Deprotonated guanine·cytosine and 9-methylguanine·cytosine base pairs and their “non-statistical” kinetics: a combined guided-ion beam and computational study

Abstract

We report a guided-ion beam mass spectrometric study on collision-induced dissociation (CID) of deprotonated guanine(G)·cytosine(C) base pairs and their 9-methylguanine (9MG) analogue with Xe, including measurements of product cross sections as a function of collision energy and determination of dissociation thresholds. DFT, RI-MP2 and DLPNO-CCSD(T) calculations and Rice–Ramsperger–Kassel–Marcus (RRKM) modeling were performed to elucidate structures and kinetics. The experiment and theoretical study have provided considerable insight into tautomerization, intra-base-pair proton transfer and dissociation of deprotonated G·C and 9MG·C. In contrast to the previously reported lowest-energy deprotonated base pair structure G·[C–H1]⁻ that consists of H-bonded neutral guanine and N1-deprotonated cytosine, we found that proton transfer from guanine N1 to cytosine N3 within G·[C–H1]⁻ (or 9MG·[C–H1]⁻) leads to another slightly more stable conformer denoted as G·[C–H1]⁻_PT1 (or 9MG·[C–H1]⁻_PT1). The conventional (non-proton-transferred) and the proton-transferred conformers are close in energy and interconvert quickly, but they can be distinguished by dissociation products. The conventional structure dissociates into deprotonated cytosine and neutral guanine, while the other dissociates into deprotonated guanine and neutral cytosine. The two dissociation asymptotes have similar threshold energies, but surprisingly the CID product mass spectra of deprotonated G·C and 9MG·C are both overwhelmingly dominated by deprotonated G or 9MG, with their branching ratios greater than RRKM predictions by one to two orders of magnitude. The proton-transferred structures of deprotonated base pairs and the “unexpected” non-statistical kinetics provide new leads for understanding purine–pyrimidine interactions, forming rare nucleobase tautomers, and base pair opening.