Small Surface, Big Effects, and Big Challenges: Toward Understanding Enzymatic Activity at the Inorganic Nanoparticle-Substrate Interface

Immobilization of Thiol-Modified Horseradish Peroxidase on Gold Nanoparticles Enhances Enzyme Stability and Prevents Proteolytic Digestion

The specificity and efficiency of enzyme-mediated reactions have the potential to positively impact many biotechnologies; however, many enzymes are easily degraded. Immobilization on a solid support has recently been explored to improve enzyme stability. This study aims to gain insights and facilitate enzyme adsorption onto gold nanoparticles (AuNPs) to form a stable bioconjugate through the installation of thiol functional groups that alter the protein chemistry. In specific, the model enzyme, horseradish peroxidase (HRP), is thiolated via Traut's reagent to increase the robustness and enzymatic activity of the bioconjugate. This study compares HRP and its thiolated analog (THRP) to deduce the impact of thiolation and AuNP-immobilization on the enzyme activity and stability. HRP, THRP, and their corresponding bioconjugates, HRP-AuNP and THRP-AuNP, were analyzed via UV-vis spectrophotometry, circular dichroism, zeta potential, and enzyme-substrate kinetics assays. Our data show a 5-fold greater adsorption for THRP on the AuNP, in comparison to HRP, that translated to a 5-fold increase in the THRP-AuNP bioconjugate activity. The thiolated and immobilized HRP exhibited a substantial improvement in stability at elevated temperatures (50 °C) and storage times (1 month) relative to the native enzyme in solution. Moreover, HRP, THRP, and their bioconjugates were incubated with trypsin to assess the susceptibility to proteolytic digestion. Our results demonstrate that THRP-AuNP bioconjugates maintain full enzymatic activity after 18 h of incubation with trypsin, whereas free HRP, free THRP, and HRP-AuNP conjugates are rendered inactive by trypsin treatment. These results highlight the potential for protein modification and immobilization to substantially extend enzyme shelf life, resist protease digestion, and enhance biological function to realize enzyme-enabled biotechnologies.

Bait and Cleave: Exosite-Binding Peptides on Quantum Dots Selectively Accelerate Protease Activity for Sensing with Enhanced Sensitivity

The advantageous optical properties of quantum dots (QDs) motivate their use in a wide variety of applications related to imaging and bioanalysis, including the detection of proteases and their activity. Recent studies have shown that surface chemistry on QDs is able to modulate protease activity, but only nonspecifically. Here, we present a strategy to selectively accelerate the activity of a particular target protease by as much as two orders of magnitude. Exosite-binding "bait" peptides were derived from proteins that span a range of biological roles─substrate, receptor, and inhibitor─and were used to increase the affinity of the QD-peptide conjugates for either thrombin or factor Xa, resulting in increased rates of proteolysis for coconjugated substrates. Unlike effects from QD surface chemistry, the acceleration was specific to the target protease with negligible acceleration of other proteases. Benefits of this "bait and cleave" sensing approach included detection limits that improved by more than an order of magnitude, reenabled detection of target protease against an overwhelming background of nontarget proteolysis, and mitigation of the action of inhibitors. The cumulative results point to a generalizable strategy, where the mechanism of acceleration, considerations for the design of bait peptides and conjugates, and routes to expanding the scope of this approach are discussed. Overall, this research represents a major step forward in the rational design of nanoparticle-based enzyme sensors that enhance sensitivity and selectivity.

Assessing the Steric Impact of Surface Ligands on the Proteolytic Turnover of Quantum Dot-Peptide Conjugates

Proteases are important biomarkers and targets for the diagnosis and treatment of disease. The advantageous properties of semiconductor quantum dots (QDs) have made these nanoparticles useful as probes for protease activity; however, the effects of QD surface chemistry on protease activity are not yet fully understood. Here, we present a systematic study of the impact of sterics on the proteolysis of QD-peptide conjugates. The study utilized eight proteases (chymotrypsin, trypsin, endoproteinase Lys C, papain, endoproteinase Arg C, thrombin, factor Xa, and plasmin) and 41 distinct surface chemistries. The latter included three molecular weights of each of three macromolecular ligands derived from dextran and polyethylene glycol, as well as anionic and zwitterionic small-molecule ligands, and an array of mixed coatings of macromolecular and small-molecule ligands. These surface chemistries spanned a diversity of thicknesses, densities, and packing organization, as characterized by gel electrophoresis, capillary electrophoresis, dynamic light scattering, and infrared spectroscopy. The macromolecular ligands decreased the adsorption of proteases on the QDs and decelerated proteolysis of the QD-peptide conjugates via steric hindrance. The properties of the QD surface chemistry, rather than the protease properties, were the main factor in determining the magnitude of deceleration. The broad scope of this study provides insights into the many ways in which QD surface chemistry affects protease activity, and will inform the development of optimized nanoparticle-peptide conjugates for sensing of protease activity and resistance to unwanted proteolysis.

