DNA nanosensor based on bipedal 3D DNA walker-driven proximal catalytic hairpin assembly for sensitive and fast TK1 mRNA detection

Hyperproliferative  diseases are the first step for tumor formation; thymidine kinase 1 (TK1) mRNA is closely related to cell proliferation. Therefore, the risk of malignant proliferation can be identified by sensitively detecting the variance in TK1 mRNA concentration, which can be used for tumor auxiliary diagnosis and monitoring tumor treatment. Owing to the low abundance and instability of TK1 mRNA in real samples, the development of a sensitive and fast mRNA detection method is necessary. A DNA nanosensor that can be used for detecting TK1 mRNA based on bipedal 3D DNA walker-driven proximal catalytic hairpin assembly (P-CHA) was developed. P-CHA hairpins were hybridized to a linker DNA strand coupled with magnetic nanoparticles to increase their local concentrations. The bipedal DNA walking on the surface of NPs accelerates reaction kinetics using the proximity effect. Taking advantage of the signal amplification of P-CHA as well as the rapid reaction rate of the DNA walker in 80 min, the proposed sensor detects TK1 mRNA with a low detection limit of 14 pM and may then be applied to clinical diagnosis.

Construction of an autofluorescence interference-free phosphorescence biosensor for the specific detection of TK1 mRNA

The anti-interference ability of biosensors is critical for detection in biological samples. Fluorescence-based sensors are subject to interference from self-luminescent substances in biological matrices. Therefore, phosphorescent sensors stand out among biosensors due to their lack of self-luminescence background. In this study, a phosphorescent sensor was constructed, which can accurately detect thymidine kinase 1 (TK1) mRNA in biological samples and avoid autofluorescence interference. When there is no target, polydopamine (PDA) is used as the phosphorescence resonance energy transfer (PRET) acceptor to quench the phosphorescence of the persistently luminescent (PL) nanomaterial. When there is a target, the DNA modified by the PL nanomaterial is replaced by the hairpin H and removed away from the PDA, resulting in a rebound in phosphorescence. The phosphorescent sensor exhibits a good linear relationship in the TK1 mRNA concentration range of 0-200 nM, and the detection limit was 1.74 nM. The sensor fabricated in this study can effectively avoid interference from spontaneous fluorescence in complex biological samples, and sensitively and precisely detect TK1 mRNA in serum samples, providing a powerful tool to more accurately detect biomarkers in biological samples.

Aptamer-based flares hybridized with single-stranded DNA-conjugated MoS2 nanosheets for ratiometric fluorescence sensing and imaging of potassium ions and adenosine triphosphate in human fluids and living cells

Addressing the limitations observed in previous studies, where the quantitative range of nanoprobes for detecting K+ and adenosine triphosphate (ATP) did not cover concentrations found within living cells, the present study aimed to develop ratiometric nanoprobes that can accurately sense changes in K+ and ATP levels in living cells and quantify them in human fluids. The proposed nanoprobes consisted of recognition flares modified with 6-carboxyfluorescein (FAM) and 5-carboxytetramethylrhodamine (TAMRA), along with thiolate single-stranded DNA (ssDNA) and molybdenum disulfide nanosheets (MoS2 NSs). The thiolate ssDNA acts as a linker between the flares and the MoS2 NSs, directly forming a functional nanostructure at room temperature. The direct conjugation of labeled flares to the MoS2 NSs simplifies the fabrication process. In the absence of K+ and ATP, the hybridization of flares and thiolate ssDNA caused FAM to move away from TAMRA, suppressing the fluorescence resonance energy transfer (FRET) process. However, upon the introduction of K+ and ATP, the flares undergo a structural transformation via the formation of G-quadruplex formation and the generation of hairpin-shaped structures, respectively. This structural change leads to the release of the flares from the ssDNA-conjugated nanosheet surface. The release of the flares brings FAM and TAMRA into close proximity, allowing FRET to occur, leading to FRET and static quenching. By monitoring the ratio between the fluorescence intensities of FAM and TAMRA, the concentration of K+ (5-100 mM) and ATP (0.3-5 mM) can be accurately determined by the proposed nanoprobes. The advantages of these nanoprobes lie in their ability to provide ratiometric measurements, which enhance the accuracy and reliability of the quantification process. The proposed nanoprobes offer potential applications as ratiometric imaging probes for monitoring K+ and ATP-related reactions in living cells, providing valuable insights into cellular processes. Additionally, they can be employed for determining the levels of K+ and ATP in human fluids, offering potential diagnostic applications in various clinical settings.

