Reverse transcription as key step in RNA in vitro evolution with unnatural base pairs

Congratulations to Eva Hoffmann and our collaborators from  Stephanie Kath-Schorr‘s lab for their insightful publication in RSC Chemical Biology!
They explored different reverse transcriptases and how they can be used to expand the genetic alphabet with unnatural bases. switchSENSE was used to monitor the binding affinities as well as the reverse transcription kinetics in real time and compare the kinetic efficacy of 2 different transcriptases on 4 different template ligand strands with 6 different natural and unnatural nucleotides. This study showcases that the heliX biosensor can be a powerful tool to study nucleic acid-modifying enzymes like reverse transcriptases and polymerases as it enables the real-time kinetic characterization of binding as well as activity.

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Repurposing the mammalian RNA-binding protein Musashi-1 as an allosteric translation repressor in bacteria

Congratulations to Roswitha Dolcemascolo and her co-authors for their publication on RNA-binding proteins in eLife!
The authors established the mammalian RNA-binding protein Musashi-1 (MSI-1) as a tool for synthetic biologists, specifically as a post-transcriptional repressor in E.coli.
switchSENSE^® was used to study binding of this two-domain RNA binding protein to RNA ligands and to determine differences between the original RNA binding motif and mutated RNA ligands

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Kinetic FRET Assay to Measure Binding-Induced Conformational Changes of Nucleic Acids

Congratulations to Anahi Higuera-Rodriguez and Mareike De Pascali for their recent publication in ACS Sensors!

They demonstrate the application of FRET in kinetic measurements for discerning binding-induced conformational changes in nucleic acids. This cutting-edge technique was applied to two distinct systems: the interaction between DNA and small molecules (MN19 aptamer with quinine) and the interaction between RNA and proteins (IMP3-KH1/2). The entire study was conducted on the heliX^® platform.

The paper not only showcases the versatility and efficacy of FRET in unraveling intricate molecular dynamics but also sheds light on the specific interactions within the DNA-small molecule and RNA-protein systems studied. This work significantly contributes to our understanding of binding-induced conformational changes in nucleic acids.

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The Fraunhofer Institute for Cellular Therapies and Immunology (IZI-BB) has published a press release highlighting how switchSENSE^® is used at the institute to characterize binding interactions of SARS-CoV-2.

The press release informs about the recent publication of Kruse et al. in Nature Scientific Reports, in which researchers investigated the interaction between the SARS-CoV-2 spike protein and its receptor hACE2. To do so, they prepared trivalent DNA-peptide nanostructures to achieve a trimeric hACE2 peptide presentation. switchSENSE^® was used to examine the binding of full-length spike protein, subdomains and even whole virus particles. They show that small changes in the amino acid sequence of the spike protein can drastically influence the binding behavior. Furthermore, they demonstrate an increased affinity of the protein to the trivalent peptide construct as compared to single peptides. Finally, they detect different binding behaviors of pseudo virus models of the Alpha and Beta variants of SARS-CoV-2 compared to the inactivated wild type virus.

This study shows the versatility of the switchSENSE^® technology, which enables the investigation of multivalent interactions and the utilization of a broad range of analytes from protein subdomains to whole virus particles.

This work was part of the project “CoronaSense” at the Fraunhofer Institute, which aims at using the switchSENSE^® technology in order to characterize binding interactions of SARS-CoV-2 Spike proteins with its receptors in more detail to aid the development of anti-viral drugs but also of diagnostic tests.