Reversible and Quantitative Photoregulation of Target Proteins

Multistage nucleic acid amplification induced nano-aggregation for 3D hotspots-improved SERS detection of circulating miRNAs

Circulating miRNAs in the blood can regulate disease development and thus indicate disease states via their various expression levels. For these reasons, circulating miRNAs constitute useful biomarkers, and an approach to the accurate detection of circulating miRNAs is attractive in the diagnosis and treatment of diseases. However, methods for clinical detecting of circulating miRNA that take both sensitivity and practicality into account are still needed. Therefore, we aimed herein to solve some inherent problems in the actual detection using a robust surface-enhanced Raman scattering (SERS) platform with integrated nucleic acid amplification and nanoparticle aggregation to construct 3D hotspots for improving performance of analyzing circulating miRNAs. After target recognition and initial signal amplification by DNAzyme, we observed that release triggered an open hairpin DNA on gold nanoparticles (AuNPs), which then promote AuNP aggregation, causing the accumulation of a large number of hotspots in three-dimention. The SERS biosensor achieved a better performance than the sandwich-type separation detection, with a low detection limit (0.37 fM) and a broad linear range (1 fM–10 nM) in liquids. This SERS platform can be used as a powerful tool for the detection of circulating miRNAs, and it can be used to improve the sensitivity and accuracy of various clinical-disease diagnoses.

Spatiotemporally Resolved Protein Detection in Live Cells Using Nanopore Biosensors

Spatiotemporal detection of proteins in living cells is a persistent challenge but is the key to understanding their cellular biology and developing theranostic technologies. We develop a dual-nanopore biosensor using affinity-tunable peptide probes, which enables label-free and spatiotemporal monitoring of protein abundance and its concentration change in single live cells. We demonstrate that by screening for peptide probes with tunable affinities, the nanopore modified with a medium-affinity peptide allowed reversible and sensitive detection of the protein kinase A (PKA) catalytic subunit with a detection limit of 0.04 nM. The sensor is shown to have the ability to effectively eliminate interferences from cell membrane resistance and coexisting species in live cell detection. Moreover, our sensor is successfully implemented in monitoring of dynamic PKA activity changes (PKA catalytic subunit dynamic concentration changes) under different stimulations in single live cells. Our design may provide a paradigm for developing nanopore biosensors for spatiotemporally resolved protein analysis in live cells.

Molecular recognition of enzymes and modulation of enzymatic activity by nanoparticle conformational sensors

Regulation of enzyme activity is key to dynamic processes in biology but is difficult to achieve with synthetic systems. We here report molecularly imprinted nanoparticles with strong binding for the N- and C-terminal peptides on lysozyme. Binding affinity for the enzyme correlated with conformational flexibility of the peptides in the protein structure. Significantly, binding at the C-terminus of lysozyme enhanced the performance of the enzyme at elevated temperatures and that at the N-terminus lowered the enzyme activity. These nanoparticles, when clicked onto magnetic nanoparticles, could also be used to fish out the protein of interest from a mixture in a single step.

Engineering DNA on the Surface of Upconversion Nanoparticles for Bioanalysis and Therapeutics

Surface modification of inorganic nanomaterials with biomolecules has enabled the development of composites integrated with extensive properties. Lanthanide ion-doped upconversion nanoparticles (UCNPs) are one class of inorganic nanomaterials showing optical properties that convert photons of lower energy into higher energy. Additionally, DNA oligonucleotides have exhibited powerful capabilities for organizing various nanomaterials with versatile topological configurations. Through rational design and nanotechnology, DNA-based UCNPs offer predesigned functionality and potential. To fully harness the capabilities of UCNPs integrated with DNA, various DNA-UCNP composites have been developed for diagnosis and therapeutics. In this review, beginning with the introduction of the UCNPs and the conjugation of DNA strands on the surface of UCNPs, we present an overview of the recent progress of DNA-UCNP composites while focusing on their applications for bioanalysis and therapeutics.

Activation of the Catalytic Activity of Thrombin for Fibrin Formation by Ultrasound

The regulation of enzyme activity is a method to control biological function. We report two systems enabling the ultrasound-induced activation of thrombin, which is vital for secondary hemostasis. First, we designed polyaptamers, which can specifically bind to thrombin, inhibiting its catalytic activity. With ultrasound generating inertial cavitation and therapeutic medical focused ultrasound, the interactions between polyaptamer and enzyme are cleaved, restoring the activity to catalyze the conversion of fibrinogen into fibrin. Second, we used split aptamers conjugated to the surface of gold nanoparticles (AuNPs). In the presence of thrombin, these assemble into an aptamer tertiary structure, induce AuNP aggregation, and deactivate the enzyme. By ultrasonication, the AuNP aggregates reversibly disassemble releasing and activating the enzyme. We envision that this approach will be a blueprint to control the function of other proteins by mechanical stimuli in the sonogenetics field.

