Express and sensitive detection of multiple miRNAs via DNA cascade reactors functionalized photonic crystal array

Excitation/emission-enhanced heterostructure photonic crystal array synergizing with "DD-A" FRET entropy-driven circuit for high-resolution and ultrasensitive analysis of ctDNA

Circulating tumor DNA (ctDNA) is an emerging biomarker of liquid biopsy for cancer. But it remains a challenge to achieve simple, sensitive and specific detection of ctDNA because of low abundance and single-base mutation. In this work, an excitation/emission-enhanced heterostructure photonic crystal (PC) array synergizing with entropy-driven circuit (EDC) was developed for high-resolution and ultrasensitive analysis of ctDNA. The donor donor-acceptor FÖrster resonance energy transfer ("DD-A" FRET) was integrated in EDC based on the introduction of simple auxiliary strand, which exhibited higher sensitivity than that of traditional EDC. The heterostructure PC array was constructed with the bilayer periodic nanostructures of nanospheres. Because the heterostructure PC has the adjustable dual photonic band gaps (PBGs) by changing nanosphere sizes, and the "DD-A" FRET can offer the excitation and emission peak with enough distance, it helps the successful matches between the dual PBGs of heterostructure PC and the excitation/emission peaks of "DD-A" FRET; thus, the fluorescence from EDC can be enhanced effectively from both of excitation and emission processes on heterostructure PC array. Besides, high-resolution of single-base mutation was obtained through the strict recognition of EDC. Benefiting from the specific spectrum-matched and synergetic amplification of heterostructure PC and EDC with "DD-A" FRET, the proposed array obtained ultrasensitive detection of ctDNA with LOD of 12.9 fM, and achieved the analysis of mutation frequency as low as 0.01%. Therefore, the proposed strategy has the advantages of simple operation, mild conditions (enzyme-free and isothermal), high-sensitivity, high-resolution and high-throughput analysis, showing potential in bioassay and clinical application.

Photonic crystal-enhanced fluorescence biosensor with logic gate operation based on one-pot cascade amplification DNA circuit for enzyme-free and ultrasensitive analysis of two microRNAs

The development of sensitive and efficient analytical methods for multiple biomarkers is crucial for cancer screening at early stage. MicroRNAs (miRNAs) are a kind of biomarkers with diagnostic potential for cancer. However, the ultrasensitive and logical analysis of multiple miRNAs with simple operation still faces some challenges. Herein, a photonic crystal (PC)-enhanced fluorescence biosensor with logic gate operation based on one-pot cascade amplification DNA circuit was developed for enzyme-free and ultrasensitive analysis of two cancer-related miRNAs. The fluorescence biosensor was performed by biochemical recognition amplification module (BCRAM) and physical enhancement module (PEM) to achieve logical and sensitive detection. In the BCRAM, one-pot cascade amplification circuit consisted of the upstream parallel entropy-driven circuit (EDC) and the downstream shared catalytic hairpin assembly (CHA). The input of target miRNA would trigger each corresponding EDC, and the parallel EDCs released the same R strand for triggering subsequent CHA; thus, the OR logic gate was obtained with minimization of design and operation. In the PEM, photonic crystal (PC) array was prepared easily for specifically enhancing the fluorescence output from BCRAM by the optical modulation capabilities; meanwhile, the high-throughput signal readout was achieved by microplate analyzer. Benefiting from the integrated advantages of two modules, the proposed biosensor achieved ultrasensitive detection of two miRNAs with easy logic gate operation, obtaining the LODs of 8.6 fM and 6.7 fM under isothermal and enzyme-free conditions. Hence, the biosensor has the advantages of high sensitivity, easy operation, multiplex and high-throughput analysis, showing great potential for cancer screening at early stage.