Trametes versicolor laccase activity modulated by the interaction with gold nanoparticles

In this study, the impact of gold nanoparticles (AuNPs) on the structure and activity of laccase from Trametes versicolor (Lc) was described. Fluorescence experiments revealed that AuNPs efficiently quench Lc's tryptophan fluorescence by a static and dynamic process. By using differential scanning microcalorimetry and circular dichroism spectroscopy, it was determined how the concentration of nanoparticles and the composition of the medium affected the secondary structure of Lc. The data revealed that upon binding with AuNPs, conformational changes take place mainly in presence of high amounts of nanoparticles. The complex kinetic analysis unveiled the Lc activity enhancement at low concentrations of AuNPs as opposed to the concentrated regime, where it can be reduced by up to 55%. The Michaelis-Menten tests highlighted that the activity of the biocatalyst is closely related to the concentration of AuNPs, while the Selwyn analysis demonstrated that even in a concentrated regime of Lc it is not deactivated regardless of the amount of AuNPs added. The thermal parameters improved by twofold in the presence of low AuNPs concentration, whereas the activation energy increased with AuNPs content, implying that not all collisions are beneficial to the enzyme structure. The effect of AuNPs on the decomposition of a recalcitrant dye (naphthol green B, NG) by Lc was also evaluated, and the Michaelis-Menten model revealed that only the high AuNPs content influenced negatively the Lc activity. The isothermal titration calorimetry revealed that hydrogen bonds are the main intermolecular forces between Lc and AuNPs, while electrostatic interactions are responsible for NG adsorption to AuNPs. The results of the docking analysis show the binding of NG near the copper T1 site of Lc with hydrogen bonds, electrostatic and hydrophobic interactions. The findings of this work provide important knowledge for laccase-based bio-nanoconjugates and their use in the field of environmental remediation.

Quantum Dots Meet Enzymes: Hydrophobicity of Surface Ligands and Size Do Matter

Colloidal quantum dots (QDs) are a class of representative fluorescent nanomaterials with tunable, bright, and sharp fluorescent emission, with promising biomedical applications. However, their effects on biological systems are not fully elucidated. In this work, we investigated the interactions between QDs with different surface ligands and different particle sizes and α-chymotrypsin (ChT) from the thermodynamic and kinetic perspectives. Enzymatic activity experiments demonstrated that the catalytic activity of ChT was strongly inhibited by QDs coated with dihydrolipoic acid (DHLA-QDs) with noncompetitive inhibitions, whereas the QDs coated with glutathione (GSH-QDs) had weak effects. Furthermore, kinetics studies showed that different particle sizes of DHLA-QDs all had high suppressive effects on the catalytic activity of ChT. It was found that DHLA-QDs with larger particle sizes had stronger inhibition effects because more ChT molecules were bound onto the surface of QDs. This work highlights the importance of hydrophobic ligands and particle sizes of QDs, which should be considered as the primary influencing factors in the assessment of biosafety. Meanwhile, the results herein can also inspire the design of nano inhibitors.

Biocatalysis versus Molecular Recognition in Sialoside-Selective Neuraminidase Biosensing

Sialic acid recognition and hydrolysis are essential parts of cellular function and pathogen infectivity. Neuraminidases are enzymes that detach sialic acid from sialosides, and their inhibition is a prime target for viral infection treatment. The connectivity and type of sialic acid influence the recognition and hydrolysis activity of the many different neuraminidases. The common strategies to evaluate neuraminidase activity, recognition, and inhibition rely on extensive labeling and require a large amount of sialylated glycans. The above limitations make the effort of finding viral inhibitors extremely difficult. We used synthetic sialylated glycans and developed a label-free electrochemical method to show that sialoside structural features lead to selective neuraminidase biosensing. We compared Neu5Ac to Neu5Gc sialosides to evaluate the organism-dependent neuraminidase selectivity-sensitivity relationship. We demonstrated that the type of surface and the glycan monolayer density direct the response to either binding or enzymatic activity. We proved that while the hydrophobic glassy carbon surface increases the interaction with the enzyme hydrophobic interface, the negatively charged interface of the lipoic acid monolayer on gold repels the protein and enables biocatalysis. We showed that the sialoside monolayers can serve as tools to evaluate the inhibition of neuraminidases both by biocatalysis and molecular recognition.

