Ligand-detected relaxation dispersion NMR spectroscopy: dynamics of preQ1-RNA binding.
An NMR-based approach to characterizing the binding kinetics of ligand molecules to biomolecules, like RNA or proteins, by ligand-detected Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments is described. A (15)N-modified preQ1 ligand is used to acquire relaxation dispersion experiments in the presence of low amounts of the Fsu class I preQ1 aptamer RNA, and increasing ligand concentrations to probe the RNA small molecule interaction. Our experimental data strongly support the conformational selection mechanism postulated. The approach gives direct access to two parameters of a ligand-receptor interaction: the off rate and the population of the small molecule-receptor complex. A detailed description of the kinetics underlying the ligand binding process is of crucial importance to fully understanding a riboswitch's function and to evaluate potential new antibiotics candidates targeting the noncoding RNA species. Ligand-detected NMR relaxation dispersion experiments represent a valuable diagnostic tool for the characterization of binding mechanisms.
Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria).
Thomas
T
Moschen
Christoph Hermann
CH
Wunderlich
Romana
R
Spitzer
Jasmin
J
Levic
Ronald
R
Micura
Martin
M
Tollinger
Christoph
C
Kreutz
D052157:Aptamers, Nucleotide / Q000737:chemistry*; D008024:Ligands; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*
D052157:Aptamers, Nucleotide; D008024:Ligands
NMR spectroscopy; aptamers; conformation analysis; nucleotides; receptors