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Tuning Riboswitch‐Mediated Gene Regulation by Rational Control of Aptamer Ligand Binding Properties
Author(s) -
Rode Ambadas B.,
Endoh Tamaki,
Sugimoto Naoki
Publication year - 2015
Publication title -
angewandte chemie
Language(s) - English
Resource type - Journals
eISSN - 1521-3757
pISSN - 0044-8249
DOI - 10.1002/ange.201407385
Subject(s) - aptamer , riboswitch , dissociation constant , chemistry , ligand (biochemistry) , rational design , small molecule , biophysics , stereochemistry , binding site , rna , combinatorial chemistry , biochemistry , biology , gene , genetics , receptor , non coding rna
Riboswitch‐mediated control of gene expression depends on ligand binding properties (kinetics and affinity) of its aptamer domain. A detailed analysis of interior regions of the aptamer, which affect the ligand binding properties, is important for both understanding natural riboswitch functions and for enabling rational design of tuneable artificial riboswitches. Kinetic analyses of binding reaction between flavin mononucleotide (FMN) and several natural and mutant aptamer domains of FMN‐specific riboswitches were performed. The strong dependence of the dissociation rate (52.6‐fold) and affinity (100‐fold) on the identities of base pairs in the aptamer stem suggested that the stem region, which is conserved in length but variable in base‐pair composition and context, is the tuning region of the FMN‐specific aptamer. Synthetic riboswitches were constructed based on the same aptamer domain by rationally modifying the tuning regions. The observed 9.31‐fold difference in the half‐maximal effective concentration (EC 50 ) corresponded to a 11.6‐fold difference in the dissociation constant ( K D ) of the aptamer domains and suggested that the gene expression can be controlled by rationally adjusting the tuning regions.