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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.; Kobitski, A. Yu.

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 o ... mehr


Zugehörige Institution(en) am KIT Institut für Angewandte Physik (APH)
Publikationstyp Zeitschriftenaufsatz
Jahr 2011
Sprache Englisch
Identifikator ISSN: 0006-2960
KITopen ID: 1000027122
Erschienen in Biochemistry
Band 50
Heft 15
Seiten 3107 - 3115
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