4.8 Article

Hidden complexity in the isomerization dynamics of Holliday junctions

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NATURE CHEMISTRY
卷 4, 期 11, 页码 907-914

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NATURE PUBLISHING GROUP
DOI: 10.1038/NCHEM.1463

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资金

  1. National Research Foundation of Korea [2010-0000602]
  2. Creative Research Initiatives (Physical Genetics Laboratory) [2009-0081562]
  3. National Science Foundation [CHE 09-14033]
  4. National Research Foundation of Korea [2008-0059125, CG035001, CG038402, 2009-0081562] Funding Source: Korea Institute of Science & Technology Information (KISTI), National Science & Technology Information Service (NTIS)

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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 (T-obs approximate to 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.

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