Abstract
Persistent heterogeneity has recently been identified in single molecule measurements of enzymes and ribozymes, but its systematic quantification and structural origin remain elusive. Here, we addressed these issues by analyzing isomerization dynamics of Holliday Junctions (HJs) as a test case. Even for HJs that retain relatively simple architectures, the molecule-to-molecule variation in dynamics persists over long observation time (Tobs), implying ergodicity breaking of HJ conformational space. An annealing experiment using Mg2+ pulse, which enables interconversion between HJ trajectories with different patterns, and the architecture of HJ suggest that the persistent heterogeneity of HJs reflects various internal multiloop topologies stabilized by Mg2+ ions.
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