Orthogonally Sequential Activation of Self-Powered DNAzymes Cascade for Reliable Monitoring of mRNA in Living Cells

Ratiometric imaging of tumor-related mRNA is significant, yet spatiotemporally resolved regulation on the ratiometric signals to avoid non-specific activation in the living cells remains challenging. Herein, orthogonally sequential activation of concatenated DNAzyme circuits is, first, developed for Spatio Temporally regulated Amplified and Ratiometric (STAR) imaging of TK1 mRNA inside living cells with enhanced reliability and accuracy. By virtue of the synthesized CuO/MnO2 nanosheets, orthogonally regulated self-powered DNAzyme circuits are operated precisely in living cells, sequentially activating two-layered DNAzyme cleavage reactions to achieve the two ratiometric signal readouts successively for reliable monitoring of low-abundance mRNA in living cells. It is found that the ratiometric signals can only be derived from mRNA over-expressed tumor cells, also irrespective of probes' delivery concentration. The presented approach could provide new insight into orthogonally regulated ratiometric systems for reliable imaging of specific biomarkers in living cells, benefiting disease precision diagnostics.

Gold nanocluster-based fluorescent sensors for in vitro and in vivo ratiometric imaging of biomolecules

Gold nanoclusters (AuNCs) are promising nanomaterials for ratiometric fluorescent probes due to their tunable fluorescence wavelengths dependent on size and structure, as well as their biocompatibility and resistance to photobleaching. By incorporating an additional fluorescence spectral peak, dual-emission AuNC-based fluorescent probes have been developed to enhance the signal output reproducibility. These probes can be fabricated by integrating various luminescent nanomaterials with AuNCs. This review focuses on the preparation methods and applications of ratiometric fluorescent probes derived from AuNCs and other fluorescent nanomaterials or fluorescent dyes for both in vitro and in vivo bioimaging of target analytes. Additionally, the review delves into the sensing mechanisms of AuNC-based ratiometric probes, their synthetic strategies, and the challenges encountered when using AuNCs for ratiometric bioimaging. Moreover, we explore the application of protein-stabilized AuNCs and thiolate-capped AuNC-based ratiometric fluorescent probes for biosensing and bioimaging. Two primary methods for assembling AuNCs and fluorophores into ratiometric fluorescent probes are discussed: triggered assembly and self-assembly. Finally, we address the challenges and issues associated with ratiometric bioimaging using AuNCs and propose future directions for further advancing AuNCs as ratiometric imaging agents.

A smartphone-based platform for ratiometric visualization of SARS-CoV-2 via an oligonucleotide probe

COVID-19 necessitates the development of reliable and convenient diagnostic tools. In this work, a facile 3D-printed smartphone platform was constructed that achieved reliable visual detection of SARS-CoV-2 by eliminating the effect of ambient light and fixing the camera position relative to the sample. The oligonucleotide probe is modified with orange-red-emitting TAMRA working as an internal standard and green-emitting FAM serving as a sensitive sensing agent. Under 365-nm UV excitation, the emission wavelengths of TAMRA and FAM are 580 nm and 518 nm, respectively. When the probes interact with the targets, the green fluorescence gradually restores while the orange-red fluorescence remains stable. Thus, a striking color transition from orange-red to green could be observed by the naked eye. The detection limit of SARS-CoV-2 nucleic acid is 0.23 nM, and the entire process of color change could be completed in 25 min. Furthermore, the RGB value analysis of the sample solution was conducted using a smartphone for reliable and reproducible discrimination of SARS-CoV-2. The proposed smartphone platform might establish a general method for visual detection of SARS-CoV-2 nucleic acid as well as other virus-related diseases.

Converting electronic nose into opto-electronic nose by mixing MoS2 quantum dots with organic reagents: Application to recognition of aldehydes and ketones and determination of formaldehyde in milk

A new colorimetric sensor array based on mixing of Molybdenum disulfide quantum dots (MoS₂ QDs) and organic reagents is introduced in this study. MoS₂ QDs shows a specific and higher affinity to oxygen functionalized volatile compounds like aldehydes and ketones. Therefore, this designed sensor array is used for classification of eight different aldehydes and ketones based on Linear Discriminate Analysis (LDA) at first. The classification accuracy of 96% and 83% was obtained for training and prediction phases, respectively. Then the introduced colorimetric sensor array is used for the semi-quantitative and quantitative analysis of formaldehyde in milk samples. Formaldehyde is an adulteration that is added to the milk for increasing the storage time. Cow milk samples were provided directly from dairy farmer and from supermarkets and were spiked by formaldehyde in the concentration range of 1-25 ppm. The response of sensor array to these samples were analyzed by partial least squares regression (PLS-R) method and were calibrated for concentration of formaldehyde. The PLSR results (R² = 0.94 and RMSEC = 2.36) shows that proposed sensor is useable in direct analysis of formaldehyde in milk as a complex matrix.

Photocaged FRET nanoflares for intracellular microRNA imaging

Herein, we developed photocaged FRET nanoflares for spatiotemporal microRNA imaging in living cells. In other words, the probes will not work until they are exposed to UV light.