Mechanical Stability of DNA Corona Phase on Gold Nanospheres

Fluorogenic Linkage Integration for Nonfluorescent Transformations (FLINT)

Since its creation, single-molecule optical imaging has revolutionized the study of catalytic processes, yet its application largely relies on probing fluorogenic reactions. To overcome this limitation, we propose the Fluorogenic Linkage Integration for Nonfluorescent Transformation (FLINT) approach, an imaging method to resolve nonfluorogenic reactions at the single-molecule level. Using glucose oxidation as a model reaction, we coupled this nonfluorogenic reaction with a fluorogenic Amplex Red (AR) → resorufin (RF) transformation to create a cascading reaction. This integration allowed us to monitor single-turnover events and extract key kinetic parameters for glucose oxidation despite their being invisible under the optical microscope. Our ensemble measurements combining cyclic voltammetry and fluorescence spectroscopy confirmed the cascade reaction mechanism and revealed first-order kinetics for both elementary reaction steps. At the single-molecule level, turnover time analysis provided detailed information on the reaction kinetics, distinguishing the relatively fast glucose oxidation from slower AR oxidation. We further confirmed the validity of the FLINT approach by comparing the catalytic performances of 5 nm gold nanoparticles (AuNPs) against that of 18 × 52 nm gold nanorods (AuNRs) and AuNP@DNA coronazymes. Furthermore, FLINT was used to evaluate the chiral selectivity of d- and l-glucose on coronazymes, suggesting the potential application of FLINT in enantioselective reactions. The FLINT approach is a significant advancement in single-molecule imaging as it enables the study of nonfluorogenic reactions with high spatiotemporal resolution.

Biphasic mechanochemistry of single-chain polymerization

Mechanical forces can induce chemical reactions, produce chemical signals, and alter reaction kinetics. Here, using magnetic tweezers-based single-molecule force spectroscopy, we study the force effects on the ring-opening metathesis polymerization (ROMP) of single-polymer chains, during which nonequilibrium conformational entanglements can form and unravel stochastically. We find a surprising, biphasic force dependence of polymerization kinetics: The single-chain polymerization rate initially slows down with increasing stretching forces, reaching a minimum, and then accelerates at higher forces. Analysis of real-time single-chain growth trajectories allows for dissecting the polymerization process into two distinct regimes, one with and the other without entanglement formation, unveiling the biphasic force dependence in both regimes. Two different mechanisms likely operate for the biphasic dependence: a force-induced entanglement tightening and then splitting and a force-induced catalyst structural distortion that switches the reaction pathway between reactant states of different stability and reactivity. These findings and insights point to opportunities of using force to manipulate polymerization reactions and tune the physiochemical properties of synthetic polymers.

Decoupling Activity and Specificity in Coronazymes

Specificity and activity are often at odds for natural enzymes. In this work, specificity and activity in coronazymes made of an Au nanoparticle (AuNP) and coated with DNA aptamer for glucose substrates are decoupled. By single-molecule fluorescent MT-HILO (magnetic tweezers coupled with highly inclined and laminated optical sheet) microscopy, it is found that this coronazyme has ≈30 times higher activity on the d-glucose compared to bare AuNP nanozymes. Significantly, the new coronazyme demonstrates long-range modulations by circularly polarized light (CPL) according to the matching chirality between the CPL and DNA corona, which follows the rule of chiral induced spin selectivity (CISS). Although the aptamer in the coronazyme is evolved against d-glucose, surprisingly, this coronazyme catalyzes l-glucose better than d-glucose, likely due to the faster rates for the aptamer to interact with the l- over d-glucose. These results demonstrate, for the first time, an artificial enzyme with its catalytic activity controlled by short-range intermolecular forces, whereas its chiral specificity is modulated by long-range CPLs. This decoupled arrangement is pivotal to forge premier catalysts with activity and specificity superior to natural enzymes by separately optimizing these two properties.

