Capture-SELEX of DNA Aptamers for Sulforhodamine B and Fluorescein

Lide, Gu

https://ror.org/00mcjh785;https://ror.org/01aff2v68

Xiamen University;University of Waterloo

https://orcid.org/0000-0002-9466-9674

Jiajie, Zheng

https://ror.org/01aff2v68

University of Waterloo

Yao, Zhang

https://ror.org/00mcjh785

Xiamen University

Deli, Wang

https://ror.org/00mcjh785

Xiamen University

Juewen, Liu

https://ror.org/01aff2v68

University of Waterloo

https://orcid.org/0000-0001-5918-9336

2023-04-01/2023-09-16

2023-09-25T13:58:07Z

2023-09-25T13:58:07Z

2023-09-25

https://www.frdr-dfdr.ca/repo/dataset/efb537e4-0c62-4a6c-86e8-7d22a79a8d0a

https://doi.org/10.20383/103.0808

While many dye binding aptamers have been reported, most of them were for light-up aptamers
that can significantly enhance the quantum yield of fluorophores. Sulforhodamine B (SRhB) was
used as a target previously to select both DNA and RNA aptamers, and the DNA aptamer was a
G-quadruplex that can bind to a number of rhodamine analogs. In addition, the previous selections were performed by immobilizing the target molecules. In this work, we used the
library immobilization method to respectively select aptamers for SRhB and fluorescein. The
SRhB aptamer has a non-G-quadruplex structure with a Kd of 1.0 µM measured from isothermal
titration calorimetry. Upon titration of the aptamer, the fluorescence of SRhB increased 2.5-fold,
and this aptamer does not require Mg2+ for binding. Rhodamine B has even tighter binding suggesting binding through the xanthene moiety of the dyes. No binding was detected for
fluorescein. For the fluorescein selection, a dominant aptamer sequence with a Kd of 147 µM was obtained. This study provides two new aptamers for two important fluorophores that can be used to study aptamer-based separation, dye detection, and catalysis. Comparison of these aptamers also provides insights into the effect of functional groups on aptamer binding.

Federated Research Data Repository / dépôt fédéré de données de recherche

Creative Commons Public Domain Dedication (CC0 1.0)

https://creativecommons.org/publicdomain/zero/1.0/

Aptamers

Biosensors

Fluorescein

Sulforhodamine B

SELEX

Capture-SELEX of DNA Aptamers for Sulforhodamine B and Fluorescein

f163c1b3-9c88-42f6-a7bb-5839ed6c4063

/2/published/publication_803/

2023

Lide Gu

Juewen Liu

2023-04-01/2023-09-16

Dataset

Natural Sciences and Engineering Research Council of Canada (NSERC)

RDF1060101

Biological sciences

Biochemistry

Analytical biochemistry

Sciences biologiques

Biochimie

Biochimie analytique