title: Selection and characterization of dimethylindole red DNA aptamers for the development of light-up fluorescent probes.
abstract: To develop novel label-free light-up probes with improved performance characteristics and low background, we selected DNA aptamers for dimethylindole red (DIR) by a modified affinity chromatography based SELEX method. DIR is an anionic propylsulfonate substituted red-emitting dye derivative of thiazole orange and exhibited weak fluorescence in fluid solution and in the presence of dsDNA. After 14 rounds of selection, a shortened 42-mer DNA aptamer with sub-micromolar dissociation constant (Kd=0.65±0.17μM) was selected. The fluorescent intensity of DIR was dramatically enhanced in the presence of the specific aptamer. The aptamer gave a 140-fold fluorescence enhancement in a saturated concentration. The DIR-aptamer pair could be potentially used as novel light-up fluorescent probe to construct sensors for various applications.
authors.affiliation: Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China.
authors.forename: Hongyan
authors.initials: H
authors.lastname: Wang
authors.affiliation: Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China.
authors.forename: Jine
authors.initials: J
authors.lastname: Wang
authors.affiliation: Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China.
authors.forename: Qinglin
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Public Health of Guangxi Medical University, Nanning 530021, China.
authors.forename: Xing
authors.initials: X
authors.lastname: Chen
authors.affiliation: Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China.
authors.forename: Min
authors.initials: M
authors.lastname: Liu
authors.affiliation: School of Life Science, Shanghai University, Shanghai 200444, China.
authors.forename: Hongxia
authors.initials: H
authors.lastname: Chen
authors.affiliation: Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China. Electronic address: rjpei2011@sinano.ac.cn.
authors.forename: Renjun
authors.initials: R
authors.lastname: Pei
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D015374:Biosensing Techniques / Q000379:methods*; D002232:Carbocyanines / Q000737:chemistry*; D004247:DNA / Q000032:analysis*; D005453:Fluorescence; D005456:Fluorescent Dyes / Q000737:chemistry*; D006801:Humans; D007211:Indoles / Q000737:chemistry*; D052156:SELEX Aptamer Technique; D013050:Spectrometry, Fluorescence
chemical_list: D052157:Aptamers, Nucleotide; D002232:Carbocyanines; D005456:Fluorescent Dyes; D007211:Indoles; C572069:dimethylindole red; D004247:DNA
keywords: Aptamer; Dimethylindole red; Light-up probes; SELEX