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Ontrack EasyRecovery Professional 188.8.131.52 SerialÂ .High-resolution, asymmetric medium resolution ion mobility spectrometry to determine neutral isomers: Application to cationized DNA oligomers.
Here we describe an analysis of the high-resolution, asymmetric-field-enabled, ion mobility spectrometry (FAIMS-H-FAIMS) and medium-resolution FAIMS (FAIMS-M) spectra of a series of long DNA oligonucleotides possessing one or two positively charged amine groups. The ions’ FAIMS spectra contain no peaks related to deprotonated DNA or cationized DNA oligomers. The FAIMS-M spectrum of cationized DNA oligomers peaks corresponding to the cationized DNA oligomers, the matching peaks in the FAIMS-H-FAIMS spectrum of cationized DNA oligomers correspond to the neutral isomers. The FAIMS spectra of DNA oligomers dually and triply cationized all contain peaks corresponding to the deprotonated DNA oligomers, which is consistent with the N-1 charge-state distribution. We were able to determine the abundance of the N-1, N-2 and N-3 deprotonated DNA oligomers for a triply cationized DNA and the N-1 deprotonated DNA oligomers for a dual cationized DNA. The FAIMS spectra of DNA oligomers singly and dually cationized show additional peaks not observed in the FAIMS spectra of their corresponding N-2 deprotonated DNA oligomers. We show that these additional peaks are related to deprotonated species of DNA that have both a hydrogen-bonded base and a protonated base (e.g., DNA: A-N3H+H). A radical-mediated deprotonation of a protonated base occurs to yield a nucleobase that remains bound to the backbone, and a nascent radical that migrates away from the backbone. The FAIMS spectra of nucleobases are similar to the FAIMS spect