Exploring the functional conformational states and their transitions in ligand binding of SAM riboswitch

Conformational transition of SAM riboswitch plays an important role in its specifically binding with S-adenosyl-L-methionine (SAM) and the regulation of downstream gene expression. Recent studies using X-ray crystallography have reported holo state of the riboswitch RNA that corresponded to regulation off. To investigate the dynamics in conformational transition, we marked multiple sets of donor and acceptor dyes on different stems of the RNA in single molecule Forster Resonance Energy Transfer (smFRET) experiments under different buffer conditions. By modeling smFRET trajectories with Hidden Markov Model (HMM), we identified multiple conformational states. Further analysis of transition kinetics, such as Transition Density Plot and dwell time statistics, was applied to explore the transitions between these states and the underlying microscopic mechanism.