Nuclear Magnetic Resonance spectroscopy provides an uncomparable method to peer into molecular structure, dynamics and interaction.  Using NMR, the NMR and Structure Analysis research unit at UGent is invested in bringing structural and dynamic insight into lipopeptide and aptamer research. Pseudomonas are ubiquitous bacteria found in soil and marine environments and are outstanding producers of bioactive secondary metabolites in support their eclectic lifestyle. Of these metabolites, cyclic lipopeptides – CLIPs in short – enjoy increasing interest because of their diverse range of bioactivities that includes antibacterial and antifungal effects. Moreover, they are involved in plant-bacteria interactions ranging from plant beneficial to plant pathogenic. Their biosynthesis through non-ribosomal peptide synthetases creates a large structural diversity (>130 distinct Pseudomonas CLiPs reported to date) that can be mined for application purposes in agriculture and medicine but also presents a daunting challenge for their structural and functional characterization. We will further develop the use of NMR spectroscopy as part of a multidisciplinary approach that aims to understand how Nature uses the same molecular blueprint to generate a swiss-army like diversity of effects. NMR based solutions for early stage dereplication of new CLiPs isolated from novel Pseudomonas sources will be further developed while solution structure determination of representative CLiPs obtained in the presence of DPC micelles will be performed in order to complete the structural library of this class of compounds. 

DNA based aptamers provide promising structures for small molecule sensing applications, demonstrating high affinity and selectivity. However, considerable challenges persist in their translation into real-world applications, for example in biosensors. We aim to assist in bridging this gap by emphasizing the importance of a detailed molecular understanding beyond simplistic descriptions of sensing mechanisms. Building on previous successes, we will employ NMR spectroscopy to uncover molecular insights within steroid based aptamer-target systems, with 3D structure determination of the tesotsterone binding TESS.1 aptamer as a first target of interest, based on its recent complete NMR assignment. Futhermore, methods based on (partially) isotope labeled oligonucleotides will be applied, to further uncover the details of the interaction, while the possibility to obtain fully and unfiromly labeled DNA constructs will be investigated. If successful, this will open up completely new avenues to the NMR based analysis of small-molecule aptamers.  From the lessons learnt, the possibility to optimise aptamer constructs through structure based guidance will be explored.