In-droplet hydrogen-deuterium exchange to examine non-canonical DNA structures

The structures of various DNA molecules have been examined using in-droplet hydrogen deuterium exchange (HDX) coupled with mass spectrometry (MS). To perform in-droplet HDX, the new ionization source, vibrating sharp-edge spray ionization (VSSI) has been utilized. In the approach, two separate cVSSI emitter tips (analyte and D2O) are employed. Overall, the Hybrid 1 topologies, 24TTG and 23TAG, exhibited the least (~12) and greatest (~23) amount of deuterium incorporation, respectively. The increased reactivity of the 23TAG species is attributed to its increased structural flexibility in solution. The parallel species Nmyc and T95 2T also exhibited increased protection with each exchanging only ~15 hydrogens. This protection level is below most other G-quadruplex structures as well as DNA duplex. Correlation analyses suggest that the relative protection arises from phosphodiester backbone sites. The results are discussed with regard to the utility of in-droplet HDX for studying the structures of intractable species such as those that undergo structural transformations on short timescales.