Photon Management Enabled by Opal and Inverse Opal Photonic Crystals: from Photocatalysis to Photoluminescence Regulation

Light is a promising renewable energy source and can be converted into heat, electricity, and chemical energy. However, the efficiency of light-energy conversion is largely hindered by limited light-absorption coefficients and the low quantum yield of current-generation materials. Photonic crystals (PCs) can adjust the propagation and distribution of photons because of their unique periodic structures, which offers a compelling platform for photon management. The periodicity of materials with an alternating refractive index can be used to manipulate the dispersion of photons to generate the photonic bandgap (PBG), in which light is reflected. The slow photon effect, i. e., photon propagation at a reduced group velocity near the edges of the PBG, is widely regarded as another valuable optical property for manipulating light. Furthermore, multiple light scattering can increase the optical path, which is a vital optical property for PCs. Recently, the light reflected by PBG, the slow photon effect, and multiple light scattering have been exploited to improve light utilization efficiency in photoelectrochemistry, materials chemistry, and biomedicine to enhance light-energy conversion efficiency. In this review, the fabrication of opal or inverse opal PCs and the theory for improving the light utilization efficiency of photocatalysis, solar cells, and photoluminescence regulation are discussed. We envision photon management of opal or inverse opal PCs may provide a promising avenue for light-assisted applications to improve light-energy-conversion efficiency.

Label-Free, High-Throughput, Sensitive, and Logical Analysis Using Biomimetic Array Based on Stable Luminescent Copper Nanoclusters and Entropy-Driven Nanomachine

The development of an array for high-throughput and logical analysis of biomarkers is significant for disease diagnosis. DNA-templated copper nanoclusters (CuNCs) have a strong potential to serve as a label-free photoluminescence source in array platforms, but their luminescent stability and sensitivity need to be improved. Herein, we report a facile, sensitive, and robust biomimetic array assay by integrating with stable luminescent CuNCs and entropy-driven nanomachine (EDN). In this strategy, the luminescent stability of CuNCs was improved by adding fructose in CuNCs synthesis to offer a reliable label-free signal. Meanwhile, the DNA template for CuNCs synthesis was introduced into EDN with excellent signal amplification ability, in which the reaction triggered by target miRNA would cause the blunt/protruding conformation change of 3'-terminus accompanied by the production or loss of luminescence. In addition, a biomimetic array fabricated by photonic crystals (PCs) physically enhanced the emitted luminescent signal of CuNCs and achieved high-throughput signal readout by a microplate reader. The proposed assay can isothermally detect as low as 4.5 pM of miR-21. Moreover, the logical EDN was constructed to achieve logical analysis of multiple miRNAs by "AND" or "OR" logic gate operation. Therefore, the proposed assay has the advantages of label-free property, high sensitivity, flexible design, and high-throughput analysis, which provides ideas for developing a new generation of facile and smart platforms in the fields of biological analysis and clinical application.

Intracellular activated logic nanomachines based on framework nucleic acids for low background detection of microRNAs in living cells

DNA molecular machines based on DNA logic circuits show unparalleled potential in precision medicine. However, delivering DNA nanomachines into real biological systems and ensuring that they perform functions specifically, quickly and logically remain a challenge. Here, we developed an efficient DNA molecular machine integrating transfer-sensor-computation-output functions to achieve high fidelity detection of intracellular biomolecules. The introduction of pH nanoswitches enabled the nanomachines to be activated after entering the cell, and the spatial-confinement effect of the DNA triangular prism (TP) enables the molecular machine to process complex information at the nanoscale, with higher sensitivity and shorter response time than diffuse-dominated logic circuits. Such cascaded activation molecular machines follow the logic of AND to achieve specific capture and detection of biomolecules in living cells through a multi-hierarchical response, providing a new insight into the construction of efficient DNA molecular machines.

Quantitative Analysis of Structure Color of Photonic Crystal Sensors Based on HSB Color Space

The photonic crystals (PhCs) have a bright structural color, but their angular dependence and naked-eye observation subjectivity only apply for qualitative analysis. The HSB color space is a three-channel color analysis technology based on hue (H)-saturation (S)-brightness (B). We use the HSB color space to analyze the structural color of the AM/NIPAM PhCs hydrogel sensor in response to temperature and organic solvents. We proved that the structural color analysis based on the hue value (H) could achieve an analysis accuracy close to the spectrum analysis. In addition, we have obtained stimulus-responsive PhCs structure color images from references and quantitatively analyzed them through the HSB color space. The results show that the H of the structural color can establish a high correlation with the specified target. In some cases, its best fitness exceeds traditional spectroscopy methods. This analysis method will provide a general and quantitative analysis technology for the structural color of PhCs by consumer-grade computers and smartphones.

