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

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.

SUBMITTER: Gustmann H

PROVIDER: S-EPMC6326822 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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

Gustmann Henrik H Segler Anna-Lena J AJ Gophane Dnyaneshwar B DB Reuss Andreas J AJ Grünewald Christian C Braun Markus M Weigand Julia E JE Sigurdsson Snorri Th ST Wachtveitl Josef J

Nucleic acids research 20190101 1

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 ...[more]

PMID: 30462266

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