Folding studies of hyperstable RNA tetraloops through molecular dynamics

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Authors
Miner, Jacob Carlson
Issue Date
2016-08
Type
Electronic thesis
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Language
ENG
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Biology
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Abstract
The direct associations of RNA with its chemical environment are responsible for stabilizing multiple alternative configurations including left-handed helices in high concentrations of neutral salt, and unfolded configurations in denaturing cosolutes such as urea. Using concentrations of KCl (100 mM, 1 M, 2 M, 3 M) and high concentrations of urea (2 M, 4 M, 6 M), the preferential associations between these solution components with each other and the gcGCAAgc molecule are described in detail with isothermal (NVT) MD simulations. The ion associations match with experiments for similar concentrations and show saturation in the highest salt concentrations measured in our work. The associations of urea show that preferential associations between RNA and these denaturants match with observations of nucleobase-specific favorability from experiment, and additional analyses into the equilibrium stability of the model RNA stem-loop system show that urea preferentially disfavors formation of alternative configurations and reduces the variability of the configurational landscape.
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August 2016
School of Science
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Rensselaer Polytechnic Institute, Troy, NY
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