Smart Nanoparticle-Based Platforms for Regulating Tumor Microenvironment and Cancer Immunotherapy

Tumor development and metastasis are closely related to the tumor microenvironment (TME). Recently, several studies indicate that modulating TME can enhance cancer immunotherapy. Among various approaches to modulating TME, nanoparticles (NPs) with unique inherent advantages and smart modified characteristics are promising candidates in delivering drugs to cancer cells, amplifying the therapeutic effects, and leading to a cascade of immune responses. In this review, several smart NP-based platforms are briefly introduced, such as responsive NPs, targeting NPs, and the composition of TME, including dendritic cells, macrophages, fibroblasts, endothelial cells, myeloid-derived suppressor cells, and regulatory T cells. Moreover, the recent applications of smart NP-based platforms in regulating TME and cancer immunotherapy are briefly introduced. Last, the advantages and disadvantages of these smart NP-based platforms in potential clinical translation are discussed.

Are We There Yet? Intracellular Sensing with Luminescent Nanoparticles and FRET

Combinations of luminescent nanoparticles (LNPs) and Förster resonance energy transfer (FRET) offer properties and features that are advantageous for sensing of biomolecular targets and activity. Despite a multitude of designs for LNP-FRET sensors, intracellular sensing applications are underdeveloped. We introduce readers to this field, summarize essential concepts, meta-analyze the literature, and offer a perspective on the bottleneck in LNP-FRET sensor development.

Spacer Matters: All-Peptide-Based Ligand for Promoting Interfacial Proteolysis and Plasmonic Coupling

Plasmonic coupling via nanoparticle assembly is a popular signal-generation method in bioanalytical sensors. Here, we customized an all-peptide-based ligand that carries an anchoring group, polyproline spacer, biomolecular recognition, and zwitterionic domains for functionalizing gold nanoparticles (AuNPs) as a colorimetric enzyme sensor. Our results underscore the importance of the polyproline module, which enables the SARS-CoV-2 main protease (M^pro) to recognize the peptidic ligand on nanosurfaces for subsequent plasmonic coupling via Coulombic interactions. AuNP aggregation is favored by the lowered surface potential due to enzymatic unveiling of the zwitterionic module. Therefore, this system provides a naked-eye measure for M^pro. No proteolysis occurs on AuNPs modified with a control ligand lacking a spacer domain. Overall, this all-peptide-based ligand does not require complex molecular conjugations and hence offers a simple and promising route for plasmonic sensing other proteases.

Viscoelasticity Investigation of Semiconductor NP (CdS and PbS) Controlled Biomimetic Nanoparticle Hydrogels

The viscoelastic properties of colloidal nanoparticles (NPs) make opportunities to construct novel compounds in many different fields. The interparticle forces of inorganic particles on colloidal NPs are important for forming a mechanically stable particulate network especially the NP-based soft matter in the self-assembly process. Here, by capping with the same surface ligand L-glutathione (GSH), two semiconductor NP (CdS and PbS) controlled biomimetic nanoparticle hydrogels were obtained, namely, CdS@GSH and PbS@GSH. The dependence of viscoelasticity of colloidal suspensions on NP sizes, concentrations, and pH value has been investigated. The results show that viscoelastic properties of CdS@GSH are stronger than those of PbS@GSH because of stronger surface bonding ability of inorganic particles and GSH. The hydrogels formed by the smaller NPs demonstrate the higher stiffness due to the drastic change of GSH configurations. Unlike the CdS@GSH hydrogel system, the changes of NP concentrations and pH value had great influence on the PbS@GSH hydrogel system. The higher the proportion of water in the small particle size PbS@GSH hydrogel system, the greater the mechanical properties. The stronger the alkalinity in the large particle size PbS@GSH hydrogel system, the greater the hardness and storage modulus. Solution˗state nuclear magnetic resonance (NMR) indicated that the ligand GSH forms surface layers with different thickness varying from different coordination modes which are induced by different semiconductor NPs. Moreover, increasing the pH value of the PbS@GSH hydrogel system will dissociate the surface GSH molecules to form Pb²⁺ and GSH complexes which could enhance the viscoelastic properties.

Highly Sensitive Fluorescence Assay for miRNA Detection: Investigation of the DNA Spacer Effect on the DSN Enzyme Activity toward Magnetic-Bead-Tethered Probes

Researchers have recently designed various biosensors combining magnetic beads (MBs) and duplex-specific nuclease (DSN) enzyme to detect miRNAs. Yet, the interfacial mechanisms for surface-based hybridization and DSN-assisted target recycling are relatively not well understood. Thus, herein, we developed a highly sensitive and selective fluorescent biosensor to study the phenomenon that occurs on the local microenvironment surrounding the MB-tethered DNA probe via detecting microRNA-21 as a model. Using the above strategy, we investigated the influence of different DNA spacers, base-pair orientations, and surface densities on DSN-assisted target recycling. As a result, we were able to detect as low as 170 aM of miR-21 under the optimized conditions. Moreover, this approach exhibits a high selectivity in a fully matched target compared to a single-base mismatch, allowing the detection of miRNAs in serum with improved recovery. These results are attributed to the synergetic effect between the DSN enzyme activity and the neutral DNA spacer (triethylene glycol: TEG) to improve the miRNA detection's sensitivity. Finally, our strategy could create new paths for detecting microRNAs since it obliterates the enzyme-mediated cascade reaction used in previous studies, which is more expensive, more time-consuming, less sensitive, and requires double catalytic reactions.

