LC-ESI-Mass Spectrometer for the Analysis of Highly-Modified RNA- and DNA-Derivatives

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One of the research focusses of the natural sciences at Goethe University Frankfurt is the investigation of RNA - ranging from the regulation of transcription, its subsequent processing (for example splicing) all the way to the regulation of translation. Of particular interest is RNA that does not code for proteins. The past 15 years are characterized by an enormous increase of knowledge especially in the latter field and the corona pandemic has shown that RNA has a large therapeutic potential. It is essential to be able to synthesize new RNA derivatives for example with increased stability or new functionalities. Such functionalities can be intelligent probes to gather new knowledge about RNA or especially also new mechanisms for the regulation of the RNA's function. For example, the development of methods for the regulation of RNA activity with light as external trigger is one of the specialities developed in Frankfurt. This research is currently funded for example by SFB 902 (Molecular Principles of RNA-Based Regulation) or GRK 1986 (Complex Light Control).For all of these projects the newly synthesized oligonucleotide derivatives need to be analyzed. The gold standard for the characterization is mass spectrometry - and this is without alternative. Also by contributions of the present applicants, an array of new modifications can now be introduced and new chemoenzymatic, solid-phase supported synthesis strategies enable the synthesis of longer and higher modified derivatives than ever before. Their analysis is very complicated and requires a mass spectrometer only for this purpose. Also analyzing other substance classes on the same device was accompanied with severe problems in the past. The currently available device is approaching its maximal life time. With a new device the detection limit needs to be lowered and the resolution needs to be enhanced. It is especially also required that the new device is now also able to perform fragmentation and fragment analysis and can hence provide sequence analysis. The former is important since with longer and more complex probes a significant part of the stock was used up for the characterization up to now. The latter will allow better analysis of the derivatives, especially in cases where the oligonucleotide is further derivatized after synthesis with reactions that need to be optimized.