title: Structure-activity studies on the fluorescent indicator in a displacement assay for the screening of small molecules binding to RNA.
abstract: A series of xanthone and thioxanthone derivatives with aminoalkoxy substituents were synthesized as fluorescent indicators for a displacement assay in the study of small-molecule-RNA interactions. The RNA-binding properties of these molecules were investigated in terms of the improved binding selectivity to the loop region in the RNA secondary structure relative to 2,7-bis(2-aminoethoxy)xanthone (X2S) by fluorimetric titration and displacement assay. An 11-mer double-stranded RNA and a hairpin RNA mimicking the stem loop IIB of Rev response element (RRE) RNA of HIV-1 mRNA were used. The X2S derivatives with longer aminoalkyl substituents showed a higher affinity to the double-stranded RNA than the parent molecule. Introduction of a methyl group on the aminoethoxy moiety of X2S effectively modulated the selectivity to the RNA secondary structure. Methyl group substitution at the C1' position suppressed the binding to the loop regions. Substitution with two methyl groups on the amino nitrogen atom resulted in reducing the affinity to the double-stranded region by a factor of 40%. The effect of methyl substitution on the amino nitrogen atom was also observed for a thioxanthone derivative. Titration experiments, however, suggested that thioxanthone derivatives showed a more prominent tendency of multiple binding to RNA than xanthone derivatives. The selectivity index calculated from the affinity to the double-stranded and loop regions suggested that the N,N-dimethyl derivative of X2S would be suitable for the screening of small molecules binding to RRE.
authors: Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
authors: Shiori
authors: S
authors: Umemoto
authors: Seongwang
authors: S
authors: Im
authors: Jinhua
authors: J
authors: Zhang
authors: Masaki
authors: M
authors: Hagihara
authors: Asako
authors: A
authors: Murata
authors: Yasue
authors: Y
authors: Harada
authors: Takeo
authors: T
authors: Fukuzumi
authors: Takahiro
authors: T
authors: Wazaki
authors: Shin-ichi
authors: S
authors: Sasaoka
authors: Kazuhiko
authors: K
authors: Nakatani
mesh_terms: D001665:Binding Sites; D005456:Fluorescent Dyes / Q000737:chemistry*; D015752:Genes, env; D015497:HIV-1 / Q000737:chemistry; D007202:Indicators and Reagents / Q000737:chemistry*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D017433:Protein Structure, Secondary; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D012330:RNA, Double-Stranded / Q000737:chemistry* / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D013329:Structure-Activity Relationship; D013892:Thioxanthenes / Q000737:chemistry; D044004:Xanthones / Q000138:chemical synthesis / Q000737:chemistry*; D054321:rev Gene Products, Human Immunodeficiency Virus / Q000737:chemistry* / Q000378:metabolism
chemical_list: C577041:2,7-bis(2-aminoethoxy)xanthone; D005456:Fluorescent Dyes; D007202:Indicators and Reagents; D012330:RNA, Double-Stranded; D012367:RNA, Viral; D013892:Thioxanthenes; D044004:Xanthones; D054321:rev Gene Products, Human Immunodeficiency Virus; D012313:RNA; C484911:thioxanthone