Single-molecule study of the CUG repeat–MBNL1 interaction and its inhibition by small molecules

Effective drug discovery and optimization can be accelerated by techniques capable of deconvoluting the complexities often present in targeted biological systems. We report a single-molecule approach to study the binding of an alternative splicing regulator, muscleblind-like 1 protein (MBNL1), to (CUG)(n)( = 4,6) and the effect of small molecules on this interaction. Expanded CUG repeats (CUG(exp)) are the causative agent of myotonic dystrophy type 1 by sequestering MBNL1. MBNL1 is able to bind to the (CUG)(n)–inhibitor complex, indicating that the inhibition is not a straightforward competitive process. A simple ligand, highly selective for CUG(exp), was used to design a new dimeric ligand that binds to (CUG)(n) almost 50-fold more tightly and is more effective in destabilizing MBNL1–(CUG)(4). The single-molecule method and the analysis framework might be extended to the study of other biomolecular interactions.