Poster abstracts

Poster number 75 submitted by Bishnu Paudel

Molecular crowding accelerates ribozyme docking and catalysis

Bishnu Paudel (Chemistry, Wayne State University), David Rueda (Chemistry, Wayne State University)

Abstract:
All biological processes take place in highly crowded cellular environments. However, how molecular crowding agents affect the folding and catalytic properties of RNA molecules remains largely unknown. Here, we have combined single-molecule fluorescence resonance energy transfer (smFRET) and bulk cleavage assays to determine the effect of a molecular crowding agent (polyethylene glycol, PEG) in the folding and catalysis of a model RNA enzyme, the hairpin ribozyme. Our single-molecule data reveal that PEG favors the formation of the docked (active) structure by increasing the docking rate constant with increasing PEG concentrations. Furthermore, Mg2+ ion induced folding in the presence of PEG takes place at ~10-fold lower concentrations, near the physiological range (~1 mM). Lastly, bulk cleavage assays show that the ribozyme’s activity accelerates by ~10-fold in the presence of the crowding agent. Our data show that molecular crowding agents can affect the structure, stability and function of the RNA enzymes, such as the hairpin ribozyme. We propose that crowding agents play an important role in stabilizing and accelerating the active structure of RNA enzymes in vivo.

Keywords: Ribozyme, smFRET, Docking and Catalysis