Label-free fluorescent DNA biosensors based on metallointercalators and nanomaterials

MXene and black phosphorus based 2D nanomaterials in bioimaging and biosensing: progress and perspectives

Bioimaging and biosensing have garnered interest in early cancer diagnosis due to the ability of gaining in-depth insights into cellular functions and providing a wide range of diagnostic parameters. Emerging 2D materials of multielement MXenes and monoelement black phosphorous nanosheets (BPNSs) with unique intrinsic physicochemical properties such as a tunable bandgap and layer-dependent fluorescence, high carrier mobility and transport anisotropy, efficient fluorescence quenching capability, desirable light absorption and thermoelastic properties, and excellent biocompatibility and biosafety properties provide promising nano-platforms for bioimaging and biosensing applications. In view of the growing attention on the rising stars of the post-graphene age in the progress of bioimaging and biosensing, and their common feature characteristics as well as complementarity for constructing complexes, the main objective of this review is to reveal the recent advances in the design of MXene or BPNS based nanoplatforms in the field of bioimaging and biosensing. The preparation and surface functionalization methods, biosafety, and other important aspects of bioimaging and biosensing applications of MXenes and BPNSs have been assessed systematically, along with highlighting the main challenges in further biomedical application. The review not only focuses on the advancements in 2D materials for use in bioimaging and biosensing but also assesses the possibility of their future potential in bioapplications.

Promiscuous dye binding by a light-up aptamer: application for label-free multi-wavelength biosensing

Light-up DNA aptamers are promising label-free signal-transducers for biosensing applications due to their high chemical stability and low synthetic cost. Herein, we demonstrate that a dapoxyl DNA aptamer DAP-10-42 can be converted into a sensor generating a fluorescence signal at different wavelengths in the range of 500-660 nm depending on the dye that is present. This results from the discovered promiscuity of DAP-10-42 in binding fluorogenic dyes including arylmethane dyes. We have designed a split DAP-10-42 aptasensor for the detection of a katG gene fragment from Mycobacterium tuberculosis with a point mutation causing isoniazid resistance. Efficient interrogation of the gene fragment after nucleic acid sequence-based amplification (NASBA) is achieved directly in a protein-containing NASBA sample. This report lays a foundation for the application of the DAP-10-42 aptamer as a versatile sensing platform.

Conformational Changes of Immobilized Polythymine due to External Stressors Studied with Temperature-Controlled Electrochemical Microdevices

Conformational changes of single-stranded DNA (ssDNA) play an important role in a DNA strand's ability to bind to target ligands. A variety of factors can influence conformation, including temperature, ionic strength, pH, buffer cation valency, strand length, and sequence. To better understand the effects of these factors on immobilized DNA structures, we employ temperature-controlled electrochemical microsensors to study the effects of salt concentration and temperature variation on the conformation and motion of polythymine (polyT) strands of varying lengths (10, 20, 50 nucleotides). PolyT strands were tethered to a gold working electrode at the proximal end through a thiol linker via covalent bonding between the Au electrode and sulfur link, which can tend to decompose between a temperature range of 60 and 90 °C. The strands were also modified with an electrochemically active methylene blue (MB) moiety at the distal end. Electron transfer (eT) was measured by square wave voltammetry (SWV) and used to infer information pertaining to the average distance between the MB and the working electrode. We observe changes in DNA flexibility due to varying ionic strength, while the effects of increased DNA thermal motion are tracked for elevated temperatures. This work elucidates the behavior of ssDNA in the presence of a phosphate-buffered saline at NaCl concentrations ranging from 20 to 1000 mmol/L through a temperature range of 10-50 °C in 1° increments, well below the decomposition temperature range. The results lay the groundwork for studies on more complex DNA strands in conjunction with different chemical and physical conditions.

Collapse of DNA Tetrahedron Nanostructure for "Off-On" Fluorescence Detection of DNA Methyltransferase Activity

As a potential detection technique, highly rigid and versatile functionality of DNA tetrahedron nanostructures is often used in biosensing systems. In this work, a novel multifunctional nanostructure has been developed as an "off-on" fluorescent probe for detection of target methyltransferase by integrating the elements of DNA tetrahedron, target recognition, and dual-labeled reporter. This sensing system is initially in an "OFF" state owing to the close proximity of fluorophores and quenchers. After the substrate is recognized by target methyltransferase, the DNA tetrahedron can be methylated to produce methylated DNA sites. These sites can be recognized and cut by the restriction endonuclease DpnI to bring about the collapse of the DNA tetrahedron, which leads to the separation of the dual-labeled reporters from the quenchers, and thus the recovery of fluorescence signal to produce an "ON" state. The proposed DNA tetrahedron-based sensing method can detect Dam methyltransferase in the range of 0.1-90 U mL^-1 with a detection limit of 0.045 U mL^-1 and shows good specificity and reproducibility for detection of Dam methyltransferase in a real sample. It has been successfully applied for screening various methylation inhibitors. Thus, this work possesses a promising prospect for detection of DNA methyltransfrase in the field of clinical diagnostics.

Bare magnetic nanoparticles as fluorescence quenchers for detection of thrombin

Rapid and sensitive detection of thrombin has very important significance in clinical diagnosis. In this work, bare magnetic iron oxide nanoparticles (magnetic nanoparticles) without any modification were used as fluorescence quenchers. In the absence of thrombin, a fluorescent dye (CY3) labeled thrombin aptamer (named CY3-aptamer) was adsorbed on the surface of magnetic nanoparticles through interaction between a phosphate backbone of the CY3-aptamer and hydroxyl groups on the bare magnetic nanoparticles in binding solution, leading to fluorescence quenching. Once thrombin was introduced, the CY3-aptamer formed a G-quartet structure and combined with thrombin, which resulted in the CY3-aptamer being separated from the magnetic nanoparticles and restoration of fluorescence. This proposed assay took advantage of binding affinity between the CY3-aptamer and thrombin for specificity, and bare magnetic nanoparticles for fluorescence quenching. The fluorescence signal had a good linear relationship with thrombin concentration in the range of 1-60 nM, and the limit of detection for thrombin was estimated as low as 0.5 nM. Furthermore, this method could be applied for other target detection using the corresponding fluorescence labeled aptamer.

Ruthenium polypyridine complexes combined with oligonucleotides for bioanalysis: a review

Ruthenium complexes are among the most interesting coordination complexes and they have attracted great attention over the past decades due to their appealing biological, catalytic, electronic and optical properties. Ruthenium complexes have found a unique niche in bioanalysis, as demonstrated by the substantial progress made in the field. In this review, the applications of ruthenium complexes coordinated with polypyridine ligands (and analogues) in bioanalysis are discussed. Three main detection methods based on electrochemistry, electrochemiluminescence, and photoluminscence are covered. The important targets, including DNA and other biologically important targets, are detected by specific biorecognition with the corresponding oligonucleotides as the biorecognition elements (i.e., DNA is probed by its complementary strand and other targets are detected by functional nucleic acids, respectively). Selected examples are provided and thoroughly discussed to highlight the substantial progress made so far. Finally, a brief summary with perspectives is included.