Effects of Preferential Counterion Interactions on the Specificity of RNA Folding

Journal Article · Thu Sep 13 00:00:00 EDT 2018 · Journal of Physical Chemistry Letters

DOI:https://doi.org/10.1021/acs.jpclett.8b02086· OSTI ID:1478094

Roh, Joon Ho ^[1]; Kilburn, Duncan ^[2]; Behrouzi, Reza ^[3]; Sung, Wokyung ^[4]; Briber, R. M. ^[5]; Woodson, Sarah A. ^[2]

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1. Univ. of Maryland, College Park, MD (United States); Johns Hopkins Univ., Baltimore, MD (United States)
2. Johns Hopkins Univ., Baltimore, MD (United States)
3. Harvard Medical School, Boston, MA (United States)
4. Pohang Univ. of Science and Technology (Korea)
5. Univ. of Maryland, College Park, MD (United States)

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, Mg²⁺ exhibits a smaller preferential interaction coefficient per charge, ΔΓ₊/Z, than Na⁺ or [Co(NH₃)₆]³⁺. The lower ΔΓ₊/Z corresponds to a smaller yield of folded RNA, although Mg²⁺ stabilizes native RNA more efficiently than other ions at equilibrium. Here, these results suggest that strong Mg²⁺–RNA interactions impede the search for globally native structure during early folding stages.

• Research Organization: Argonne National Laboratory (ANL), Argonne, IL (United States)
• Sponsoring Organization: NIH; USDOE Office of Science (SC)
• Grant/Contract Number: AC02-06CH11357
• OSTI ID: 1478094
• Journal Information: Journal of Physical Chemistry Letters, Journal Name: Journal of Physical Chemistry Letters Journal Issue: 19 Vol. 9; ISSN 1948-7185
• Publisher: American Chemical Society
• Country of Publication: United States
• Language: ENGLISH

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
counterions
cytosine
genetics
ions
kinetics