RNA play crucial roles in the cellular network. The numbers of identified RNA molecules that are actively transcribed is constantly raising whereas their functional analysis still lack far behind. To study RNA interaction networks molecular tools are by far not as evolved as in the protein world. RNA aptamers that can bind small molecule chromophores provided a great step into the right direction. Still their potential is by far not exhaustively used. So we are working on the development and optimization methods to qualitatively and quantitatively study RNA-interactions by the use of fluorescent RNA aptamers.
The green fluorescent 'Spinach RNA' is able to radiationless transfer (FRET) its excited state energy to an acceptor molecule (quencher). We show that it is even able to transfer its energy to the genetical encodable and fluorescent protein mCherry (scheme in figure 1). This system can be used to study direct, bimolecular binding events as the energy transfer is highly distance dependend and will just sufficiently occur if RNA and protein are in close proximity (Roszyk, Hennig et. al., ACS Chem. Biol. 2017).