Research

Small-molecule modulators of RNAs is a key activity of the group. With a multi-disciplinary team of collaborators, we are exploring the target potential of LIN28, an oncogenic RNA-binding protein (RBP) which controls biogenesis of let-7 miRNAs.

We began with characterization of the protein-RNA complex using NMR spectroscopy (external page Nat Struct Mol Biol 2012) and novel in vitro assays (external page Nucleic Acids Res 2013), as well as a miniaturized one for small-molecule screening.

One hit molecule (from 16'000 screened) was successfully validated in embryonic stem cells and cancer tumor spheres (external page ACS Chem Biol 2016).

Currently, we are investigating its use in two disease areas: prostate cancer (external page Cancer Res 2016) and myotonic dystrophies, in collaboration with clinical researchers at the Institute of Oncology Research, Bellinzona and the neurology dept. of LMU (DE), respectively.

A spate of recent approvals for oligonucleotide drugs in the last few years has rewarded perseverance of the field. These drugs are isomeric mixtures due to their chiral phosphorothioate (PS) linkages.

In Stereochemical bias introduced during RNA synthesis modulates the activity of PS-siRNAs (external page Nat Commun 2015), we described an unexpected observation that low levels of stereoselectivity in coupling during solid phase synthesis produced additive effects in the biophysical properties of siRNAs, and affected their properties in cells.

We later extended the investigation to single-stranded PS-oligonucleotides (external page Chem Commun 2017), and published the first account of cellular activity from stereopure reagents.

Several years ago, we began to work on RNA G-quadruplexes, a fascinating but contentious structure because of difficulties to prove its formation in vivo.

We discovered an unusual set of G-rich motifs in the untranslated regions of several genes from the polyamine biosynthesis pathway. Polyamines are often perceived simply as polycations, but they also play important roles mediating RNA structure and function.

Using an all-encompassing set of biophysical and cellular assays, together with NMR spectroscopy, we i) confirmed the formation of many new G-quadruplexes, ii) demonstrated that they regulate polyamine levels in cells and iii) showed that their formation is affected by cellular polyamines in feedback loops (external page eLife 2018).

The discovery of microRNAs (miRNAs) and their regulation of mRNAs uncovered a genome-wide mechanism of gene regulation.

It initiated intense efforts to identify the mRNA targets of miRNAs, which have been partly successful for many miRNAs using sequence-based prediction tools. However, miRNAs often have non-canonical functions, and to help identify these we developed an RNA chemistry (external page Angew Chem 2013) to capture by cross-linking all mRNA binding partners of a miRNA in cells (external page Nat Chem Biol 2015).

Indeed, this approach revealed new roles of some miRNAs, including an exciting interplay between two families of tumor suppressor and oncogenic miRNAs.

In this study, we adapted the RNA-binding FAB BL3-6, originally developed in the Joseph Piccirilli Lab, for the crystallization of DNAzymes. We had to synthesize large quantities of clean DNA-RNA mixmers to facilitate the crystallization of DNAzyme structures in their pre-catalytical state. Finally we demonstrated that FAB BL3-6 binds to the engineered DNAzyme-RNA mixmers without compromising their catalytic functions.