title: Optimization of RNA-based c-di-GMP fluorescent sensors through tuning their structural modules.
abstract: Cyclic diguanylate (c-di-GMP) is a second messenger of bacteria and its detection is an important issue in basic and applied microbiology. As c-di-GMP riboswitch ligand-binding domains (aptamer domains) capture c-di-GMP with high affinity and selectivity, they are promising platforms for the development of RNA-based c-di-GMP sensors. We analyzed two previously reported c-di-GMP sensor RNAs derived from the Vc2 riboswitch. We also designed and tested their variants, some of which showed improved properties as RNA-based c-di-GMP sensors.
authors.affiliation: Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan.
authors.forename: Saki
authors.initials: S
authors.lastname: Inuzuka
authors.affiliation: Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan.
authors.forename: Shigeyoshi
authors.initials: S
authors.lastname: Matsumura
authors.affiliation: Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan. Electronic address: yikawa@sci.u-toyama.ac.jp.
authors.forename: Yoshiya
authors.initials: Y
authors.lastname: Ikawa
mesh_terms: D052157:Aptamers, Nucleotide / Q000032:analysis* / Q000737:chemistry / Q000235:genetics; D001483:Base Sequence; D015374:Biosensing Techniques / Q000379:methods* / Q000592:standards; D006152:Cyclic GMP / Q000031:analogs & derivatives* / Q000032:analysis / Q000737:chemistry; D005453:Fluorescence; D008024:Ligands; D012313:RNA / Q000032:analysis* / Q000737:chemistry* / Q000235:genetics; D058928:Riboswitch; D015290:Second Messenger Systems; D018724:Spinacia oleracea / Q000235:genetics
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D058928:Riboswitch; C062025:bis(3',5')-cyclic diguanylic acid; D012313:RNA; D006152:Cyclic GMP
keywords: Fluorescent sensor; RNA-based sensor; Riboswitch; Spinach RNA; c-Di-GMP