DNAzyme–aptamer or aptamer–DNAzyme paradigm: Biochemical approach for aflatoxin analysis

Abstract

DNAzyme and aptamer conjugations have already been used for sensitive and accurate detection of several molecules. In this study, we tested the relationship between conjugation orientation of DNAzyme and aflatoxin B1 aptamer and their subsequent peroxidase activity. Circular dichroism (CD) spectroscopy and biochemical analysis were used here to differentiate between these two conjugation patterns. Results showed that DNAzyme-aptamer has more catalytic activity and efficiency than aptamer-DNAzyme. Thereby, DNAzyme-aptamer with its superior efficiency can be used for design and development of more sensitive aflatoxin B1 DNA based biosensors.

Recent advances in computational methods for biosensor design

“…Frequently, aptamers can refold to their native structures after changing the denaturing conditions to the natural ones. Besides, they can maintain their functionality under some denaturing conditions, such as urine (M. Jafari et al, 2018; Khoshbin, Housaindokht, et al, 2018; Khoshbin, Verdian, et al, 2018; Y. Li et al, 2018; J. Liu et al, 2014; Verdian, 2018).…”

“…Aptamers are obtained from the random oligonucleotide libraries through the systematic evolution of ligands by the exponential enrichment (SELEX) process including the repetitive processes of binding, selection, and amplification of oligonucleotides (Bai et al, 2017; Bostan et al, 2017; M. Jafari et al, 2018; Khoshbin, Housaindokht, Izadyar, Verdian, et al, 2019; S.‐E. Wang & Si, 2013).…”

Optimization of Aflatoxin B1 Aptasensing

“…DNAzyme sequence can attach to either 5′ or 3′ ends of aptamer sequence yield DNAzyme-aptamer or aptamer-DNAzyme ( Table 1 and Figure 1 ). In our previous study, we investigated the relationship between the orientation of the DNAzyme and aptamer conjugation and their final peroxidase activities [ 27 ]. As seen in Table 2 , DNAzyme-aptamer displayed a higher enzymatic activity than 3′ oriented conjugation.…”

Practical Application of Aptamer-Based Biosensors in Detection of Low Molecular Weight Pollutants in Water Sources

“…Some sensing platforms using Pb 2+ specific DNAzyme base on quartz crystal microbalance with dissipation (QCM-D) [ 132 ] and ZnO nanoflower (NF) photoelectrochemical (PEC) analysis [ 133 ] are also used in detecting Pb 2+ in water samples. In comparison with enzymes and antibodies, DNAzymes and aptamers have remarkable advantages [ 31 ]. As mentioned above, aptamers and DNAzymes are mainly used for detecting Pb 2+ in water sample, thus nucleic acids-based biosensors can be further developed for Pb 2+ pollutant monitoring.…”

“…Compared to the generation of antibodies, SELEX processes allow greater control over binding conditions, and allows selection under non-physiological conditions [ 4 , 30 ]. In addition, DNA has higher stability and tolerance in different physical and chemical conditions than proteins (e.g., high temperature or extreme pH) [ 31 , 32 ]. How to generate aptamers for low weight molecules has been well reported or reviewed recently by Yang et al [ 33 ], Pfeiffer and Mayer [ 4 ], and Kin and Gu [ 30 ].…”