Open AccessSelective recognition of parallel and anti-parallel thrombin-binding aptamer G-quadruplexes by different fluorescent dyes
Author(s) -
Dan Zhao,
Xiongwei Dong,
Nan Jiang,
Dan Zhang,
Changlin Liu
Publication year - 2014
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/gku833
Subject(s) - aptamer , g quadruplex , fluorescence , circular dichroism , oligonucleotide , molecular recognition , thrombin , biomolecule , green fluorescent protein , combinatorial chemistry , biophysics , biology , biochemistry , stereochemistry , chemistry , dna , molecule , microbiology and biotechnology , gene , physics , platelet , organic chemistry , quantum mechanics , immunology
G-quadruplexes (G4) have been found increasing potential in applications, such as molecular therapeutics, diagnostics and sensing. Both Thioavin 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 uorescence 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.