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Single-molecule FRET Studies of Counterion Effects on the Free Energy Landscape of Human Mitochondrial Lysine tRNA

Dammertz, K.; Hengesbach, M.; Helm, M.; Nienhaus, G. U. ORCID iD icon 1; Kobitski, A. Yu. 1
1 Center for Functional Nanostructures (CFN), Karlsruher Institut für Technologie (KIT)

Abstract:

The folding energy landscape of RNA is greatly affected by interactions between the RNA and counterions that neutralize the backbone negative charges and may also participate in tertiary contacts. Valence, size, coordination number, and electron shell structure can all contribute to the energetic stabilization of specific RNA conformations. Using single-molecule fluorescence resonance energy transfer (smFRET), we have examined the folding properties of the RNA transcript of human mitochondrial tRNALys, which possesses two different folded states in addition to the unfolded one under conditions of thermodynamic equilibrium. We have quantitatively analyzed the degree of RNA tertiary structure stabilization for different types of cations based on a thermodynamic model that accounts for multiple conformational states and RNA−ion interactions within each state. We have observed that small monovalent ions stabilize the tRNA tertiary structure more efficiently than larger ones. More ions were found in close vicinity of compact RNA structures, independent of the type of ion. The largest conformation-dependent binding specificity of ions of the same charge was found for divalent ions, for which the ionic radii and coordination properties were responsible for shaping the folding free energy.


Originalveröffentlichung
DOI: 10.1021/bi101804t
Scopus
Zitationen: 10
Web of Science
Zitationen: 12
Dimensions
Zitationen: 11
Zugehörige Institution(en) am KIT Institut für Angewandte Physik (APH)
Publikationstyp Zeitschriftenaufsatz
Publikationsjahr 2011
Sprache Englisch
Identifikator ISSN: 0006-2960
KITopen-ID: 1000027122
Erschienen in Biochemistry
Verlag American Chemical Society (ACS)
Band 50
Heft 15
Seiten 3107 - 3115
Nachgewiesen in Dimensions
Scopus
Web of Science
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