is also associated with this enzyme. Glycosylic removal of 5-meC from DNA by this activity could be involved in the regulation of transcription, replication, differentiation, and development through resultant hypomethylation of DNA.

Photochemistry of DNA and related biomolecules: quantum yields and consequences of photoionization

The reactions of nucleic acids and constituents, which can be induced by laser UV irradiation, are described. Emphasis is placed on the quantum yields of various stable photoproducts of DNA and model compounds upon irradiation at 193, 248, 254 or 266 nm. In particular, those quantum yields and processes are discussed which involve photoionization as the initial step and occur in aqueous solution under well defined conditions, e.g. type of atmosphere. The efficiencies of some photoproducts, with respect to photoionization using irradiation at 193 or 248 nm, are presented. Radical cations of nucleobases are important sources of damage of biological substrates since they can cause lesions other than dimers and adducts, e.g. strand breakage, abasic sites, crosslinks or inactivation of plasmid and chromosomal DNA. While competing photoreactions, such as hydration, dimerization or adduct formation, diminish the selectivity of the photoionization method, a combination with model studies on pyrimidine- and purine-containing constituents of DNA has brought about an enhanced insight into the reaction mechanisms. The knowledge concerning the lethal events in plasmid and cellular DNA has been greatly improved by correlation with the chemical effects obtained by gamma-radiolysis, vacuum-UV (< 190 nm) and low-intensity irradiation at 254 nm.

Formation of cyclobutane dimers and (6-4) photoproducts upon far-UV photolysis of 5-methylcytosine-containing dinucleotide monophosphates

The far-UV photochemistry of 5-methylcytosine, a minor DNA base, was studied in three dinucleoside monophosphates, including m5dCpT, Tpm5dC, and m5dCpdC. The model compounds were exposed to 254-nm radiation, and the resulting photoproducts were isolated by reverse-phase HPLC and characterized as cyclobutane dimers, (6-4) adducts, and the related Dewar valence isomers by UV, mass, and 1H NMR spectroscopies. The rate of formation of the different photoproducts was compared with those obtained by photolysis of TpT and the corresponding cytosine dinucleoside monophosphates, including dCpT, TpdC, and dCpdC. The formation of deaminated m5dC-containing photoproducts was observed in each of the far-UV irradiated solution of m5dCpT, Tpm5dC, and m5dCpdC. They were shown to be generated mainly through a photochemical process since methylation of the C5 atom of the cytosine ring appeared to dramatically decrease the deamination rate of the C5-C6 saturated photoproducts.