期刊
RNA BIOLOGY
卷 15, 期 10, 页码 1376-1383出版社
TAYLOR & FRANCIS INC
DOI: 10.1080/15476286.2018.1534526
关键词
RNA ligand recognition; modifications; riboswitches; kinetics; thermodynamics; RNA biosensor tools; preQ(1) derivatives
资金
- Austrian Science Fund FWF [I1040, P27947, P27024]
- Austrian Research Promotion Agency FFG [West Austrian BioNMR] [858017]
- Austrian Science Fund (FWF) [P27024] Funding Source: Austrian Science Fund (FWF)
For this study, we utilized class-I and class-II preQ(1)-sensing riboswitches as model systems to decipher the structure-activity relationship of rationally designed ligand derivatives in vitro and in vivo. We found that synthetic preQ(1) ligands with amino-modified side chains that protrude from the ligand-encapsulating binding pocket, and thereby potentially interact with the phosphate backbone in their protonated form, retain or even increase binding affinity for the riboswitches in vitro. They, however, led to significantly lower riboswitch activities in a reporter system in vivo in E. coli. Importantly, when we substituted the amino- by azido-modified side chains, the cellular activities of the ligands were restored for the class-I conditional gene expression system and even improved for the class-II counterpart. Kinetic analysis of ligand binding in vitro revealed enhanced on-rates for amino-modified derivatives while they were attenuated for azido-modified variants. This shows that neither high affinities nor fast on-rates are necessarily translated into efficient cellular activities. Taken together, our comprehensive study interconnects in vitro kinetics and in vitro thermodynamics of RNA-ligand binding with the ligands' in vivo performance and thereby encourages azido- rather than amino-functionalized design for enhanced cellular activity.
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