Dresden 2014 – wissenschaftliches Programm
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BP: Fachverband Biologische Physik
BP 2: DNA/RNA and related enzymes
BP 2.5: Vortrag
Montag, 31. März 2014, 10:30–10:45, ZEU 250
Complex RNA folding kinetics revealed by single molecule FRET and hidden Markov models — •Bettina Keller1, Andrei Kobitski2, G. Ulrich Nienhaus2, and Frank Noé3 — 1Freie Universität Berlin, Institut für Chemie, Takustr. 3, 14195 — 2Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany — 3Freie Universität Berlin, Institut für Mathematik, Arnimallee 6, 14195
We have developed a hidden Markov model and optimization procedure for photon-based single-molecule FRET data, which takes into account the trace-dependent background intensities. This analysis technique reveals an unprecedented amount of detail in the folding kinetics of the Diels-Alderase ribozyme. Depending on the Mg2+ concentration, 7 to 9 states can be distinguished, including putative native, near-native and misfolded states. Some states exist only at either low or high Mg2+ concentrations, while other states exhibit little sensitivity to Mg2+. There is a general tendency for structures to become more compact upon the addition of Mg2+. A hierarchy of timescales was found, including dynamics of 10 ms or faster, likely due to tertiary structure fluctuations, and slow dynamics on the seconds timescale, presumably associated with significant changes in secondary structure. The folding pathways proceed through a series of intermediate secondary structures. There exist both, compact pathways and more complex ones in which structures show tertiary unfolding, then secondary refolding, and subsequently tertiary refolding.