The Elusive Noncanonical Isomers of Ionized 9-Methyladenine and 2′-Deoxyadenosine

Noncanonical nucleobases and nucleosides represent newly discovered species of relevance for DNA ionization. We report a targeted synthesis of gas-phase 9-methylene(1H)adenine cation radical (2(+center dot)) as a low-energy isomer of ionized 9-methyladenine. Ion 2(+center dot) showed unique collision-induced dissociation and UV-vis photodissociation action spectra that distinguished it from other cation radical isomers. Ab initio energy calculations with coupled cluster theory extrapolated to the complete basis set limit, CCSD(T)/CBS, identified cation radical 2(+center dot) as the global energy minimum of the adenine-related C6H7N5+center dot isomers. The action spectrum of 2(+center dot) was assigned on the basis of vibronic absorption spectra that were calculated with time-dependent density functional theory for multiple vibrational configurations of thermal ions. The major dissociation of 2(+center dot) proceeded by hydrogen loss that was elucidated by deuterium labeling at the exchangeable N-1 and NH2 positions and C-8 position and by kinetic analysis. The dissociation involved a reversible rearrangement to intermediate dihydropteridine structures, yielding a protonated aminopteridine as the product, which was identified by multistep UV-vis action spectroscopy. We also report a computational study of related noncanonical isomers of 2'-deoxyadenosine cation radical having the radical defect at C-1' that were found to be thermodynamically more stable than the canonical isomer in both the gas phase and aqueous solution. The noncanonical isomers were calculated to have extremely low ion-electron recombination energies of 4.42-5.10 eV that would make them dead-end hole traps if produced by DNA ionization.

Automated summary

The study reports the targeted synthesis of gas-phase 9-methylene(1H)adenine cation radical and its unique collision-induced dissociation and UV-vis photodissociation action spectra. Computational analysis was performed to identify the global energy minimum of the cation radical and to explain the dissociation mechanisms. Additionally, a computational study of noncanonical isomers of 2'-deoxyadenosine cation radical was conducted to investigate their stability and ion-electron recombination energies.