Effect of Interfacial Properties on Impedimetric Biosensing of the Sialylation Process with a Biantennary N-Glycan-Based Monolayer

Sensing enzymatic sialylation provides new tools for the evaluation of pathological events and pathogen invasion. Enzymatic sialylation is usually monitored via fluorescence or metabolic labeling, which requires relatively large amounts of the glycan substrate with limited availability. Using a label-free biosensor requires smaller quantities of substrates because the interactions induce measurable changes to an interface, which can be translated into a signal. The downside of label-free biosensors is that they are very sensitive to changes at the interface, and the properties of the surface layer can play a major role. Electrochemical impedance spectroscopy was used here to follow the enzymatic sialylation of a biantennary N-glycan acceptor in mixed monolayers. The surfaces contained either neutral, positively or negatively charged, or zwitterionic functional groups. The systems were characterized by contact potential difference, ellipsometry, and contact angle analyses. We found that the characteristics of the mixed monolayer have a profound effect on the biosensing of the enzymatic sialylation. Positively charged layers were found to adsorb the enzyme under the reaction conditions. Negatively charged and zwitterionic surfaces were nonresponsive to enzymatic sialylation. Only the neutral mixed monolayers provided signals that were related directly to enzymatic sialylation. This work demonstrates the importance of appropriate interface properties for monitoring enzymatic sialylation processes.

Regulation of the Enzymatic Activities of Lysozyme by the Surface Ligands of Ultrasmall Gold Nanoclusters: The Role of Hydrophobic Interactions

Nanomaterials for biological applications would inevitably encounter and interact with biomolecules, which have a profound impact on the properties, functions, and even fates of both nanomaterials and biomolecules. Among the biomolecules, lysozyme (Lys) is of great importance in defending the bacterial intruder and maintaining health. Here, the interactions between fluorescent gold nanoclusters (AuNCs) (∼2 nm) capped with different surface ligands and Lys were thoroughly investigated. Fluorescence spectroscopic studies showed that dihydrolipoic acid (DHLA)-capped and glutathione (GSH)-capped AuNCs both quenched the intrinsic fluorescence of Lys by different quenching mechanisms. Agarose gel electrophoresis and zeta-potential assays showed that statistically one DHLA-AuNC could bind one Lys, while one GSH-AuNC could bind 3-4 Lys, providing new examples for the concept of a "protein complex". Activity assays indicated that DHLA-AuNCs heavily inhibited the enzymatic activity of Lys, while GSH-AuNCs had little effect. By synchronous fluorescence and circular dichroism spectroscopic studies, it was deduced that both AuNCs would interact with Lys by electrostatic attractions due to the distinct surface charges, and then DHLA-AuNCs would further interact with Lys by hydrophobic interactions, probably due to the hydrophobic carbon chain of DHLA and the hydrophobic side chains of amino acid residues in Lys, which was proved by the significant secondary structure changes caused by DHLA-AuNCs. Meanwhile, conformational changes induced by GSH-AuNCs with zwitterionic ligands were neglectable. Therefore, this work provided a comprehensive study of the consequences and mechanisms of the interactions between Lys and AuNCs, which was essential for the design and better use of nanomaterials as biological agents.

Stimuli-Responsive Three-Dimensional DNA Nanomachines Engineered by Controlling Dynamic Interactions at Biomolecule-Nanoparticle Interfaces

Stimuli-responsive nanomachines are attractive tools for biosensing, imaging, and drug delivery. Herein, we demonstrate that the orientation of macromolecules and subsequent dynamic interactions at the biomolecule-nanoparticle (bio-nano) interfaces can be rationally controlled to engineer stimuli-responsive DNA nanomachines. The success of this design principle was demonstrated by engineering a series of antibody-responsive DNA walkers capable of moving persistently on a three-dimensional track made of DNA functionalized gold nanoparticles. We show that drastically different responses to antibodies could be achieved using DNA walkers of identical sequences but with varying number or sites of modifications. We also show that multiple interfacial factors could be combined to engineer stimuli-responsive DNA nanomachines with high sensitivity and modularity. The potential of our strategy for practical uses was finally demonstrated for the amplified detection of antibodies and small molecules in both buffer and human serum samples. Unlike many DNA-based nanomachines, the performance of which could be significantly hindered by the matrix of serum, our system shows a matrix-enhanced sensitivity as a result of the engineering approach at the bio-nano interface.

