Poster abstracts
Poster number 70 submitted by Prabuddha Madubashitha
Mass spectrometry-based mapping of RNA-binding molecules
Prabuddha Madubashitha (Department of Chemistry, Wayne State University), Rasoul Daliri (Department of Chemistry, Wayne State University), M. T. Rodgers (Department of Chemistry, Wayne State University), Christine S. Chow (Department of Chemistry, Wayne State University)
Abstract:
Recent advances in rational design of small molecules and biochemical screening methods have identified novel RNA targeting molecules including peptides and small molecules. Meanwhile, characterization of the binding sites of RNA targeting molecules remains a major challenge. In this study, we have employed a mass spectrometry (MS) based method to map the binding sites of a basic peptide and an aminoglycoside to the transactivation responsive (TAR) RNA as a model system.1,2 Fourier Transform Ion Cyclotron Resonance (FT-ICR) MS was used to study complex formation and to map the binding sites of the peptide and aminoglycoside with TAR RNA. The MS data show concentration-dependent complex formation between the peptide and RNA. Moreover, 1:2 and 1:3 stoichiometric complexes between RNA and the peptide are formed with increasing peptide concentration. Similarly, our data show 1:1, 1:2, and 1:3 stoichiometric complexes of TAR RNA and the aminoglycoside. The complex between the aminoglycoside and TAR RNA was mapped by collision-induced dissociation, which allowed multiple binding sites to be identified. This MS-based mapping strategy is being extended to reveal important molecular details of the interactions between other small molecules and their RNA targets.
References:
1. Richter, S., Cao, H., Rana, T. M. Biochemistry 2002, 41, 6391-6397.
2. Sannes-Lowery, K. A., Mei, H-Y., Loo, J. A. Int. J. Mass Spectrom. 1999, 193, 115–122.
Keywords: mass spectrometry, peptides, aminoglycosides, TAR RNA