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- Title
Hidden complexity in the isomerization dynamics of Holliday junctions.
- Authors
Hyeon, Changbong; Lee, Jinwoo; Yoon, Jeseong; Hohng, Sungchul; Thirumalai, D.
- Abstract
A plausible consequence of the rugged folding energy landscapes inherent to biomolecules is that there may be more than one functionally competent folded state. Indeed, molecule-to-molecule variations in the folding dynamics of enzymes and ribozymes have recently been identified in single-molecule experiments, but without systematic quantification or an understanding of their structural origin. Here, using concepts from glass physics and complementary clustering analysis, we provide a quantitative method to analyse single-molecule fluorescence resonance energy transfer (smFRET) data, thereby probing the isomerization dynamics of Holliday junctions, which display such heterogeneous dynamics over a long observation time (Tobs ? 40 s). We show that the ergodicity of Holliday junction dynamics is effectively broken and that their conformational space is partitioned into a folding network of kinetically disconnected clusters. Theory suggests that the persistent heterogeneity of Holliday junction dynamics is a consequence of internal multiloops with varying sizes and flexibilities frozen by Mg2+ ions. An annealing experiment using Mg2+ pulses lends support to this idea by explicitly showing that interconversions between trajectories with different patterns can be induced.
- Subjects
BIOMOLECULES; CATALYTIC RNA; CLUSTER analysis (Statistics); ISOMERIZATION; HOLLIDAY junctions; GENETIC recombination; FLUORESCENCE resonance energy transfer
- Publication
Nature Chemistry, 2012, Vol 4, Issue 11, p907
- ISSN
1755-4330
- Publication type
Article
- DOI
10.1038/nchem.1463