The Acidity and Proton Affinity of the Damaged Base 1,N⁶-Ethenoadenine in the Gas Phase versus in Solution: Intrinsic Reactivity and Biological Implications

Abstract

1,N(6)-ethenoadenine (epsilonA) is a highly mutagenic lesion that is excised from human DNA by the enzyme alkyladenine DNA glycosylase (AAG). In an effort to understand the intrinsic properties of 1,N(6)-ethenoadenine, we examined its gas phase acidity and proton affinity using quantum mechanical calculations and mass spectrometric experimental methods. We measure two acidities for epsilonA: a more acidic site (DeltaH(acid) = 332 kcal mol(-1); DeltaG(acid) = 325 kcal mol(-1)) and a less acidic site (DeltaH(acid) = 367 kcal mol(-1); DeltaG(acid) = 360 kcal mol(-1)). We also find that the proton affinity of the most basic site of 1,N(6)-ethenoadenine is 232-233 kcal mol(-1) (GB = 224 kcal mol(-1)). These measurements, when compared to calculations, establish that, under our experimental conditions, we have only the canonical tautomer of 1,N(6)-ethenoadenine present. We also compare the gas phase acidic properties of epsilonA with that of the normal bases adenine and guanine and find that epsilonA is the most acidic. This supports the theory that AAG and other related enzymes may cleave damaged bases as anions. Furthermore, comparison of the gas phase and aqueous acidities indicates that the nonpolar environment of the enzyme enhances the acidity differences of epsilonA versus adenine and guanine.

Gas-Phase Studies of Substrates for the DNA Mismatch Repair Enzyme MutY

“…Furthermore, based on our studies with other glycosylases, we postulate that MutY may provide a nonpolar active site that serves to enhance the differences in acidity among nucleobases, and in doing so, aids in the discrimination of substrate bases over nonsubstrate bases. 18,19,21,23,40 Thus, studies in the gas phase, which is the ultimate nonpolar environment, are relevant.…”

“…18,19,29,30,50 Proton transfer reactions were conducted in both directions. For example, for Z3 acidity bracketing, hydroxide is used to deprotonate neutral Z3.…”

“…Reading the pressure of the neutral compounds from the ion gauges is not always accurate; therefore, we “back out” the neutral substrate pressure from fast control reactions (described previously). 19,22,23,30,51,52 …”

Reactivity of carbene•phosphine dimers: proton affinity revisited

“…Proton affinity measurement of 1b was also conducted in a linear trap quadrupole mass spectrometer using the Cooks kinetic method . The procedure for conducting these experiments in our lab has been described previously . Briefly, for PA experiments, this method involves the formation of a proton‐bound complex, or dimer, of the unknown and a reference base of known PA (Eqn 1, where “A” is the unknown substrate and “B i ” is a series of reference bases).…”

Nucleotides and Nucleic Acids; Oligo- and Polynucleotides

“…229 1,N 6 -Ethenoadenine (48) is a mutagenic lesion formed by the reaction with aldehydes (chloroacetaldehyde) or vinyl chloride, and is a substrate for the repair enzyme alkyladenine DNA glycosylase (AAG). The acidity and basicity of the analogue (48) in gas and solution phase has been measured, 230 and the mechanism by which AAG repairs (48) has been investigated. 231 A comparison of the mutagenicity of (48) with 8-oxoguanine showed that 8-oxoguanine is about 10 times more mutagenic in human cell extracts.…”