Synthetic approaches to the understanding of DNA nucleobase methylation

DNA methylation is a major source of genetic variation and cancer. Methylation occurs when nucleophilic DNA bases react with methylating agent methyl methanesulfonate (MMS), dimethyl sulfate (DMS), N-methyl-N-nitrosourea (MNU), N-methyl-N-nitro-N-nitrosoguanidine (MNNG), etc. N7-methyl-2\u27-deoxyguanosine (N7-methyl-dG, or 7MedG) adduct is the most abundant DNA methylation products for most methylating agents. DNA polymerase actions on 7MedG are difficult to study due to its instability against ring- opening hydrolysis and deglycosyl ati on. Oligonucleotides containing a single chemical adduct of 7MedG cannot be chemically synthesized. In addition, 7MedG is unstable in vivo due to the presence of DNA repair enzymes. This work explores the possibility of using stable analogues of N7-methyl-dG to study the polymerase bypass. The chemical synthesis of N7-methyl-9-deaza- dG (7Me9CdG) has been developed and the nucleoside has been successfully incorporated into oligonucleotides. Thermal melting studies show that replacement of dG by 7Me9CdG only slightly decreases DNA duplex stability. Replication of the DNA templates containing 7Me9CdG and the related 7- methyl -7-deaza- dG (7Me7CdG) and 7-deaza- dG (7CdG) by Klenow fragment of E. coli DNA polymerase I is examined. The misincorporation frequencies on the 7Me9CdG, 7Me7CdG, and 7CdG templates are comparable to the dG template, although the 7-methyl group slows down the turnover rate of the polymerase when dCTP is incorporated. The stability of 7Me9CdG and 7Me7CdG against the actions of formamidopyrimidine DNA N- glycosylase (Fpg) and human alkyladenine DNA Glycosylase (hAAG) are also studied. 7Me9CdG is stable in the presence of both enzymes. In contrast, 7Me7CdG is cleaved by Fpg, and possibly by hAAG but in an extremely slow rate. This work demonstrates that 7Me9CdG is a better analogue than 7Me7CdG for future cellular studies. Epigenetic mechanisms regulate the expression of genetic information. A major epigenetic event is DNA cytosine methylation, which is catalyzed by the DNA methyltransferases (DNMTs). Among different mammalian DNMTs, DNMT1 is the most abundant and active, and plays multiple roles in carcinogenesis, embryonic development, and several other biological functions. Reactivation of silenced tumor suppressor genes by DNMT inhibitors (DNMTi) is provides a relatively new approach to cancer therapy. A couple of irreversible nucleoside DNMT inhibitors have been developed clinically. However, due to their low specificity and high cellular toxicity, there is a clear need for the development of reversible inhibitors. S-adenosyl homocysteine (SAH) is a known strong inhibitor of DNA methyltransferases. Based on the crystal structure of SAH bound to human DNMT1-DNA complex, a series of transition state analogues have been designed to occupy the SAH binding site and the cytosine binding site simultaneously. These analogues have been successfully synthesized from adenosine using a modular approach. Inhibition of DNMT1 by these analogues will be studied in the future

Cleavage of pyrene-stabilized RNA bulge loops by trans-(±)-cyclohexane-1,2-diamine

Chemical agents that cleave HIV genome can be potentially used for anti-HIV therapy. In this report, the cleavage of the upper stem-loop region of HIV-1 TAR RNA was studied in a variety of buffers containing organic catalysts. trans-(±)-Cyclohexane-1,2-diamine was found to cleave the RNA with the highest activity (31%, 37°C, 18 h). Cleavage of the RNA in trans-(±)-cyclohexane-1,2-diamine buffer was also studied when the RNA was hybridized with complementary DNAs. A pyrene-modified C3 spacer was incorporated to the DNA strand to facilitate the formation of a RNA bulge loop in the RNA/DNA duplex. In contrast, unmodified DNAs cannot efficiently generate RNA bulge loops, regardless of the DNA sequences. The results showed that the pyrene-stablized RNA bulge loops were efficiently and site-specifically cleaved by trans-(±)-cyclohexane-1,2-diamine