Investigating the interaction of ionic liquids with fungal and bacterial cell envelopes, proteins and nucleic acids
In recent years, molecular diagnostics of health-relevant microorganisms have become more and more based on the detection and quantification of their nucleic acids (NAs), DNA and RNA. The extraction of NAs from clinical or environmental samples is a necessary preliminary step to allow for NA-based tests.
DNA/RNA extraction is a complex, laborious process for many target organisms that also has to be adapted to different sample types. It often takes several hours and requires expensive equipment or hazardous chemicals and is therefore considered a major bottleneck for molecular diagnostic workflow. Over the last years, ionic liquids (ILs), salts with a melting temperature below 100°C, have emerged as environmental benign solvents.
ILs have the capability to efficiently dissolve biomass (cellulose, lignin, chitin) and have been used for the extraction of active plants ingredients, proteins, and cells. They have also been reported to stabilize DNA and small RNAs and to denature and reconstitute proteins.
![[Translate to English:] Ionic liquids](fileadmin/icc_images/ionic_liquids.png "[Translate to English:] Ionic liquids")
Recently, our group has shown that hydrophilic ILs can effectively and rapidly lyse plant, animal, and bacterial cells, demonstrating their potential for the extraction of NAs in molecular diagnostics. However, unfortunately the mechanisms of interaction of ILs with the microbial cell wall leading to cell lysis, and the effects of ILs on cell lysate components such as DNA, RNA, and proteins are very poorly understood. For fungal cells IL-based cell lysis has not even been attempted up to date.
In this project we aim at finding hydrophilic ILs that are capable of lysing fungal and bacterial cells and attempt to shed some light on their mode of interaction. Firstly, we plan to investigate the interaction of hydrophilic ILs with the components of the microbial cell wall that results in cell lysis. We will also aim at elucidating how ILs stabilize NAs and interact with proteins that are relevant for molecular diagnostics (nucleases, polymerases). We believe that understanding the interaction of hydrophilic ILs with cell wall components could allow future tailored design of ILs for the rapid and quantitative extraction of NAs from a broad range of microbial targets.
Additionally, understanding the interaction of ILs with NAs, nucleases, and polymerases and how that interaction might interfere in downstream reactions such as hybridisation, PCR or sequencing is essential for the selection of ILs to be used in molecular diagnostics workflows.
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