Title
Structure guided fluorescence labeling reveals a two-step binding mechanism of neomycin to its RNA aptamer
Author
Henrik Gustmann,q Anna-Lena J Segler, Dnyaneshwar B Gophane, Andreas J Reuss, Christian Grünewald, Markus Braun, Julia E Weigand, Snorri Th Sigurdsson, Josef Wachtveitl
Year
2018
Journal
Nucleic Acids Research
Abstract
The ability of the cytidine analog Çmf to act as a position specific reporter of RNA-dynamics was spectroscopically evaluated. Çmf-labeled single- and double-stranded RNAs differ in their fluorescence lifetimes, quantum yields and anisotropies. These observables were also influenced by the nucleobases flanking Çmf. This conformation and position specificity allowed to investigate the binding dynamics and mechanism of neomycin to its aptamer N1 by independently incorporating Çmf at four different positions within the aptamer. Remarkably fast binding kinetics of neomycin binding was observed with stopped-flow measurements, which could be satisfactorily explained with a two-step binding. Conformational selection was identified as the dominant mechanism.
Full Article
Instrument
V-650, FP-8500
Keywords
RNA structure, Thermal stability, Thermodynamics, Biochemistry, Fluorescence, Quantum yield, Stopped flow, Kinetics, Anisotropy