Structure guided fluorescence labeling reveals a two-step binding mechanism of neomycin to its RNA aptamer 

April 9, 2019

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.

Instrument

V-650, FP-8500

Keywords

RNA structure, Thermal stability, Thermodynamics, Biochemistry, Fluorescence, Quantum yield, Stopped flow, Kinetics, Anisotropy