Fluorescence Correlation Spectroscopy (FCS)-Based Characterisation of Aptamer Ligand Interaction

Fluorescence correlation spectroscopy (Bacia and Schwille (2007) Nat. Protoc. 2 , 2842–2856) reveals molecular mobilities, enabling to identify molecular interactions based on a change of diffusion times (Rigler and Elson, (2001) Fluorescence Correlation Spectroscopy: Theory and Applications . Springer, Berlin; Haustein, and Schwille, (2004) Curr. Opin. Struct. Biol. 14 , 531–540). This technique can be applied to determine the dissociation constant of a complex formed by a fluorescence-labelled target and its corresponding RNA aptamer selected via systematic evolution of ligands by exponential enrichment (SELEX) (Sch�rer, et al. (2001) Biol. Chem . 382 , 47948). Here, an FCS titration experiment is described in detail, where the binding properties of tetramethylrhodamine (TMR) labelled Moenomycin A to its corresponding RNA aptamer were determined (Sch�rer, et al. (2001) Biol. Chem . 382 , 47948).