Abstract: Aptamers are short, synthetic DNA or RNA molecules that are characterized by a specific 3D conformation which enables specific target recognition. Aptamers are promising tools in many application fields from sensing to therapeutics. One of the major challenges in the aptamer field is understanding the relationship between the sequence and what determines the higher-order structure and specific interactions with targets. Therefore, this PhD thesis focuses on the use of different mass spectrometry (MS) based approaches to characterize aptamers and their interactions. Several of these approaches are already widely applied to study other biomolecules, such as proteins, but are still largely unexplored for aptamers and oligonucleotides in general. A first focus was put on obtaining information on the higher-order structure and conformational stability of aptamers using a combination of MS and with ion mobility (IM) spectrometry by performing collision-induced unfolding (CIU) experiments. CIU was shown to hold great promise to analyze the conformational dynamics and gas-phase stabilities of aptamers. Next, the capabilities and limitations of native IM-MS for the analysis of noncovalent interactions of aptamers were demonstrated. The conformational behavior and interactions of cocaine-binding aptamers were studied and it was found that relative binding affinities of aptamers that only differ slightly in sequence and structure can be determined using native MS. Moreover, native IM-MS allowed the detection of small conformational changes upon binding of a target, which were found to be dependent on the binding mode of the aptamer. An adaptive binding mechanism was suggested for flexible aptamers that require more reorganization upon binding. In the final part of this thesis, the importance of thoroughly characterizing and validating aptamer-target interactions before using them in an application was emphasized. Moreover, the gathered insights were applied in our own development of a proof-of-concept aptamer-based sensor. This was shown by investigating the interactions of ampicillin aptamers which were found to not bind the target they were selected for in the first place. A multi-analytical approach combining complementary techniques was used for this purpose since no single technique is generally applicable to characterize all aptamers and their interactions and to obtain a comprehensive picture of the aptamer-target interactions. Furthermore, such multi-analytical approach was used to characterize a testosterone-binding aptamer while developing an aptamer-based electrochemiluminescent sensing strategy for this target. This shows the importance of native MS, in combination with other techniques, to thoroughly understand the aptamer-target interactions in the development of a designed application.

Abstract: Although the analysis of thermal water by spark-source mass spectrometry (SSMS) is rather timeconsuming, it allows the detection of about 20 elements of geochemical interest down to the ppb-level. A physical preconcentration is proposed in order to collect elements having quite different chemical properties, e.g. alkalis, transition elements, and elements occurring in anionic form. The relative sensitivity factors appear to be rather independent of the salt content of the graphite electrodes. Contrary to neutron activation analysis, SSMS has a quite uniform elemental sensitivity, and allows to determine elements for which neutron activation is not suitable, e.g. Sn and Pb. The precision of SSMS is however by a factor of about 2 worse than that obtained for neutron activation.

Abstract: Sensitive multi‐element analytical techniques were applied to determine 24 dissolved trace components in 25 different water samples from a 10 km2 zone in Brittany, France. Correspondence factor and multiple regression analyses showed that the elements considered are influenced mainly by the presence of: Fe‐Mn oxide accumulations, a local poly‐metallic sulfide mineralization, and non‐mineralized host rocks, agricultural activity and abundant organic material in local swamps. Via these numerical techniques the location of the poly‐metallic ore body can be derived from the data set.