Masatora Fukuda

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The structural characteristics of RNA-peptide (RNP) complexes are suitable for molding of a ligand-binding pocket of the RNP complex in a stepwise manner. The first step involves molding of the RNA subunit by in vitro selection of an RNP pool originating from an RNA library and the peptide, as previously reported for the construction of an ATP-binding RNP(More)
Fluorescent biosensors that facilitate reagentless sensitive detection of small molecules are crucial tools in the areas of therapeutics and diagnostics. However, construction of fluorescent biosensors with desired characteristics, that is, detection wavelengths and concentration ranges for ligand detection, from macromolecular receptors is not a(More)
Tools for selective recognition and sensing of specific phosphorylated tyrosine residues on the protein surface are essential for understanding signal transduction cascades in the cell. A stable complex of RNA and peptide, a ribonucleopeptide (RNP), provides effective approaches to tailor RNP receptors and fluorescent RNP sensors for small molecules. In(More)
We describe here a novel strategy to create a ribonucleopeptide (RNP) receptor with defined substrate-binding geometry. RNP library was generated by introducing randomized nucleotide sequences in the RNA subunit of the structurally well-defined complex of RRE-RNA and the Rev peptide by a structure-based design. ATP-binding RNP receptors were selected from(More)
A stable complex of a peptide and RNA, ribonucleopeptide (RNP), provides a new framework to construct a macromolecular receptor for small molecules. The RNP receptor functionalized by a fluorophore-labeled Rev peptide exerts an optical signal associated with the ligand binding events. Replacing the Rev peptide of the ATP-binding RNP with a(More)
We describe here analyses of the secondary structure of ATP-binding ribonucleopeptide (RNP) receptors. Mapping of the RNA structure of ATP-binding RNP receptors by using hydrolytic enzymes, chemical probing with dimethyl sulfate (DMS), and in-line probing indicated that ATP-binding RNP receptors take the loop structure at the nucleotide position of the(More)
Fluorescent biosensors based on the biological macromolecule are convenient tools for investigating the event occurring in the living cell. As for one of the candidates of such biosensors, we have reported a fluorescent sensor by utilizing a ribonucleopeptide (RNP) framework. Fluorescent RNP sensors are obtained from the fluorescent RNP library constructed(More)
We describe here a ribonucleopeptide (RNP) receptor targeting a tetra-amino-acid motif containing phosphotyrosine, GpYSR. GpYSR-binding RNP receptors were obtained from an RNA-based RNP library by in vitro selection. These receptors have a higher affinity than those of previously obtained pY-binding RNP receptors. One of these RNP receptors exhibited unique(More)
We describe here a novel strategy to create a stable functional ribonucleopeptide (RNP) complex by the covalent linking method. Adenosine-5'-triphosphate (ATP)-binding RNP receptors were selected from the RNP library by in vitro selection. The RNA subunit of RNP is utilized to construct a ligand-binding cavity, while the peptide subunit can be(More)