title: Selective recognition of parallel and anti-parallel thrombin-binding aptamer G-quadruplexes by different fluorescent dyes.
abstract: G-quadruplexes (G4) have been found increasing potential in applications, such as molecular therapeutics, diagnostics and sensing. Both Thioﬂavin T (ThT) and N-Methyl mesoporphyrin IX (NMM) become fluorescent in the presence of most G4, but thrombin-binding aptamer (TBA) has been reported as the only exception of the known G4-forming oligonucleotides when ThT is used as a high-throughput assay to identify G4 formation. Here, we investigate the interactions between ThT/NMM and TBA through fluorescence spectroscopy, circular dichroism and molecular docking simulation experiments in the absence or presence of cations. The results display that a large ThT ﬂuorescence enhancement can be observed only when ThT bind to the parallel TBA quadruplex, which is induced to form by ThT in the absence of cations. On the other hand, great promotion in NMM fluorescence can be obtained only in the presence of anti-parallel TBA quadruplex, which is induced to fold by K+ or thrombin. The highly selective recognition of TBA quadruplex with different topologies by the two probes may be useful to investigate the interactions between conformation-specific G4 and the associated proteins, and could also be applied in label-free fluorescent sensing of other biomolecules.
authors.affiliation: Key Laboratory of Pesticide and Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan 430079, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Pesticide and Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan 430079, China.
authors.forename: Xiongwei
authors.initials: X
authors.lastname: Dong
authors.affiliation: Key Laboratory of Pesticide and Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan 430079, China.
authors.forename: Nan
authors.initials: N
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Pesticide and Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan 430079, China danzhang@mail.ccnu.edu.cn.
authors.forename: Dan
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Pesticide and Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan 430079, China danzhang@mail.ccnu.edu.cn.
authors.forename: Changlin
authors.initials: C
authors.lastname: Liu
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D052160:Benzothiazoles; D005456:Fluorescent Dyes / Q000737:chemistry*; D054856:G-Quadruplexes; D008652:Mesoporphyrins / Q000737:chemistry*; D062105:Molecular Docking Simulation; D013844:Thiazoles / Q000737:chemistry*
chemical_list: D052157:Aptamers, Nucleotide; D052160:Benzothiazoles; D005456:Fluorescent Dyes; D008652:Mesoporphyrins; D013844:Thiazoles; C065420:N-methylmesoporphyrin IX; C081676:thrombin aptamer; C009462:thioflavin T