Two-dimensional biomaterials: material science, biological effect and biomedical engineering applications

To date, nanotechnology has increasingly been identified as a promising and efficient means to address a number of challenges associated with public health. In the past decade, two-dimensional (2D) biomaterials, as a unique nanoplatform with planar topology, have attracted explosive interest in various fields such as biomedicine due to their unique morphology, physicochemical properties and biological effect. Motivated by the progress of graphene in biomedicine, dozens of types of ultrathin 2D biomaterials have found versatile bio-applications, including biosensing, biomedical imaging, delivery of therapeutic agents, cancer theranostics, tissue engineering, as well as others. The effective utilization of 2D biomaterials stems from the in-depth knowledge of structure-property-bioactivity-biosafety-application-performance relationships. A comprehensive summary of 2D biomaterials for biomedicine is still lacking. In this comprehensive review, we aim to concentrate on the state-of-the-art 2D biomaterials with a particular focus on their versatile biomedical applications. In particular, we discuss the design, fabrication and functionalization of 2D biomaterials used for diverse biomedical applications based on the up-to-date progress. Furthermore, the interactions between 2D biomaterials and biological systems on the spatial-temporal scale are highlighted, which will deepen the understanding of the underlying action mechanism of 2D biomaterials aiding their design with improved functionalities. Finally, taking the bench-to-bedside as a focus, we conclude this review by proposing the current crucial issues/challenges and presenting the future development directions to advance the clinical translation of these emerging 2D biomaterials.

Photoluminescent Nanoparticles for Chemical and Biological Analysis and Imaging

Research related to the development and application of luminescent nanoparticles (LNPs) for chemical and biological analysis and imaging is flourishing. Novel materials and new applications continue to be reported after two decades of research. This review provides a comprehensive and heuristic overview of this field. It is targeted to both newcomers and experts who are interested in a critical assessment of LNP materials, their properties, strengths and weaknesses, and prospective applications. Numerous LNP materials are cataloged by fundamental descriptions of their chemical identities and physical morphology, quantitative photoluminescence (PL) properties, PL mechanisms, and surface chemistry. These materials include various semiconductor quantum dots, carbon nanotubes, graphene derivatives, carbon dots, nanodiamonds, luminescent metal nanoclusters, lanthanide-doped upconversion nanoparticles and downshifting nanoparticles, triplet-triplet annihilation nanoparticles, persistent-luminescence nanoparticles, conjugated polymer nanoparticles and semiconducting polymer dots, multi-nanoparticle assemblies, and doped and labeled nanoparticles, including but not limited to those based on polymers and silica. As an exercise in the critical assessment of LNP properties, these materials are ranked by several application-related functional criteria. Additional sections highlight recent examples of advances in chemical and biological analysis, point-of-care diagnostics, and cellular, tissue, and in vivo imaging and theranostics. These examples are drawn from the recent literature and organized by both LNP material and the particular properties that are leveraged to an advantage. Finally, a perspective on what comes next for the field is offered.

Biological and Medical Applications of Calcium Phosphate Nanoparticles

Calcium phosphate nanoparticles have a high biocompatibility and biodegradability due to their chemical similarity to human hard tissue, for example, bone and teeth. They can be used as efficient carriers for different kinds of biomolecules such as nucleic acids, proteins, peptides, antibodies, or drugs, which alone are not able to enter cells where their biological effect is required. They can be loaded with cargo molecules by incorporating them, unlike solid nanoparticles, and also by surface functionalization. This offers protection, for example, against nucleases, and the possibility for cell targeting. If such nanoparticles are functionalized with fluorescing dyes, they can be applied for imaging in vitro and in vivo. Synthesis, functionalization and cell uptake mechanisms of calcium phosphate nanoparticles are discussed together with applications in transfection, gene silencing, imaging, immunization, and bone substitution. Biodistribution data of calcium phosphate nanoparticles in vivo are reviewed.

