Háskóli ÍslandsUniversity of IcelandGustmann, HenrikSegler, Anna-Lena JGophane, Dnyaneshwar BReuss, Andreas JGrünewald, ChristianBraun, MarkusWeigand, JuliaSigurdsson, SnorriWachtveitl, Josef2020-05-282020-05-282018-11-20Henrik Gustmann, Anna-Lena J Segler, Dnyaneshwar B Gophane, Andreas J Reuss, Christian Grünewald, Markus Braun, Julia E Weigand, Snorri Th Sigurdsson, Josef Wachtveitl, Structure guided fluorescence labeling reveals a two-step binding mechanism of neomycin to its RNA aptamer, Nucleic Acids Research, Volume 47, Issue 1, 10 January 2019, Pages 15–280305-10481362-4962 (eISSN)https://hdl.handle.net/20.500.11815/1856Publisher's version (útgefin grein)The ability of the cytidine analog Ç m f to act as a position specific reporter of RNA-dynamics was spectroscopically evaluated. Ç m f-labeled single-and double-stranded RNAs differ in their fluorescence lifetimes, quantum yields and anisotropies. These observables were also influenced by the nucleobases flanking Ç m f. This conformation and position specificity allowed to investigate the binding dynamics and mechanism of neomycin to its aptamer N1 by independently incorporating Ç m f 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.15-28eninfo:eu-repo/semantics/openAccessGeneticsRNAErfðafræðiDNA-rannsóknirinfo:eu-repo/semantics/articleNucleic Acids Research10.1093/nar/gky1110