Selection and characterization of a DNA aptamer to crystal violet

Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society for Photobiology
Yang ChenRenjun Pei

Abstract

Aptamers are short single-stranded DNA or RNA, which can be selected in vitro by systematic evolution of ligands by exponential enrichment (SELEX). In order to develop novel light-up probes to substitute G-quadruplex (G4), we selected a DNA aptamer for crystal violet (CV), a triphenylmethane light-up dye, by a modified affinity chromatography-based SELEX. The ssDNA pool was first coupled on streptavidin-coated agarose beads through a biotin labeled complementary oligonucleotide, and then the aptamer sequences would be released from agarose beads by CV affinity. This method is simple, straightforward and effective. The aptamer sequence with a low micromolar dissociation constant (Kd) and good specificity was achieved after 11 rounds of selection. The light-up properties of the CV-aptamer were also investigated, and the CV showed dramatic fluorescence enhancement. The CV-aptamer pair could be further used as a novel light-up fluorescent probe to design biosensors.

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Citations

Jul 3, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Mubarak I UmarChun Kit Kwok
Aug 26, 2020·Chemistry : a European Journal·Yanwei CaoRenjun Pei
Mar 26, 2020·Angewandte Chemie·Dmitry M Kolpashchikov, Alexander A Spelkov
Mar 17, 2021·Chemical Communications : Chem Comm·Ryan P ConnellyYulia V Gerasimova

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Methods Mentioned

BETA
biosensors
SELEX
PCR
electrophoresis
Fluorescence
fluorescence spectroscopy

Software Mentioned

Clustalx
GENEWIZ
MEME
fold
Origin

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