DNA Nanostructure Sequence-Dependent Binding of Organophosphates

Simple and fast colorimetric detection of lipopolysaccharide based on aptamer and SYBR Green I mediated aggregation of gold nanoparticles

Lipopolysaccharide (LPS) poses a considerable threat to food safety and human health. A colorimetric assay for LPS detection based on LPS binding aptamer (LBA) and SYBR Green I (SG) mediated aggregation of gold nanoparticles (AuNPs) was established. In the absence of LPS, the LBA was absorbed onto the AuNPs surface which prevented SG-induced aggregation of AuNPs, and the sensing system exhibited red color. When LPS was added, it interacted with the LBA, forming a complex. At higher LPS concentration, many LBAs were exhausted resulting in SG-induced aggregation of AuNPs, and color change from red to blue. The range of colorimetric detection of LPS was linear in 0-12 EU/mL, with a limit of detection of 0.1698 EU/mL. Spiked LPS in real samples and interfering substances were also identified. This assay ingeniously using the fluorescent dye SG as an effective trigger of AuNPs aggregation, is rapid and facile than most of those earlier reported LBA-based LPS assays, and there is potential to be modified to construct assays for other targets.

Ligand-binding assays with OBPs and CSPs

Assessing the ligand-binding properties of OBPs and CSPs is essential for understanding their physiological function. It also provides basic information when these proteins are used as biosensing elements for instrumental measurement of odors. Although different approaches have been applied in the past to evaluate the affinity of receptors and soluble binding proteins to their ligands, using a fluorescent reporter represents the method of choice for OBPs and CSPs. It offers the advantages of working at the equilibrium, being simple, fast and inexpensive, without requiring the use of radioactive tracers. However, as an indirect method, the fluorescence competitive binding approach presents drawbacks and sometimes requires an elaborate analysis to explain unexpected results. Here, after a brief survey of the different approaches to evaluate affinity constants, we focus on the fluorescence binding assay as applied to OBPs and CSPs, discussing situations that may require closer inspection of the results.

Molecular binding scaffolds increase local substrate concentration enhancing the enzymatic hydrolysis of VX nerve agent

Kinetic enhancement of organophosphate hydrolysis is a long-standing challenge in catalysis. For prophylactic treatment against organophosphate exposure, enzymatic hydrolysis needs to occur at high rates in the presence of low substrate concentrations and enzymatic activity should persist over days and weeks. Here, the conjugation of small DNA scaffolds was used to introduce substrate binding sites with micromolar affinity to VX, paraoxon, and methyl-parathion in close proximity to the enzyme phosphotriesterase (PTE). The result was a decrease in K_M and increase in the rate at low substrate concentrations. An optimized system for paraoxon hydrolysis decreased K_M by 11-fold, with a corresponding increase in second-order rate constant. The initial rates of VX and methyl-parathion hydrolysis were also increased by 3.1- and 6.7-fold, respectively. The designed scaffolds not only increased the local substrate concentration, but they also resulted in increased stability and PTE-DNA particle size tuning between 25 and ~150 nm. The scaffold engineering approach taken here is focused on altering the local chemical and physical microenvironment around the enzyme and is therefore compatible with active site engineering via combinatorial and computational approaches.

Engineering enzyme microenvironments for enhanced biocatalysis

Protein engineering provides a means to alter protein structure leading to new functions. Much work has focused on the engineering of enzyme active sites to enhance catalytic activity, however there is an increasing trend towards engineering other aspects of biocatalysts as these efforts can also lead to useful improvements. This tutorial discusses recent advances in engineering an enzyme's local chemical and physical environment, with the goal of enhancing enzyme reaction kinetics, substrate selectivity, and activity in harsh conditions (e.g., low or high pH). By introducing stimuli-responsiveness to these enzyme modifications, dynamic control of activity also becomes possible. These new biomolecular and protein engineering techniques are separate and independent from traditional active site engineering and can therefore be applied synergistically to create new biocatalyst technologies with novel functions.

From radioactive ligands to biosensors: binding methods with olfactory proteins

In this paper, we critically review the binding protocols currently reported in the literature to measure the affinity of odorants and pheromones to soluble olfactory proteins, such as odorant-binding proteins (OBPs), chemosensory proteins (CSPs) and Niemann-Pick class C2 (NPC2) proteins. The first part contains a brief introduction on the principles of binding and a comparison of the techniques adopted or proposed so far, discussing advantages and problems of each technique, as well as their suitable application to soluble olfactory proteins. In the second part, we focus on the fluorescent binding assay, currently the most widely used approach. We analyse advantages and drawbacks, trying to identify the causes of anomalous behaviours that have been occasionally observed, and suggest how to interpret the experimental data when such events occur. In the last part, we describe the state of the art of biosensors for odorants, using soluble olfactory proteins immobilised on biochips, and discuss the possibility of using such approach as an alternative way to measure binding events and dissociation constants.

Quantifying Small Molecule Binding Interactions with DNA Nanostructures

DNA nanostructures and hybrid DNA-protein materials are attractive solutions to many applications in biotechnology and material science because of their controllable molecule-level features. Critical to a complete description and characterization of these technologies is the quantification of binding affinity between DNA nanostructures and small molecules relevant to the application at hand. This protocols chapter described a series of experimental and in silico analyses that can be used to described and quantify ligand binding interactions between DNA nanostructures (DNA DX tiles), short double stranded DNA fragments, and arbitrary small molecules. The described methods include microscale thermophoresis, ligand completion assays, circular dichroism spectroscopy, and AutoDock simulations. The protocols use organophosphates and model chemical nerve agents as examples, but the methods described here are broadly applicable.

Enhancing Enzyme Activity and Immobilization in Nanostructured Inorganic-Enzyme Complexes

Understanding the chemical and physical interactions at the interface of protein surfaces and inorganic crystals has important implications in the advancement of immobilized enzyme catalysis. Recently, enzyme-inorganic hybrid complexes have been demonstrated as effective materials for enzyme immobilization. The precipitation of phosphate nanocrystals in the presence of enzymes creates enzyme-Cu₃(PO₄)₂·3H₂O particles with high surface-to-volume ratios, enhanced activity, and increased stability. Here, we begin to develop a mechanistic understanding of enzyme loading in such complexes. Using a series of enzymes including horseradish peroxidase (HRP), a thermostable alcohol dehydrogenase (AdhD), diaphorase, catalase, glucose oxidase (GOx), and the protein bovine serum albumin (BSA), we identified a correlation between particle synthesis temperature, overall enzyme charge, and enzyme loading. The model enzyme HRP has a high predicted pI of ∼7.5 and maintains an overall positive charge under the synthesis conditions, phosphate buffer pH 7.4. HRP loading in HRP-Cu₃(PO₄)₂ complexes was enhanced by 4.2-fold when synthesis was carried out at 37 °C in comparison with synthesis at 4 °C. HRP loading was further enhanced with synthesis at pH 8.0, correlating with a decrease in overall enzyme charge. Proteins with lower predicted pI values and negative overall charge (AdhD, pI of 5.6; diaphorase, pI of 6.8; GOx, pI of 5.2; catalase, pI of 6.9; and, BSA, pI of 5.7) exhibited higher enzyme loadings with 4 °C synthesis, 2.7-, 2.6-, 2.5-, 1.8-, and 1.7-fold protein loading enhancements, respectively. Using HRP as a model system, we also demonstrate that activity increased concomitantly with enzyme loading, and that particle nanostructure was minimally affected by synthesis temperature. Combined, the results presented here demonstrate the control of enzyme loading in enzyme-inorganic particles opening up new possibilities in enzyme and multienzyme catalysis.