Bistable secondary structures of small RNAs and their structural probing by comparative imino proton NMR spectroscopy.
We investigate 25-34 nucleotide RNA sequences, that have been rationally designed to adopt two different secondary structures that are in thermodynamic equilibrium. Experimental evidence for the co-existence of the two conformers results from the NH...N 1H NMR spectra. When compared to the NH...N 1H NMR spectra of appropriate reference sequences the equilibrium position is easily quantifiable even without the assignment of the individual NH resonances. The reference sequences represent several Watson-Crick base-paired double helical segments, each encountered in either of the two conformers of the bistable target sequence. In addition, we rationalize the influence of nucleotide mutations on the equilibrium position of one of the bistable RNA sequences. The approach further allows a detailed thermodynamic analysis and the evaluation of secondary structure predictions for multistable RNAs obtained by computational methods.
Höbartner
Claudia
C
Institute of Organic Chemistry, Leopold Franzens University, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria.
Micura
Ronald
R
D001482:Base Composition; D020029:Base Pairing; D001483:Base Sequence; D007098:Imino Acids / Q000737:chemistry* / Q000378:metabolism; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D020871:RNA Stability; D013696:Temperature; D013816:Thermodynamics
D007098:Imino Acids; D012313:RNA