https://iopscience.iop.org/article/10.1149/2.0252003JES/pdf

Review—Measurement and Analysis of Cancer Biomarkers Based on Electrochemical Biosensors

Due to their relative synthetic and chemical simplicity compared to antibodies, aptamers afford enhanced stability and functionality for the detection of environmental contaminants and for use in environmental monitoring. Furthermore, nucleic acid aptamers can be selected for toxic targets which may prove difficult for antibody development. Of particular relevance, aptamers have been selected and used to develop biosensors for environmental contaminants such as heavy metals, small-molecule agricultural toxins, and water-borne bacterial pathogens. This review will focus on recent aptamer-based developments for the detection of diverse environmental contaminants. Within this domain, aptamers have been combined with other technologies to develop biosensors with various signal outputs. The goal of much of this work is to develop cost-effective, user-friendly detection methods that can complement or replace traditional environmental monitoring strategies. This review will highlight recent examples in this area. Additionally, with innovative developments such as wearable devices, sentinel materials, and lab-on-a-chip designs, there exists significant potential for the development of multifunctional aptamer-based biosensors for environmental monitoring. Examples of these technologies will also be highlighted. Finally, a critical perspective on the field, and thoughts on future research directions will be offered.

/pdf/aptamer-based-biosensors-for-environmental-monitoring-196jl1ch67.pdf

Aptamer-Based Biosensors for Environmental Monitoring.

Biosensors for the detection of pathogenic bacteria in food are a promising alternative to conventional methods of analysis. This review focuses on the electrochemical biosensors reported in recent years for use with food samples. It highlights the performance parameters of these sensors, and provides a critical discussion of current and future trends, including future commercialization.

Electrochemical biosensors for the detection of pathogenic bacteria in food

This article provides a comprehensive review of biosensing with DNAzymes, providing an overview of different sensing applications while highlighting major progress and seminal contributions to the field of portable biosensor devices and point-of-care diagnostics. Specifically, the field of functional nucleic acids is introduced, with a specific focus on DNAzymes. The incorporation of DNAzymes into bioassays is then described, followed by a detailed overview of recent advances in the development of in vivo sensing platforms and portable sensors incorporating DNAzymes for molecular recognition. Finally, a critical perspective on the field, and a summary of where DNAzyme-based devices may make the biggest impact are provided.

Biosensing with DNAzymes

Catalytic Nucleic Acids: Biochemistry, Chemical Biology, Biosensors, and Nanotechnology

Enhancing the limit of detection (LOD) is significant for crucial diseases. Cancer development could take more than 10 years, from one mutant cell to a visible tumor. Early diagnosis facilitates more effective treatment and leads to higher survival rate for cancer patients. Rolling circle amplification (RCA) is a simple and efficient isothermal enzymatic process that utilizes nuclease to generate long single stranded DNA (ssDNA) or RNA. The functional nucleic acid unit (aptamer, DNAzyme) could be replicated hundreds of times in a short period, and a lower LOD could be achieved if those units are combined with an enzymatic reaction, Surface Plasmon Resonance, electrochemical, or fluorescence detection, and other different kinds of biosensor. Multifarious RCA-based platforms have been developed to detect a variety of targets including DNA, RNA, SNP, proteins, pathogens, cytokines, micromolecules, and diseased cells. In this review, improvements in using the RCA technique for medical biosensors and biomedical applications were summarized and future trends in related research fields described.

Research Progress on Rolling Circle Amplification (RCA)-Based Biomedical Sensing

Pathogenic bacteria contamination can cause many problems, such as infections in humans and animals and environmental pollution. Early prevention and detection of pathogenic bacteria outbreaks is crucial to managing these problems. Some traditional detection methods such as cell culturing and polymerase chain reaction (PCR) are time-consuming, labor-intensive, insensitive, and inconvenient for detection. Therefore, simple and efficient pathogenic bacteria detection methods involving DNAzymes signaling mechanisms have been reported, including fluorescence and color detection. DNAzymes are divided into cases as a molecular recognition element (RNA-cleaving DNAzyme) and as a reporter element (peroxidase mimicking DNAzyme), which have proven compatible with isothermal amplification technology for pathogenic bacteria detection. In this review, we summarize the current methods of detecting pathogenic bacteria based on various DNAzyme sensors. We include the design principles, working mechanisms, and detection applications of these sensors and discuss the experimental and theoretical bases for their application in the diagnosis and prevention of diseases caused by pathogenic bacteria.

DNAzyme biosensors for the detection of pathogenic bacteria

Selection of a metal ligand modified DNAzyme for detecting Ni2.

Vibrio anguillarum is a bacterial pathogen that causes serious damage to aquatic fish, and its rapid detection and prevention are critical. DNAzymes are DNA-based catalysts with excellent stability. In this study, in vitro selection of DNAzymes was performed using the crude extracellular matrix (CEM) of V. Anguillarum as the target. Different from previous selections targeting bacterial CEM, this work used an unmodified DNA library, allowing easier adoption of the technology. After seven rounds of selection, a DNAzyme named VAE-2 with high activity and specificity was obtained. It showed the highest activity toward V. Anguillarum among eight types of tested bacterial strains. Polyvalent metal ions are needed for its activity. Protease treatment of the CEM and filtration studies indicated that the target is a protein with a molecular weight between 50 k and 100 k Da. A fluorescent biosensor was designed for V. anguillarum with a detection limit down to 4000 cfu/mL, and detection was demonstrated for real fish tissue and feeding water samples. Being the first work of DNAzyme-based sensing of aquatic bacteria, this study indicates that unmodified DNA can be used for targeting bacterial CEM, and it provides a new framework for developing other RNA-cleaving DNAzymes for rapid detection of pathogenic bacteria and water pollution.

Selection of DNAzymes for Sensing Aquatic Bacteria: Vibrio Anguillarum.

The crystal structure of Dextranase from the marine bacterium Arthrobacter oxidans KQ11 (Aodex) was determined at a resolution of 1.4 A. The crystal structure of the conserved Aodex fragment (Ala52-Thr638) consisted of an N-terminal domain N and a C-terminal domain C. The N-terminal domain N was identified as a β-sandwich, connected to a right-handed parallel β-helix at the C-terminus. Sequence comparisons, cavity regions, and key residues of the catalytic domain analysis all suggested that the Aodex was an inverting enzyme, and the catalytic acid and base were Asp439 and Asp420, respectively. Asp440 was not a general base in the Aodex catalytic domain, and Asp396 in Dex49A may not be a general base in the catalytic domain. The thermostability of the S357F mutant using semirational design based on B-factors was clearly better than that of wild-type Aodex. This process may promote the aromatic-aromatic interactions that increase the thermostability of mutant Phe357.

Crystal Structure of GH49 Dextranase from Arthrobacter oxidans KQ11: Identification of Catalytic Base and Improvement of Thermostability Using Semirational Design Based on B-Factors

Shujun Wang

Papers

Research Progress on Rolling Circle Amplification (RCA)-Based Biomedical Sensing

DNAzyme biosensors for the detection of pathogenic bacteria

Selection of a metal ligand modified DNAzyme for detecting Ni2.

Selection of DNAzymes for Sensing Aquatic Bacteria: Vibrio Anguillarum.

Crystal Structure of GH49 Dextranase from Arthrobacter oxidans KQ11: Identification of Catalytic Base and Improvement of Thermostability Using Semirational Design Based on B-Factors