Divergent mechanisms for enzymatic excision of 5-formylcytosine and 5-carboxylcytosine from DNA.

5-Methylcytosine (mC) is an epigenetic mark that impacts transcription, development, and genome stability, and aberrant DNA methylation contributes to aging and cancer. Active DNA demethylation involves stepwise oxidation of mC to 5-hydroxymethylcytosine, 5-formylcytosine (fC), and potentially 5-carboxylcytosine (caC), excision of fC or caC by thymine DNA glycosylase (TDG), and restoration of cytosine via follow-on base excision repair. Here, we investigate the mechanism for TDG excision of fC and caC.

Gas-phase studies of substrates for the DNA mismatch repair enzyme MutY.

The gas-phase thermochemical properties (tautomeric energies, acidity, and proton affinity) have been measured and calculated for adenine and six adenine analogues that were designed to test features of the catalytic mechanism used by the adenine glycosylase MutY. The gas-phase intrinsic properties are correlated to possible excision mechanisms and MutY excision rates to gain insight into the MutY mechanism. The data support a mechanism involving protonation at N7 and hydrogen bonding to N3 of adenine.

Gas-phase studies of purine 3-methyladenine DNA glycosylase II (AlkA) substrates.

3-Methyladenine DNA glycosylase II (AlkA) is an enzyme that cleaves a wide range of damaged bases from DNA. The gas-phase thermochemical properties (tautomerism, acidity, and proton affinity) have been measured and calculated for a series of AlkA purine substrates (7-methyladenine, 7-methylguanine, 3-methyladenine, 3-methylguanine, purine, 6-chloropurine, xanthine) that have not been heretofore examined. The damaged nucleobases are found to be more acidic than the normal nucleobases adenine and guanine.

2-Pyridone and derivatives: gas-phase acidity, proton affinity, tautomer preference, and leaving group ability.

The fundamental properties of the parent and substituted 2-pyridones (2-pyridone, 3-chloro-2-pyridone, and 3-formyl-2-pyridone) have been examined in the gas phase using computational and experimental mass spectrometry methods. Newly measured acidities and proton affinities are reported and used to ascertain tautomer preference. These particular substrates (as well as additional 3-substituted pyridones) were chosen in order to examine the correlation between leaving group ability and acidity for moieties that allow resonance delocalization versus those that do not, which is discussed herein.