Development of aptamere based RNA labeling techniques for analysis of RNA dynamics inside living cells via FRET

• Applicant: Dr. Markus Hirsch
• Subject Area: Biophysics ; Biochemistry ; Cell Biology
• Term: from 2015 to 2017
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 284039133

Many cellular processes are regulated and influenced by different RNA species, like non-coding RNA, mRNA and toxic RNA. For a detailed understanding of these processes and for investigation of RNA and RNA interaction with other biomacromolecules, an imaging approach that allows real-time analysis inside cells is essential. The Jaffrey lab recently developed the spinach aptamer which enables to label and study RNA inside living cells. The spinach aptamere represents the first approach to develop a green fluorescent RNA aptamer tag. Further research and development is necessary to create a repertoire of techniques, similar to fluorescent proteins, that allow the study of RNA-RNA or RNA-protein interactions. Most important is hereby the possibility of performing direct observation of RNA and its interaction partners inside living cells.During my research project in the group of Prof. Jaffrey I will develop (1) new red fluorescent variant of the spinach aptamer that mimics red fluorescent proteins and expands the repertoire of available aptamer tags towards the red light spectrum. Based on this new red shifted aptamer I will start to establish (2) a FRET-System between fluorescent protein tags and RNA aptamer tags. This system will be used to study protein-RNA interaction inside living cells by fluorescence microscopy.

• DFG Programme: Research Fellowships
• International Connection: USA
• Host: Professor Samie R. Jaffrey, Ph.D.