Biomolecular interactions of ultrasmall metallic nanoparticles and nanoclusters

The use of nanoparticles (NPs) in biomedicine has made a gradual transition from proof-of-concept to clinical applications, with several NP types meeting regulatory approval or undergoing clinical trials. A new type of metallic nanostructures called ultrasmall nanoparticles (usNPs) and nanoclusters (NCs), while retaining essential properties of the larger (classical) NPs, have features common to bioactive proteins. This combination expands the potential use of usNPs and NCs to areas of diagnosis and therapy traditionally reserved for small-molecule medicine. Their distinctive physicochemical properties can lead to unique in vivo behaviors, including improved renal clearance and tumor distribution. Both the beneficial and potentially deleterious outcomes (cytotoxicity, inflammation) can, in principle, be controlled through a judicious choice of the nanocore shape and size, as well as the chemical ligands attached to the surface. At present, the ability to control the behavior of usNPs is limited, partly because advances are still needed in nanoengineering and chemical synthesis to manufacture and characterize ultrasmall nanostructures and partly because our understanding of their interactions in biological environments is incomplete. This review addresses the second limitation. We review experimental and computational methods currently available to understand molecular mechanisms, with particular attention to usNP-protein complexation, and highlight areas where further progress is needed. We discuss approaches that we find most promising to provide relevant molecular-level insight for designing usNPs with specific behaviors and pave the way to translational applications.

Tuning DNA-nanoparticle conjugate properties allows modulation of nuclease activity

Enzyme-nanoparticle interactions can give rise to a range of new phenomena, most notably significant enzymatic rate enhancement. Accordingly, the careful study and optimization of such systems is likely to give rise to advanced biosensing applications. Herein, we report a systematic study of the interactions between nuclease enzymes and oligonucleotide-coated gold nanoparticles (spherical nucleic acids, SNAs), with the aim of revealing phenomena worthy of evolution into functional nanosystems. Specifically, we study two nucleases, an exonuclease (ExoIII) and an endonuclease (Nt.BspQI), via fluorescence-based kinetic experiments, varying parameters including enzyme and substrate concentrations, and nanoparticle size and surface coverage in non-recycling and a recycling formats. We demonstrate the tuning of nuclease activity by SNA characteristics and show that the modular units of SNAs can be leveraged to either accelerate or suppress nuclease kinetics. Additionally, we observe that the enzymes are capable of cleaving restriction sites buried deep in the oligonucleotide surface layer and that enzymatic rate enhancement occurs in the target recycling format but not in the non-recycling format. Furthermore, we demonstrate a new SNA phenomenon, we term 'target stacking', whereby nucleic acid hybridization efficiency increases as enzyme cleavage proceeds during the beginning of a reaction. This investigation provides important data to guide the design of novel SNAs in biosensing and in vitro diagnostic applications.

Affinity Immobilization of Semiconductor Quantum Dots and Metal Nanoparticles on Cellulose Paper Substrates

Colloidal semiconductor quantum dots (QDs), metal nanoparticles, and cellulose paper are materials with numerous applications in bioanalysis and beyond. The functional properties of QDs and metal NPs are substantially different than those of cellulose, such that their integration with cellulose paper is potentially enabling for many applications. Here, we characterize and evaluate multiple chemistries that modify cellulose paper substrates for the affinity-based immobilization of QDs, gold nanoparticles (Au NPs), and platinum nanoparticles (Pt NPs). These chemistries include grafting of cellulose fibers with imidazole and dithiol groups, as well as the aminosilanization of cellulose fibers (both with and without subsequent grafting with dithiol groups). Cellulose modifications and nanoparticle immobilization are characterized by multiple techniques, including, but not limited to, X-ray photoelectron spectroscopy, scanning electron microscopy, and optical imaging, extinction, and fluorescence measurements. We demonstrate the on-paper immobilization of color-tuned mixtures of QDs, on-paper patterning of QDs by microcontact printing, and post-immobilization enhancement of energy transfer and model assays of protease activity. The robustness of QD photoluminescence is also evaluated between immobilization chemistries. Paper-immobilized Au NPs and Pt NPs are evaluated as potential substrates for SERS and as supported catalysts for a model decolorization reaction. Our cumulative results indicate that there may not be a one-size-fits-all immobilization chemistry. Instead, the immobilization chemistry should be tailored and optimized for the downstream application.

Regulation of Thrombin Activity with Ultrasmall Nanoparticles: Effects of Surface Chemistry

Nanomaterials displaying well-tailored sizes and surface chemistries can provide novel ways with which to modulate the structure and function of enzymes. Recently, we showed that gold nanoparticles (AuNPs) in the ultrasmall size regime could perform as allosteric effectors inducing partial inhibition of thrombin activity. We now find that the nature of the AuNP surface chemistry controls the interactions to the anion-binding exosites 1 and 2 on the surface of thrombin, the allosterically induced changes to the active-site conformation, and, by extension, the enzymatic activity. Ultrasmall AuNPs passivated with p-mercaptobenzoic acid ligands (AuMBA) and a peptide-based (Ac-ECYN) biomimetic coat (AuECYN) were utilized in our investigations. Remarkably, we found that while AuMBA binds to exosites 1 and 2, AuECYN interacts primarily with exosite 2. It was further established that AuMBA behaves as a "mild denaturant" of thrombin leading to catalytic dysfunction over time. Conversely, AuECYN resembles a proper allosteric effector leading to partial and reversible inhibition of the activity. Collectively, our findings reveal how the distinct binding modes of different AuNP types may uniquely influence thrombin structure and catalysis. The present study further contributes to our understanding of how synthetic nanomaterials could be exploited in the allosteric regulation of enzymes.

