"Plug and Play" logic gate construction based on chemically triggered fluorescence switching of gold nanoparticles conjugated with Cy3-tagged aptamer

A Sensitive and Portable Double-Layer Microfluidic Biochip for Harmful Algae Detection

Harmful algal blooms (HABs) are common disastrous ecological anomalies in coastal waters. An effective algae monitoring approach is important for natural disaster warning and environmental governance. However, conducting rapid and sensitive detection of multiple algae is still challenging. Here, we designed an ultrasensitive, rapid and portable double-layer microfluidic biochip for the simultaneous quantitative detection of six species of algae. Specific DNA probes based on the 18S ribosomal DNA (18S rDNA) gene fragments of HABs were designed and labeled with the fluorescent molecule cyanine-3 (Cy3). The biochip had multiple graphene oxide (GO) nanosheets-based reaction units, in which GO nanosheets were applied to transfer target DNA to the fluorescence signal through a photoluminescence detection system. The entire detection process of multiple algae was completed within 45 min with the linear range of fluorescence recovery of 0.1 fM-100 nM, and the detection limit reached 108 aM. The proposed approach has a simple detection process and high detection performance and is feasible to conduct accurate detection with matched portable detection equipment. It will have promising applications in marine natural disaster monitoring and environmental care.

A review of spectroscopic probes constructed from aptamer-binding gold/silver nanoparticles or their dimers in environmental pollutants' detection

The issue of environmental pollutant residues has gained wide public attention all along. Therefore, it is necessary to develop simple, rapid, economical, portable, and sensitive detection techniques, which have become the focus of research in the pollutants detection field. Spectroscopy is one of the most convenient, simple, rapid, and intuitive analytical tools that can provide accurate information, such as ultraviolet spectroscopy, fluorescence spectroscopy, Raman spectroscopy, plasmon resonance spectroscopy, etc. Gold nanoparticles, silver nanoparticles, and their dimers with unique optical properties are commonly used in the construction of spectroscopic probes. As a class of oligonucleotides that can recognize specific target molecules, aptamers also have a strong ability to recognize small-molecule pollutants. The application of aptamer-binding metal nanoparticles in biosensing detection presents significant advantages for instance high sensitivity, good selectivity, and rapid analysis. And many spectroscopic probes constructed by aptamer-binding gold nanoparticles, silver nanoparticles, or their dimers have been successfully demonstrated for detecting pollutants. This review summarizes the progress, advantages, and disadvantages of aptamer sensing techniques constructed by visual colorimetric, fluorescence, Raman, and plasmon resonance spectroscopic probes combining gold/silver nanoparticles or their dimers in the field of pollutants detection, and discusses the prospects and challenges for their future.

Rapid and Highly Sensitive Detection of Target DNA Related to COVID-19 Virus With a Fluorescent Bio-conjugated Probe via a FRET Mechanism

A novel cyanine 3 (Cy3)-based bio-conjugated sensor has been developed to detect target DNA or extracted RNA from COVID -19 samples using the fluorescence resonance energy transfer (FRET) experiment. A special sequence of the COVID -19 genome was selected as a complementary DNA (target DNA) part. The opposite chain of this target sequence was designed in 2 parts; one part was attached to the Cy3 organic dye (capture DNA or Cy3- DNA), and the other part was attached to the BHQ₂ molecule (quencher DNA or BHQ₂- DNA). The Cy3 molecule acts as a donor pair, and BHQ₂ acts as an acceptor pair in the FRET experiment. The capture DNA and quencher DNA can form a sandwiched complex in the presence of target DNA. The formation of the entitled sandwiched hybrid causes the decrement of emission intensity of the Cy3 donor in bio-conjugated Cy3-DNA via energy transfer from Cy3 (as a donor) to BHQ₂ (as an acceptor). Indeed, in the presence of non-complementary DNA, the pairing of DNA strands does not occur, the FRET phenomenon does not exist, and therefore fluorescence intensity of Cy3 does not decrease. Moreover, this biosensor was successfully applied to analyze real samples containing extracted RNA of COVID -19 prepared for the reverse transcriptase-polymerase chain reaction (RT-PCR) test, and the results were promising.

Development of gold nanoparticles-aptamer nanocomposite for multiplexed analysis of antibiotics and design of molecular logic gates

The widespread use of antibiotics caused severe problems of antibiotic residues in foodstuffs and water, posing a serious threat to public health and thus urging the development of sensitive, selective, and rapid detection methods for antibiotics. In this study, a fluorescence resonance energy transfer (FRET)-based system is developed for the multiplexed analysis of chloramphenicol (CAP) and streptomycin (Strep) with detection limits of 2.51 and 8.69μg l^-1, respectively. The FRET-based system consists of Cy3-tagged anti-CAP aptamer-conjugated gold nanoparticles (AuNPs) (referred to as AuNPs-AptCAP) and Cy5-tagged anti-Strep aptamer-conjugated AuNPs (referred to as AuNPs-AptStrep). In addition, AuNPs-AptCAP and AuNPs-AptStrep have been demonstrated to serve as signal transducers for implementing a series of logic operations such as YES, NOT, INH, OR, (2-4)-Decoder and even more complicated multi-level logic gates (OR-INH). Based on the outputs of logic operations, it could be figured out whether targeted analytes were present or not, thus enabling multiplex sensing and evaluation of pollution status. This proof of concept study might provide a new route for the enhanced sensing performance to distinguish different pollution status as well as the design of molecular mimics of logic elements to demonstrate better applicability.

Label-free Electrochemical Impedance Spectroscopy Aptasensor for Ultrasensitive Detection of Lung Cancer Biomarker Carcinoembryonic Antigen

In this work, an integrated electrode system consisting of a graphene working electrode, a carbon counter electrode and an Ag/AgCl reference electrode was fabricated on an FR-4 glass fiber plate by a polyethylene self-adhesive mask stencil method combined with a manual screen printing technique. The integrated graphene electrode was used as the base electrode, and AuNPs were deposited on the working electrode surface by cyclic voltammetry. Then, the carcinoembryonic antigen aptamer was immobilized using the sulfhydryl self-assembly technique. The sensor uses [Fe(CN)6]3-/4- as a redox probe for label free detection of carcinoembryonic antigen based on the impedance change caused by the difference in electron transfer rate before and after the binding of carcinoembryonic antigen aptamer and the target carcinoembryonic antigen. The results showed a good linear relationship when the CEA concentration is in the range of 0.2-15.0 ng/ml. The detection limit was calculated to be 0.085 ng/ml (S/N = 3).

Logic Gates Based on DNA Aptamers

DNA bio-computing is an emerging trend in modern science that is based on interactions among biomolecules. Special types of DNAs are aptamers that are capable of selectively forming complexes with target compounds. This review is devoted to a discussion of logic gates based on aptamers for the purposes of medicine and analytical chemistry. The review considers different approaches to the creation of logic gates and identifies the general algorithms of their creation, as well as describes the methods of obtaining an output signal which can be divided into optical and electrochemical. Aptameric logic gates based on DNA origami and DNA nanorobots are also shown. The information presented in this article can be useful when creating new logic gates using existing aptamers and aptamers that will be selected in the future.