Peroxidase-mimicking DNAzyme modulated growth of CdS nanocrystalline structures in situ through redox reaction: application to development of genosensors and aptasensors

A magnified aptamer fluorescence sensor based on the metal organic frameworks adsorbed DNA with enzyme catalysis amplification for ultra-sensitive determination of ATP and its logic gate operation

With the development of frame materials, metal organic frameworks (MOFs) have been successfully applied in the fields of biological small molecule analysis and fluorescent DNA detection. In this work, in view of the good adsorption characteristics of MIL-101(Cr), the highly sensitive detection of adenosine triphosphate (ATP) assisted nucleic acid exonuclease amplification by MIL-101(Cr) on the different affinity of single stranded DNA and double stranded DNA was investigated. The detection limit of ATP reaches 1.7 μM, and the platform has good applicability in biological samples. On this basis, an "AND" logic gate was successfully constructed. Superior sensitivity to ATP in the presence of exonuclease was reflected, which greatly enhanced the system's fluorescence. Importantly, the fluorescence sensing application of this nanomaterial inspired other target detection and enriched the building blocks of fluorescence sensing platform.

Comparison of turn-on and ratiometric fluorescent G-quadruplex aptasensor approaches for the detection of ATP

Two fluorescent aptasensor methods were developed for the detection of ATP in biochemical systems. The first method consisted of a label-free fluorescent "turn-on" approach using a guanine-rich ATP aptamer sequence and the DNA-binding agent berberine complex. In the presence of ATP, the ATP preferentially binds with its aptamer and conformationally changes into a G-quadruplex structure. The association of berberine with the G-quadruplex results in the enhancement of the fluorescence signal of the former. The detection limit of ATP was found to be 3.5 μM. Fluorescence, circular dichroism and melting temperature (T_m) experiments were carried out to confirm the binding specificity and structural changes. The second method employs the ratiometric fluorescent approach based on the Forster resonance energy transfer (FRET) for the detection of ATP using berberine along with a quencher (AuNRs, AgNPs) and a fluorophore (red quantum dots (RQDs), carbon dots (CDs)) labeled at 5' and 3' termini of the ATP-binding aptamer sequence. Upon addition of ATP and berberine, ATP specifically binds with its aptamer leading to the formation of G-quadruplex, and similarly, berberine also binds to the G-quadruplex. This leads to an enhancement of fluorescence of berberine while that of RQD and CDs were significantly quenched via FRET. The respective detection limits calculated were 3.6 μM and 3.8 μM, indicating these fluorescent aptasensor methods may be used for a wide variety of small molecules. Graphical abstract.

Biosensing strategies based on enzymatic reactions and nanoparticles

Application of new nanomaterials to detection of enzymatic activities allows the development of new sensitive and selective bioanalytical assays based on enzymes for recognition and signal amplification.

Optical Aptasensors for Adenosine Triphosphate

Nucleic acids are among the most researched and applied biomolecules. Their diverse two- and three-dimensional structures in conjunction with their robust chemistry and ease of manipulation provide a rare opportunity for sensor applications. Moreover, their high biocompatibility has seen them being used in the construction of in vivo assays. Various nucleic acid-based devices have been extensively studied as either the principal element in discrete molecule-like sensors or as the main component in the fabrication of sensing devices. The use of aptamers in sensors - aptasensors, in particular, has led to improvements in sensitivity, selectivity, and multiplexing capacity for a wide verity of analytes like proteins, nucleic acids, as well as small biomolecules such as glucose and adenosine triphosphate (ATP). This article reviews the progress in the use of aptamers as the principal component in sensors for optical detection of ATP with an emphasis on sensing mechanism, performance, and applications with some discussion on challenges and perspectives.

Supramolecular micelle-based nucleoapzymes for the catalytic oxidation of dopamine to aminochrome

Lipidated DNAzymes or a lipidated Cu(ii)-complex and lipidated aptamer sequences form supramolecular assemblies of micellar nucleoapzymes for the enhanced oxidation of dopamine to aminochrome.

CdS/MoS2 heterojunction-based photoelectrochemical DNA biosensor via enhanced chemiluminescence excitation

This work developed a CdS/MoS2 heterojunction-based photoelectrochemical biosensor for sensitive detection of DNA under the enhanced chemiluminescence excitation of luminol catalyzed by hemin-DNA complex. The CdS/MoS2 photocathode was prepared by the stepwise assembly of MoS2 and CdS quantum dots (QDs) on indium tin oxide (ITO), and achieved about 280% increasing of photocurrent compared to pure CdS QDs electrode due to the formation of heterostructure. High photoconversion efficiency in the photoelectrochemical system was identified to be the rapid spatial charge separation of electron-hole pairs by the extension of electron transport time and electron lifetime. In the presence of target DNA, the catalytic hairpin assembly was triggered, and simultaneously the dual hemin-labeled DNA probe was introduced to capture DNA/CdS/MoS2 modified ITO electrode. Thus the chemiluminescence emission of luminol was enhanced via hemin-induced mimetic catalysis, leading to the physical light-free photoelectrochemical strategy. Under optimized conditions, the resulting photoelectrode was proportional to the logarithm of target DNA concentration in the range from 1 fM to 100 pM with a detection limit of 0.39 fM. Moreover, the cascade amplification biosensor demonstrated high selectivity, desirable stability and good reproducibility, showing great prospect in molecular diagnosis and bioanalysis.

Target-driven self-assembly of stacking deoxyribonucleic acids for highly sensitive assay of proteins

In this paper, we report a new signal amplification strategy for highly sensitive and enzyme-free method to assay proteins based on the target-driven self-assembly of stacking deoxyribonucleic acids (DNA) on an electrode surface. In the sensing procedure, binding of target protein with the aptamer probe is used as a starting point for a scheduled cycle of DNA hairpin assembly, which consists of hybridization, displacement and target regeneration. Following numbers of the assembly repeats, a great deal of DNA duplexes can accordingly be formed on the electrode surface, and then switch on a succeeding propagation of self-assembled DNA concatemers that provide further signal enhancement. In this way, each target binding event can bring out two cascaded DNA self-assembly processes, namely, stacking DNA self-assembly, and therefore can be converted into remarkably intensified electrochemical signals by associating with silver nanoparticle-based readout. Consequently, highly sensitive detection of target proteins can be achieved. Using interferon-gamma as a model, the assay method displays a linear range from 1 to 500 pM with a detection limit of 0.57 pM, which is comparable or even superior to other reported amplified assays. Moreover, the proposed method eliminates the involvement of any enzymes, thereby enhancing the feasibility in clinical diagnosis.