DNA module platform for developing colorimetric aptamer sensors

Abstract

Here we present a DNA module platform for developing simple aptamer sensors based on a microarray format combined with secondary structure prediction in silico. The platform comprises four parts: (i) aptamer, (ii) joint module, (iii) terminal stem, and (iv) a DNAzyme that catalyzes a redox reaction controlled by a structural change induced by aptamer/target binding. First, we developed a joint module, capable of sensing a conformational change in the aptamer region, that was linked to the signal transmission activity of a DNAzyme as the reporter in a concentration-dependent manner with the AMP aptamer. This module design was then used to generate an arginine sensor simply by replacing the AMP aptamer region with a previously reported arginine aptamer. Using this DNA module platform, we were also able to customize a microarray containing >10,000 sequences designed by in silico secondary structure prediction and successfully identify a new aptamer against patulin. Our results show that the DNA module platform can be used to readily devise sensors based on known aptamers as well as create new aptamer sensors by array-based screening.

An Aptamer-Based Biosensor for Direct, Label-Free Detection of Melamine in Raw Milk

“…Most of the sequences containing no aptamer block sequence showed better S/N ratios ( Supplementary Figure S2 ). This specific case was different from that of the streptavidin biosensor, the AMP biosensor [ 13 ], and the patulin biosensor [ 14 ].…”

“…The aptamer-DNAzyme conjugated biosensor requires block sequences of appropriate length, for both the aptamer and the DNAzyme, and for the internal loop sequences, to couple the aptamer and DNAzyme to the block sequences. Owing to the numerous combinations of the sequence lengths, redox activity microarray technology has been used to screen biosensors [ 14 , 15 ]. Moreover, the DNAzyme activity increases the fluorescence signal intensity of N -methylmesoporphyrin IX (NMM) [ 16 , 17 ].…”

Fast Detection of Chloramphenicol in Raw Milk Using a Hairpin Aptamer-templated Silver Nanoclusters

“…Based on the above designs, our plan will combine more strategies, having a wider range of application in the future. It is expected to achieve better results when combined with other strategies, such as electrochemical adapter sensor [90,91], colorimetric aptamer sensor [92][93][94][95][96][97][98][99], strand displacement amplification reaction (SDA) [100][101][102], hybridization chain reaction (HCR) [103][104][105][106] and catalyzed hairpin assembly (CHA) [107][108][109]. In addition, through the recovery test in milk, the practicability was verified successfully.…”

Mycotoxin Contamination of Beverages Obtained from Tropical Crops

“…Aptamer-based technologies are an example of a recent approach [223]. As an example of a novel non-chromatographic analytical method, an aptamer-based technology for the detection of PAT has been described [224]. A comprehensive review of other techniques applied to the mycotoxin analysis in fruits can be found elsewhere [7].…”

“…For example, in Iran, non-alcoholic beverages have been evaluated for mycotoxins using ELISA, and higher levels were found in local samples (5.00 × 10 −4 -5.54 × 10 −1 µg L −1 ) than those that were imported (9.00 × 10 −4 -2.29 × 10 −1 µg L −1 ) [225]. Most of the immunology-based research for mycotoxin detection is based on the preparation of monoclonal antibodies against the metabolite; these antibodies can be further applied in ELISA techniques and immunoaffinity columns for sample preparation before fluorimetry of HPLC [224]. For example, monoclonal antibodies against OTB were prepared to assay coffee samples [226].…”