Docking-aided rational tailoring of a fluorescence- and affinity-enhancing aptamer for a label-free ratiometric malachite green point-of-care aptasensor

Keren Chen; Longjiao Zhu; Zaihui Du; Xinyue Lan; Kunlun Huang; Wenqiang Zhang; Wentao Xu

doi:10.1016/j.jhazmat.2023.130798

Docking-aided rational tailoring of a fluorescence- and affinity-enhancing aptamer for a label-free ratiometric malachite green point-of-care aptasensor

J Hazard Mater. 2023 Apr 5:447:130798. doi: 10.1016/j.jhazmat.2023.130798. Epub 2023 Jan 14.

Authors

Keren Chen¹, Longjiao Zhu², Zaihui Du¹, Xinyue Lan¹, Kunlun Huang³, Wenqiang Zhang⁴, Wentao Xu⁵

Affiliations

¹ Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modiﬁed Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
² Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China.
³ Key Laboratory of Safety Assessment of Genetically Modiﬁed Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
⁴ Department of Mechanical Design and Manufacturing, College of Engineering, China Agricultural University, Beijing 100083, China.
⁵ Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modiﬁed Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China. Electronic address: xuwentao@cau.edu.cn.

PMID: 36669418
DOI: 10.1016/j.jhazmat.2023.130798

Abstract

Although nucleic acid aptasensors are increasingly applied in the detection of environmentally hazardous biomolecules, several formidable challenges remain with this technique because of their vulnerability, high cost and suboptimal sensitivity. Here, a docking-aided rational tailoring (DART) strategy was established at three levels and in two dimensions for the refinement of malachite green (MG) DNA aptamers. Guided by in silico molecular docking, coarse and fine tailoring were conducted at three levels each, to significantly enhance fluorescence activation intensity and binding affinity in two dimensions. Empowered by the results of the rational tailoring, a mechanistic view of the MG DNA aptamer-target interaction was thoroughly analyzed via four types of interactions. To meet the demand for point-of-care testing (POCT), a label-free and ratiometric fluorescent aptasensor was developed leveraging the tailored MG aptamer, based on the binding site competition-equilibrium effect via the introduction of a reference dye. This sensitive, specific, low-cost and rapid aptasensor subsequently demonstrated outstanding detection performance, achieving an ideal signal response range of 5 nmol·L^-1 - 6 μmol·L^-1 and a low limit of detection (LOD) of 1.49 nmol·L^-1. The DART strategy and systematic exploration of the MG DNA luminescent aptamers herein will provide a valuable reference in the field of aptamer tailoring, biosensing and bioimaging. The proposed label-free ratiometric aptasensor also provides a highly generalizable strategy for hazardous biomolecular detection.

Keywords: Label-free ratiometric biosensor; Malachite green; Molecular docking; Nucleic acid aptamers; Point-of-care testing; Rational tailoring.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Aptamers, Nucleotide* / chemistry
Biosensing Techniques* / methods
Hydrolases
Limit of Detection
Molecular Docking Simulation
Point-of-Care Systems
Rosaniline Dyes

Substances

malachite green
Aptamers, Nucleotide
Rosaniline Dyes
Hydrolases