Exploring the Trans-Cleavage Activity of CRISPR/Cas12a on Gold Nanoparticles for Stable and Sensitive Biosensing

Taking advantage of the excellent trans-cleavage activity, CRISPR-based diagnostics (CRISPR-Dx) has shown great promise in molecular diagnostics. However, the single-stranded DNA reporter of the current CRISPR-Dx suffers from poor stability and limited sensitivity, which make their application in complex biological environments difficult. Herein, we, for the first time, explore the trans-cleavage activity of CRISPR/Cas12a toward the substrate on gold nanoparticles and apply the new phenomenon to develop a spherical nucleic acid (SNA) reporter for stable and sensitive CRISPR-Dx biosensing. By anchoring the DNA substrate on gold nanoparticles, we discovered different trans-cleavage activities of different types of the Cas12a system (e.g., LbCas12a and AsCas12a) on a nanoparticle surface. The further study suggests that the trans-cleavage activity of LbCas12a on the nanoparticle surface is highly dependent on the density and length of DNA strands. Based on these interesting discoveries, we furthermore develop SNA reporter-based fluorescent CRISPR-Dx for stable and sensitive biosensing application. Compared to traditional ssDNA reporters, the SNA reporter exhibits improved stability, which enables the stable application in a complex serum environment. In addition, the SNA reporter system with tunable density exhibits high sensitivity with a detection limit of 10 fM, which is about 2 orders of magnitude lower than that of the ssDNA reporter system. Finally, the practical application of SNA reporter-based CRISPR-Dx in clinical serum was successfully achieved. These results indicate their significant potential in future research on biology science and medical diagnoses.

Determination of adenosine triphosphate based on the use of fluorescent terbium(III) organic frameworks and aptamer modified gold nanoparticles

A thiol-labeled adenosine triphosphate (ATP) binding aptamer is covalently linked on the surface of gold nanoparticles (AuNPs). This warrants protection of the red AuNPs from aggregation in high salt condition. The dispersed AuNPs can quench the fluorescence of the Tb(III)-MOFs at 547 nm with the excitation wavelength of 290 nm. This is ascribed to the combined action of inner filter effect, dynamic quenching and fluorescence resonance energy transfer. If the aptamer binds ATP to form folded structures, the AuNPs aggregate in high salt medium and the green fluorescence of the Tb(III)-MOFs is recovered. This method shows good sensitivity and selectivity for ATP, and the linear range is from 0.5 to 10 μM of ATP with the detection limitat of 0.32 μM. It was applied to the determination of ATP in (spiked) human plasma with satisfactory recoveries (from 93.2% to 106.3%). Oppositely, when the unlabeled aptamer is used instead of thiol-labeled aptamer in this process, the ATP-aptamer complexes rather than unlabeled aptamer provide greater protection for AuNPs against salt-induced aggregation. It is found that when the aptamer covalently binds to AuNPs, the steric hindrance is dominant for the stabilization of AuNPs; for unlabeled aptamer, the electrostatic repulsion is responsible for their stability, irrespective of whether ATP is present or not. These two different forces lead to the aggregation or dispersion of AuNPs with addition of target in salt solution. Graphical abstractThe impact of two repulsive forces (electrostatic repulsion and steric repulsion) on the stabilization of gold nanoparticles, and its application in fluorescent terbium metal-organic frameworks as a nanoprobe for adenosine triphosphate.

Enhancing Enzyme Immobilization on Carbon Nanotubes via Metal-Organic Frameworks for Large-Substrate Biocatalysis

Biocatalysis of large-sized substrates finds wide applications. Immobilizing the involved enzymes on solid supports improves biocatalysis yet faces challenges such as enzyme structural perturbation, leaching, and low cost-efficiencies, depending on immobilization strategies/matrices. Carbon nanotubes (CNTs) are attractive matrices but challenged by enzyme leaching (physical adsorption) or perturbation (covalent linking). Zeolitic imidazolate frameworks (ZIFs) overcome these issues. However, our recent study [ J. Am. Chem. Soc., 2018, 140, 16032-16036] showed reduced cost-efficiency as enzymes trapped below the ZIF surfaces cannot participate in biocatalysis; the enzyme-ZIF composites are also unstable under acidic conditions. In this work, we demonstrate the feasibility of using ZIFs to immobilize enzymes on CNT surfaces on two model enzymes, T4 lysozyme and amylase, both of which showed negligible leaching and retained catalytic activity under neutral and acidic conditions. To better understand the behavior of enzymes on CNTs and CNT-ZIF, we characterized enzyme orientation on both matrices using site-directed spin-labeling (SDSL)-electron paramagnetic resonance (EPR), which is immune to the complexities caused by CNT and ZIF background signals and enzyme-matrix interactions. Our structural investigations showed enhanced enzyme exposure to the solvent compared to enzymes in ZIFs alone; orientation of enzymes in matrices itself is directly related to substrate accessibility and, therefore, essential for understanding and improving catalytic efficiency. To the best of our knowledge, this is the first time ZIFs and one-pot synthesis are employed to anchor large-substrate enzymes on CNT surfaces for biocatalysis. This is also the first report of enzyme orientation on the CNT surface and upon trapping in CNT-ZIF composites. Our results are essential for guiding the rational design of CNT-ZIF combinations to improve enzyme stabilization, loading capacity, and catalytic efficiency.