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: Wall paintings make up an important section of cultural heritage. They resemble time portals that can be used to travel back into the past and witness the life of our ancestors. In these paintings, the ancient artists depicted the different aspects of their life, such as cooking, baking, farming, manufacturing, as well as thoughts and beliefs. Unfortunately, wall paintings are susceptible to degradation over time in the form of the accumulations of dirt and deposits on the painted surfaces and loss of adhesion of the paint layers at the surface. Therefore, the removal of these deposits is one of the primary duties of conservator-restorers. Such operations are intended to restore the painted surface to a condition close enough to its original state. Since cleaning artworks may cause undesirable physicochemical alterations and is nonreversible, the proper cleaning procedure should be adopted. In this regard, numerous gels have been developed and exploited for the cleaning of various artwork surfaces. Lately, polyvinyl alcohol-borax (PVA-B) and agarose (AG) hydrogels have been widely employed as cleaning materials by conservator-restorers. However, both hydrogels have shown limitations in specific cleaning practices. In this work, we investigated a new double network hydrogel based on blending PVA-B and agarose to avoid the limitations posed by the constituting hydrogels. For this reason, a detailed characterization of the PVA–B/AG double network hydrogel was performed, including chemical structure, liquid phase retention, mechanical strength, rheological behavior, and self-healing behavior of various PVA-B/AG hydrogels. These new hydrogels revealed better properties than PVA-B and agarose hydrogels and obviated their limitations. A laboratory experiment on the removal of deteriorated Paraloid® B72 proved that the PVA-B/AG hydrogel loaded 10%/10% MEK/1-PeOH was able to remove these layers efficiently. Therefore, the hydrogel was tested on a wall painting from the Temple of Seti I in Abydos – Egypt. It removed the glossy/darkened consolidant from the wall painting and restored the original matt appearance of the painted surface. In another application on the painted ceiling of the same temple, the hydrogel was tested for removing thick soot layers. The hydrogel formulation (loaded with 5% ammonia, 0.3% ammonium carbonate, and 0.3% EDTA) removed these layers with no noticeable damage to the paint layers. In a wide-scale application of the hydrogel (loaded with 10% propylene carbonate), it removed a highly deteriorated varnish layer from a 19-c wall painting. All the traditional cleaning methods employed caused damage to the paint layers, proving that gel cleaning can be a safer cleaning alternative in some cases.

Abstract: The discovery of antibiotics represented one of the greatest breakthroughs in medicine. Their success combined with an increasing intensive use is apparently bound to be also their undoing. This is due to the development of acquired antibiotic resistance, leading to inefficient antibiotherapy and even to the impossibility of treatment and death. The development and spread of antibiotic resistance are fueled by the widespread presence of trace levels of antibiotics residue, in various media, from environment to aliments. One of the solutions is the rigorous monitoring of the levels of antibiotics, which in term requires an almost constant development of new, more accessible analytical methods, especially screening methods, capable of decentralized analysis. In this direction, the electrochemical detection of antibiotics represents a very viable alternative. In this context, the aim of this thesis was to develop new electrochemical methods for the detection of antibiotics by employing and expanding on several strategies, like biomimetic sensors and electrochemical fingerprinting. Five studies were described in this thesis, that can be roughly divided in three categories, based on the analytical strategy employed. The first group is represented by direct electrochemical methods. The second group focuses on the use of biomimetic elements, molecularly imprinted polymers and aptamers. The hyphenation of electrochemical methods with other analytical methods was explored in the last group. In the last study, included in this group, the singlet oxygen-based photoelectrochemical approach was used for the detection of a phenolic antibiotic, rifampicin. The originality of the thesis consists in the testing and development of new approaches to various strategies used in electrochemical detection, revealing new insights in the field of electrochemical detection of antibiotics. The complex electrochemical fingerprint and the mechanism of the electrochemical oxidation were created and investigated, respectively, for the antibiotic vancomycin. New sensitive nanoplatforms were prepared by employing and combining new protocols. Additionally, important contributions were brought through the study involving the singlet oxygen-based detection of rifampicin. We demonstrated how a photocatalyst can exhibit analyte selectivity by strongly interacting with a complex phenolic compound, rifampicin. Summing up, the studies presented in this thesis will have an important impact in the field of electrochemical detection of antibiotics.

Abstract: During the conservation treatment of Memling’s Christ with Singing and Music-making Angels, three panel paintings that are among the most monumental works in early Netherlandish art, the conservators came across insoluble surface layers containing calcium oxalates. A very thin and irregular layer of this type, hardly visible to the naked eye, was spread across the surface of all three panels. A much thicker layer forming an opaque and highly disfiguring crust that obscured the composition (Figs. 15.1 and 15.7) was locally present on areas of dark copper-containing paint, where multiple layers of old discolored coatings and accretions remained in place before the most recent cleaning. This article describes the application of a wide range of analytical techniques in order to fully understand the stratigraphy and composition of the crusts on the Memling paintings. FTIR spectroscopy in transmission and reflection mode, micro-ATR-FTIR imaging and macro-rFTIR scanning, SEM-EDX, mobile XRD, and SR-μXRD showed that the crusts contained two related Ca-based oxalate salts, whewellite and weddellite, and were separated from the original paint surface by varnish, indicating that they did not originate from degradation of the original paint but from a combination of microbial action and a thick accumulation of dirt. Supported by the results from these different analytical techniques, which when used together proved to be very effective in providing complementary information that addressed this specific conservation problem, and aided by the presence of the intermediate varnish layer(s), the conservators were able to remove most of the crusts with spectacular results.

Abstract: This chapter lays out a conservation timeline, from past to future, for the Amsterdam version of Van Gogh's Sunflowers. It starts by considering the restoration history of the painting in order to assess its current physical state, and looks ahead to formulate an appropriate strategy for future conservation treatment and display. Due attention is paid to the two recorded episodes of restoration performed in 1927 and 1961 by the Dutch restorer, Jan Cornelis Traas. Based on physical and chemical investigation of Sunflowers we attempt to reconstruct what these former treatments (which are barely documented) entailed and consider the repercussions for the present condition of the painting. The former interventions by Traas also serve as a benchmark to reflect on current choices made, highlighting the extent to which ideas and methodologies have continued to evolve over the past century as conservation has moved further away from being a singularly craft-based activity to become an established historical and scientific discipline underpinned by ethical guidelines. Jan Cornelis Traas (1898–1984) As mentioned, the two main recorded interventions to the Amsterdam Sunflowers may be associated with the Dutch restorer, Jan Cornelis Traas, who treated the picture in 1927, close to the start of his career, and again in 1961, shortly before he retired. Traas was the first restorer to be appointed at the Mauritshuis in The Hague where he worked from 1931 to 1962 and treated hundreds of paintings, including iconic masterpieces such as Girl with a Pearl Earring by Johannes Vermeer. Yet despite the magnitude and importance of his restoration oeuvre, J.C. Traas (as he is usually referred to in surviving documents), has remained somewhat obscure. He is shown here in the only known surviving photograph of him at work, shortly before he retired (fig. 7.1). Unlike his illustrious contemporaries, A. Martin de Wild (1899–1969) and Helmut Ruhemann (1891–1973), for example, Traas did not publish anything, he appears to have kept no records of his work and no personal archive is known. However, the study of some newly discovered historical documents, combined with physical examination of Sunflowers and a large number of other works he treated, allows us to recover an idea of his working practices and approaches viewed within the context of his day.