Open AccessEffects of Preferential Counterion Interactions on the Specificity of RNA Folding
Author(s) -
Joon Ho Roh,
Duncan Kilburn,
Reza Behrouzi,
Wonyong Sung,
Robert M. Briber,
Sarah A. Woodson
Publication year - 2018
Publication title -
the journal of physical chemistry letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.563
H-Index - 203
ISSN - 1948-7185
DOI - 10.1021/acs.jpclett.8b02086
Subject(s) - ribozyme , rna , counterion , folding (dsp implementation) , chemistry , chemical physics , biophysics , population , crystallography , protein folding , ion , biology , biochemistry , demography , organic chemistry , sociology , electrical engineering , gene , engineering
The real-time search for native RNA structure is essential for the operation of regulatory RNAs. We previously reported that a fraction of the Azoarcus ribozyme achieves a compact structure in less than a millisecond. To scrutinize the forces that drive initial folding steps, we used time-resolved SAXS to compare the folding dynamics of this ribozyme in thermodynamically isostable concentrations of different counterions. The results show that the size of the fast-folding population increases with the number of available counterions and correlates with the flexibility of initial RNA structures. Within 1 ms of folding, Mg 2+ exhibits a smaller preferential interaction coefficient per charge, ΔΓ + / Z, than Na + or [Co(NH 3 ) 6 ] 3+ . The lower ΔΓ + / Z corresponds to a smaller yield of folded RNA, although Mg 2+ stabilizes native RNA more efficiently than other ions at equilibrium. These results suggest that strong Mg 2+ -RNA interactions impede the search for globally native structure during early folding stages.