A universal array platform for ultrasensitive, high-throughput and microvolume detection of heavy metal, nucleic acid and bacteria based on photonic crystals combined with DNA nanomachine

The development of a universal, sensitive, and rapid assay platform to achieve detections of heavy metal, nucleic acid and bacteria is of great significance but it also faces a thorny challenge. Herein, a novel and universal array platform was developed by combining photonic crystals (PCs) and DNA nanomachine. The developed array platform integrated the physical and biological signal amplification ability of PCs and DNA nanomachine, resulting in ultrasensitive detections of Hg²⁺, DNA, and Shigella sonnei with limits of detection (LODs) of 22.1 ppt, 31.6 fM, and 9 CFU/mL, respectively. More importantly, by utilizing a microplate reader as signal output device, the array achieved high-throughput scanning (96 samples/3 min) with only 2 μL loading sample, which is advantageous for the detection of infectious dangerous targets. In addition, the PCs array could be obtained easily and rapidly based on self-assembly of colloidal nanospheres, and the DNA nanomachine was operated with enzyme-free and time-saving features. Benefiting from these merits, the proposed PCs array offered a powerful universal platform for large-scale detection of various analytes in the fields of pollution monitoring, epidemic control, and public health.

Triggered Dimerization and Trimerization of DNA Tetrahedra for Multiplexed miRNA Detection and Imaging of Cancer Cells

The reversible and switchable triggered reconfiguration of tetrahedra nanostructures from monomer tetrahedra structures into dimer or trimer structures is introduced. The triggered bridging of monomer tetrahedra by K⁺ -ion-stabilized G-quadruplexes or T-A•T triplexes leads to dimer or trimer tetrahedra structures that are separated by crown ether or basic pH conditions, respectively. The signal-triggered dimerization/trimerization of DNA tetrahedra structures is used to develop multiplexed miRNA-sensing platforms, and the tetrahedra mixture is used for intracellular sensing and imaging of miRNAs.

A two-dimensional photonic crystal hydrogel biosensor for colorimetric detection of penicillin G and penicillinase inhibitors

A simple penicillinase functionalized two-dimensional photonic crystal hydrogel (2DPPCH) biosensor was developed for colorimetric detection of penicillin G and penicillinase inhibitors. The penicillinase can specifically recognize penicillin G and catalyze it to produce penicilloic acid, which decreases the pH of the hydrogel microenvironment and shrinks the pH-sensitive hydrogel. The particle spacing decrease of the 2D photonic crystal array induced by the hydrogel shrinkage further causes a blue-shift in the diffraction wavelength. While the hydrolysis reaction is repressed upon treatment with clavulanate potassium (a kind of penicillinase inhibitor), no significant change in the diffraction wavelength is found. The detection of targets can be achieved by measuring the Debye diffraction ring diameter or observing the structural color change in the visible region. The lowest detectable concentrations for penicillin G and clavulanate potassium are 1 μM and 0.1 μM, respectively. Moreover, the 2DPPCH is proved to exhibit high selectivity and an excellent regeneration property, and it shows satisfactory performance for penicillin G analysis in real water samples.

Construction of Molecular Sensing and Logic Systems Based on Site-Occupying Effect-Modulated MOF-DNA Interaction

Interactions between metal-organic frameworks (MOFs) and nucleic acids are of great importance in molecular assembly. However, current MOF-nucleic acid interactions lack diversity and are normally realized in an uncontrollable manner. Herein, the interaction of zirconium-based MOFs (Zr-MOFs) with nucleic acids is enabled by the formation of Zr-O-P bonds and further manipulated by a phosphate-induced site-occupying effect. Covering Zr ions in clusters of MOFs with phosphates impedes the formation of Zr-O-P bonds with nucleic acids, rendering the MOF-nucleic acid interaction tunable and stimulus-responsive. Notably, the experimental results demonstrate that various phosphates, Zr-MOFs, and nucleic acids can all be adopted in the tunable interaction. On the basis of these findings, fluorescent DNA and typical Zr-MOFs are proposed as functional probe-quencher pairs to establish molecular sensing and logic systems. Accordingly, alkaline phosphatase and inorganic pyrophosphatase can be quantified simultaneously, and the overall relation of different phosphates and phosphatases is facilely displayed. The work provides a general strategy for modulating MOF-nucleic acid interactions, which is conducive to the development of molecular intelligent systems.