Research

The Helm group conducts highly interdisciplinary research in the backdrop of Pharmaceutical Chemistry and Molecular Biotechnology, as is suggested by the name-forming initials of the IPMB. Ranging from organic chemistry over biochemistry and molecular biology to aspects of cell biology and pharmakokinetics, we investigate the various aspects of molecular movement and of RNA modifications that confer function to ribonucleic acids.

There is a huge variety of different RNA molecules such as tRNAs, ribozymes, and siRNAs, whose functions are largely more sophisticated than the simple transport of genomic information commonly assigned to RNA. Proper functioning of these molecules relies on their ability to interconvert between different structures, depending on the type of molecular partner which they interact with. It is this ability of interconversion between different structures which is of special interest to us, because it becomes more and more apparent that nature uses it as a tool for regulation of function.

Our investigations concern topics with biomedical and pharmaceutical background:

I) RNA Modifications in mitochondrial neuromuscular disorders: Caused by a variety of over 80 different point mutations in mitochondrial tRNA genes, these diseases share a respiratory deficiency, caused by insufficient levels of functional tRNAs in mitochondrial protein synthesis. We are about to prove that most of the tRNA deficiencies result from incomplete tRNA modification (ref. R1). Our greatest achievement up to date is the demonstration of the structural influence of a mitochondrial tRNA modification by single-molecule FRET. We could demonstrate that a single methylation shifts a dynamic equilibrium towards the functional cloverleaf tRNA structure (24, 27). We are now in a position to assess the effect of pathogenic mutations, as well as that of protein binding to tRNA by smFRET. These experiments are paralleled by the related biochemistry (14) and cell biology investigations in cybrid cell lines, which contain homoplasmic mutant mitochondrial DNA (19,20). The smFRET work in particular produced a strong resonance in the community, resulting in numerous invitations to conferences and secondary literature contributions. Click here for MORE details in GERMAN.

II) RNA methylation in epigenetics: Dnmt2 is a somewhat enigmatic protein originally belonging to a family of DNA methyltransferase involved in epigenetic regulation of gene expression. Surprisingly, Dnmt2 shows strong tRNA methylating activity in vivo and in vitro. With the epigenetic functional implications of this unclear, we are investigating the RNA substrate specificity of Dnmt2 in order to identify alternative small RNA substrates, presumably with regulatory functions (25,28).

III) Modulation of immunostimulation by modified RNA: In this as yet unpulished work we have identified a differential interferon response of dendritic cells towards various purified bacterial and eukaryotic tRNA species. Post-transcriptional modifications clearly determine the extend of TLR-7-mediated immunostimulation, which strongly varies even among different bacterial tRNA species.

IV) Tracing the degradation of siRNA in cells: Using microinjection of FRET-labeled siRNAs, we can trace minute amounts of intact siRNA inside cells, in order to study pharmacological aspects of intracellular distribution (23). The labeling is also suitable to monitor in real-time the incorporation of siRNAs in liposomal formulations in very small batch sizes. This work has raised substantial interest in the field.

	Structural Dynamics in natural RNA		Structural Dynamics in artificial RNA		Structural integrity of siRNA
	tRNA in the pathogenesis of mitochondrial diseases		in synthetic ribozymes		in cells and tissues

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