Applications of DNA functionalized gold nanozymes in biosensing

In recent years, nanozymes have emerged as highly potential substitutes, surpassing the performance of natural enzymes. Among them, gold nanoparticles (AuNPs) and their metal hybrids have become a hot topic in nanozyme research due to their facile synthesis, easy surface modification, high stability, and excellent enzymatic activity. The integration of DNA with AuNPs, by precisely controlling the assembly, arrangement, and functionalization of nanoparticles, greatly facilitates the development of highly sensitive and selective biosensors. This review comprehensively elaborates on three core strategies for the combination of DNA with AuNPs, and deeply analyzes two widely applied enzyme activities in the field of sensing technology and the catalytic principles behind them. On this basis, we systematically summarize various methods for regulating the activity of gold nanozymes by DNA. Following that, we comprehensively review the latest research trends of DNA-Au nanozymes in the field of biosensing, with a particular focus on several crucial application areas such as food safety, environmental monitoring, and disease diagnosis. In the conclusion of the article, we not only discuss the main challenges faced in current research but also look forward to potential future research directions.

DNA Catalysis: Design, Function, and Optimization

Catalytic DNA has gained significant attention in recent decades as a highly efficient and tunable catalyst, thanks to its flexible structures, exceptional specificity, and ease of optimization. Despite being composed of just four monomers, DNA's complex conformational intricacies enable a wide range of nuanced functions, including scaffolding, electrocatalysis, enantioselectivity, and mechano-electro spin coupling. DNA catalysts, ranging from traditional DNAzymes to innovative DNAzyme hybrids, highlight the remarkable potential of DNA in catalysis. Recent advancements in spectroscopic techniques have deepened our mechanistic understanding of catalytic DNA, paving the way for rational structural optimization. This review will summarize the latest studies on the performance and optimization of traditional DNAzymes and provide an in-depth analysis of DNAzyme hybrid catalysts and their unique and promising properties.

Catalytic Relaxation of Kinetically Trapped Intermediates by DNA Chaperones

Common in biomacromolecules, kinetically trapped misfolded intermediates are often detrimental to the structures, properties, or functions of proteins or nucleic acids. Nature employs chaperone proteins but not nucleic acids to escort intermediates to correct conformations. Herein, we constructed a Jablonski-like diagram of a mechanochemical cycle in which individual DNA hairpins were mechanically unfolded to high-energy states, misfolded into kinetically trapped states, and catalytically relaxed back to ground-state hairpins by a DNA chaperone. The capacity of catalytic relaxation was demonstrated in a 1D DNA hairpin array mimicking nanoassembled materials. At ≥1 μM, the diffusive (or self-walking) DNA chaperone converted the entire array of misfolded intermediates to correct conformation in less than 15 s, which is essential to rapidly prepare homogeneous nanoassemblies. Such an efficient self-walking amplification increases the signal-to-noise ratio, facilitating catalytic relaxation to recognize a 1 fM DNA chaperone in 10 min, a detection limit comparable to the best biosensing strategies.

Amalgamation of DNAzymes and Nanozymes in a Coronazyme

Artificial enzymes such as nanozymes and DNAzymes are economical and stable alternatives to natural enzymes. By coating Au nanoparticles (AuNPs) with a DNA corona (AuNP@DNA), we amalgamated nanozymes and DNAzymes into a new artificial enzyme with catalytic efficiency 5 times higher than AuNP nanozymes, 10 times higher than other nanozymes, and significantly greater than most of the DNAzymes on the same oxidation reaction. The AuNP@DNA demonstrates excellent specificity as its reactivity on a reduction reaction does not change with respect to pristine AuNP. Single-molecule fluorescence and force spectroscopies and density functional theory (DFT) simulations indicate a long-range oxidation reaction initiated by radical production on the AuNP surface, followed by radical transport to the DNA corona, where the binding and turnover of substrates take place. The AuNP@DNA is named coronazyme because of its natural enzyme mimicking capability through the well-orchestrated structures and synergetic functions. By incorporating different nanocores and corona materials beyond DNAs, we anticipate that the coronazymes represent generic enzyme mimics to carry out versatile reactions in harsh environments.