Cation-induced kinetic heterogeneity of the intron-exon recognition in single group II introns

Proceedings of the National Academy of Sciences of the United States of America
Danny KowerkoRoland K O Sigel

Abstract

RNA is commonly believed to undergo a number of sequential folding steps before reaching its functional fold, i.e., the global minimum in the free energy landscape. However, there is accumulating evidence that several functional conformations are often in coexistence, corresponding to multiple (local) minima in the folding landscape. Here we use the 5'-exon-intron recognition duplex of a self-splicing ribozyme as a model system to study the influence of Mg(2+) and Ca(2+) on RNA tertiary structure formation. Bulk and single-molecule spectroscopy reveal that near-physiological M(2+) concentrations strongly promote interstrand association. Moreover, the presence of M(2+) leads to pronounced kinetic heterogeneity, suggesting the coexistence of multiple docked and undocked RNA conformations. Heterogeneity is found to decrease at saturating M(2+) concentrations. Using NMR, we locate specific Mg(2+) binding pockets and quantify their affinity toward Mg(2+). Mg(2+) pulse experiments show that M(2+) exchange occurs on the timescale of seconds. This unprecedented combination of NMR and single-molecule Förster resonance energy transfer demonstrates for the first time to our knowledge that a rugged free energy landscape coincides with inco...Continue Reading

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Citations

Oct 17, 2015·Journal of the American Chemical Society·Krishna C SuddalaNils G Walter
Jun 19, 2016·Proceedings of the National Academy of Sciences of the United States of America·Michael HinczewskiD Thirumalai
Dec 28, 2016·PLoS Computational Biology·Wonseok HwangChangbong Hyeon
Oct 27, 2016·Physical Chemistry Chemical Physics : PCCP·Fabio D SteffenRichard Börner
Apr 14, 2018·PloS One·Richard BörnerRoland K O Sigel
Oct 26, 2018·Nature Communications·Wonseok HwangGwangrog Lee
Aug 18, 2017·Wiley Interdisciplinary Reviews. RNA·Louis G SmithDouglas H Turner
Jun 15, 2020·The Journal of Chemical Physics·Nadine Schwierz
Jun 15, 2021·Analytical Chemistry·Anisa KaurSoma Dhakal
Jan 4, 2018·Chemical Reviews·Jiří ŠponerMichal Otyepka
May 6, 2020·Langmuir : the ACS Journal of Surfaces and Colloids·Sergio Cruz-León, Nadine Schwierz

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