Quantum Dot Lipase Biosensor Utilizing a Custom-Synthesized Peptidyl-Ester Substrate

Lipases are an important class of lipid hydrolyzing enzymes that play significant roles in many aspects of cell biology and digestion; they also have large roles in commercial food and biofuel preparation and are being targeted for pharmaceutical development. Given these, and many other biotechnological roles, sensitive and specific biosensors capable of monitoring lipase activity in a quantitative manner are critical. Here, we describe a Förster resonance energy transfer (FRET)-based biosensor that originates from a custom-synthesized ester substrate displaying a peptide at one end and a dye acceptor at the other. These substrates were ratiometrically self-assembled to luminescent semiconductor quantum dot (QD) donors by metal affinity coordination using the appended peptide's terminal hexahistidine motif to give rise to the full biosensing construct. This resulted in a high rate of FRET between the QD donor and the proximal substrate's dye acceptor. The lipase hydrolyzed the intervening target ester bond in the peptide substrate which, in turn, displaced the dye acceptor containing component and altered the rate of FRET in a concentration-dependent manner. Specifics of the substrate's stepwise synthesis are described along with the sensors assembly, characterization, and application in a quantitative proof-of-concept demonstration assay that is based on an integrated Michaelis-Menten kinetic approach. The utility of this unique nanoparticle-based architecture within a sensor configuration is then discussed.

Concentric DNA Amplifier That Streamlines In-Solution Biorecognition and On-Particle Biocatalysis

Colloidal nanoparticle biosensors capable of on-particle biocatalysis are powerful tools for amplified detection of biomolecules. The development and practical uses of such concentric amplifiers can be complicated because of the on-particle biorecognition that involves varying interfacial factors at the biomolecule-nanoparticle interfaces. Herein, we reason that a nanoparticle biosensor equipped with an in-solution biorecognition element may be better fabricated, predicted, controlled, and performed. The in-solution biorecognition shall also be streamlined with the on-particle biocatalysis so that the overall analytical and kinetic performance is not compromised. As a testbed, we introduce a concentric DNA amplifier driven by an enzyme-powered three-dimensional DNA nanomachine, where a DNA walker can be instantly assembled onto a spherical nucleic acid (SNA) track through a polyadenosine anchor. As such, the free DNA walker can participate in reactions in a homogeneous solution before assembling to the SNA track. The instant and stable assembly enabled by both adsorption and complementary base pairing also ensures rapid on-particle biocatalysis. We demonstrate that the in-solution biorecognition effectively eliminates the binding hindrance encountered by the on-particle biorecognition and thus significantly reduced energy barriers for the detection of nucleic acids and proteins. Because of the in-solution biorecognition, our system can also be plugged readily into complex DNA strand displacement networks for rapid signal amplification.

Property-Activity Relationship of Black Phosphorus at the Nano-Bio Interface: From Molecules to Organisms

As a novel member of the two-dimensional nanomaterial family, mono- or few-layer black phosphorus (BP) with direct bandgap and high charge carrier mobility is promising in many applications such as microelectronic devices, photoelectronic devices, energy technologies, and catalysis agents. Due to its benign elemental composition (phosphorus), large surface area, electronic/photonic performances, and chemical/biological activities, BP has also demonstrated a great potential in biomedical applications including biosensing, photothermal/photodynamic therapies, controlled drug releases, and antibacterial uses. The nature of the BP-bio interface is comprised of dynamic contacts between nanomaterials (NMs) and biological systems, where BP and the biological system interact. The physicochemical interactions at the nano-bio interface play a critical role in the biological effects of NMs. In this review, we discuss the interface in the context of BP as a nanomaterial and its unique physicochemical properties that may affect its biological effects. Herein, we comprehensively reviewed the recent studies on the interactions between BP and biomolecules, cells, and animals and summarized various cellular responses, inflammatory/immunological effects, as well as other biological outcomes of BP depending on its own physical properties, exposure routes, and biodistribution. In addition, we also discussed the environmental behaviors and potential risks on environmental organisms of BP. Based on accumulating knowledge on the BP-bio interfaces, this review also summarizes various safer-by-design strategies to change the physicochemical properties including chemical stability and nano-bio interactions, which are critical in tuning the biological behaviors of BP. The better understanding of the biological activity of BP at BP-bio interfaces and corresponding methods to overcome the challenges would promote its future exploration in terms of bringing this new nanomaterial to practical applications.

Quantum Dots and Gold Nanoparticles as Scaffolds for Enzymatic Enhancement: Recent Advances and the Influence of Nanoparticle Size

Nanoparticle scaffolds can impart multiple benefits onto immobilized enzymes including enhanced stability, activity, and recoverability. The magnitude of these benefits is modulated by features inherent to the scaffold–enzyme conjugate, amongst which the size of the nanoscaffold itself can be critically important. In this review, we highlight the benefits of enzyme immobilization on nanoparticles and the factors affecting these benefits using quantum dots and gold nanoparticles as representative materials due to their maturity. We then review recent literature on the use of these scaffolds for enzyme immobilization and as a means to dissect the underlying mechanisms. Detailed analysis of the literature suggests that there is a “sweet-spot” for scaffold size and the ratio of immobilized enzyme to scaffold, with smaller scaffolds and lower enzyme:scaffold ratios generally providing higher enzymatic activities. We anticipate that ongoing studies of enzyme immobilization onto nanoscale scaffolds will continue to sharpen our understanding of what gives rise to beneficial characteristics and allow for the next important step, namely, that of translation to large-scale processes that exploit these properties.

Clickable gold nanoparticles for streamlining capture, enrichment and release of alkyne-labelled proteins

Alkyne-labelled proteins are generated as key intermediates in the chemical probe-based approaches to proteomics analysis. Their efficient and selective detection and isolation is an important problem. We designed and synthesized azide-functionalized gold nanoparticles as new clickable capture reagents to streamline click chemistry-mediated capture, enrichment and release of the alkyne-labelled proteins in one-pot to expedite the post-labelling analysis. Because hydrophobic surface functionalities are known to render gold nanoparticles poorly water-dispersible, hydrophilic PEG linkers with two different lengths were explored to confer colloidal stability to the clickable capture reagents. We demonstrated the ability of the capture reagents to conjugate the alkyne containing proteins at a nanomolar concentration via click chemistry, which can be immediately followed by their enrichment and elution. Furthermore, a bifunctional clickable capture reagent bearing sulforhodamine and azide groups was shown to conveniently attach a fluorophore to the alkyne-labelled protein upon click capture, which facilitated their rapid detection in the gel analysis.

Valency-Controlled Molecular Spherical Nucleic Acids with Tunable Biosensing Performances

Spherical nucleic acids (SNAs) play critical roles in many fields, such as molecular diagnostics, disease therapeutics, and materials application. Due to the important role of DNA density on the properties of SNAs, the controlled synthesis of monodisperse SNAs with precise DNA density is an important approach for the structure-function relationship study and finite functions regulation of SNAs. In particular, the construction of monodisperse SNAs in a valency-tunable and site-specific manner is highly important; however, it is still challenging. Herein, on the basis of the high controllability, nanometer precision, and addressable modification ability of framework nucleic acid (FNA), we develop the concept of valency-controlled framework nucleic acid core-based molecular spherical nucleic acids (FNA-mSNAs) with tunable biosensing performances. The FNA-mSNAs consist of a valency-tunable FNA-based DNA nanocube as the core and a controlled, precise number of DNA strands per core. By simply alternating the binding site number for shell DNA strands on the DNA nanocube, homogeneous FNA-mSNAs with different valencies were easily designed, which enabled the molecular level study of the effect of valency on their properties, such as nuclease stability and cellular uptake. Furthermore, taking advantage of the addressable modification ability of FNA, the first heterogeneous molecular SNAs with tunable valency were demonstrated. Importantly, the valency of heterogeneous FNA-mSNAs was able to tune their biosensing performance, such as response dynamics, detection sensitivity, and response range. With these remarkable features, FNA-mSNAs provide new research methods for the development of functional SNAs at the molecular level for a wide range of biological applications.

Probing and Controlling Dynamic Interactions at Biomolecule-Nanoparticle Interfaces Using Stochastic DNA Walkers

Herein, we report a bottom-up approach to assemble a series of stochastic DNA walkers capable of probing dynamic interactions occurring at the bio-nano interface. We systematically investigated the impact of varying interfacial factors, including intramolecular interactions, orientation, cooperativity, steric effect, multivalence, and binding hindrance on enzymatic behaviors at the interfaces of spherical nucleic acids. Our mechanistic study has revealed critical roles of various interfacial factors that significantly alter molecular binding and enzymatic behaviors from bulk solutions. The improved understanding of the bio-nano interface may facilitate better design and operation of nanoparticle-based biosensors and/or functional devices. We successfully demonstrate how improved understanding of the bio-nano interface help rationalize the design of amplifiable biosensors for nucleic acids and antibodies.