Control of Nanoscale Environment to Improve Stability of Immobilized Proteins on Diamond Surfaces

Advancements of CRISPR technology in public health-related analysis

Pathogens and contaminants in food and the environment present significant challenges to human health, necessitating highly sensitive and specific diagnostic methods. Traditional approaches often struggle to meet these requirements. However, the emergence of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system has revolutionized nucleic acid diagnostics. The present review provides a comprehensive overview of the biological sensing technology based on the CRISPR/Cas system and its potential applications in public health-related analysis. Additionally, it explores the enzymatic cleavage capabilities mediated by Cas proteins, highlighting the promising prospects of CRISPR technology in addressing bioanalysis challenges. We discuss commonly used CRISPR-Cas proteins and elaborate on their application in detecting foodborne bacteria, viruses, toxins, other chemical pollution, and drug-resistant bacteria. Furthermore, we highlight the advantages of CRISPR-based sensors in the field of public health-related analysis and propose that integrating CRISPR-Cas biosensing technology with other technologies could facilitate the development of more diverse detection platforms, thereby indicating promising prospects in this field.

In silico study of substrate chemistry effect on the tethering of engineered antibodies for SARS-CoV-2 detection: Amorphous silica vs gold

The influence of the properties of different solid substrates on the tethering of two antibodies, IgG1-CR3022 and IgG1-S309, which were specifically engineered for the detection of SARS-CoV-2, has been examined at the molecular level using conventional and accelerated Molecular Dynamics (cMD and aMD, respectively). Two surfaces with very different properties and widely used in immunosensors for diagnosis, amorphous silica and the most stable facet of the face-centered cubic gold structure, have been considered. The effects of such surfaces on the structure and orientation of the immobilized antibodies have been determined by quantifying the tilt and hinge angles that describe the orientation and shape of the antibody, respectively, and the dihedrals that measure the relative position of the antibody arms with respect to the surface. Results show that the interactions with amorphous silica, which are mainly electrostatic due to the charged nature of the surface, help to preserve the orientation and structure of the antibodies, especially of the IgG1-CR3022, indicating that the primary sequence of those antibodies also plays some role. Instead, short-range van der Waals interactions with the inert gold surface cause a higher degree tilting and fraying of the antibodies with respect to amorphous silica. The interactions between the antibodies and the surface also affect the correlation among the different angles and dihedrals, which increases with their strength. Overall, results explain why amorphous silica substrates are frequently used to immobilize antibodies in immunosensors.

Bioinks and Bioprinting Strategies for Skeletal Muscle Tissue Engineering

Skeletal muscles play important roles in critical body functions and their injury or disease can lead to limitation of mobility and loss of independence. Current treatments result in variable functional recovery, while reconstructive surgery, as the gold-standard approach, is limited due to donor shortage, donor-site morbidity, and limited functional recovery. Skeletal muscle tissue engineering (SMTE) has generated enthusiasm as an alternative solution for treatment of injured tissue and serves as a functional disease model. Recently, bioprinting has emerged as a promising tool for recapitulating the complex and highly organized architecture of skeletal muscles at clinically relevant sizes. Here, skeletal muscle physiology, muscle regeneration following injury, and current treatments following muscle loss are discussed, and then bioprinting strategies implemented for SMTE are critically reviewed. Subsequently, recent advancements that have led to improvement of bioprinting strategies to construct large muscle structures, boost myogenesis in vitro and in vivo, and enhance tissue integration are discussed. Bioinks for muscle bioprinting, as an essential part of any bioprinting strategy, are discussed, and their benefits, limitations, and areas to be improved are highlighted. Finally, the directions the field should expand to make bioprinting strategies more translational and overcome the clinical unmet needs are discussed.

Tag-Free Site-Specific BMP-2 Immobilization with Long-Acting Bioactivities via a Simple Sugar-Lectin Interaction

The construction of a biomaterial matrix with biological properties is of great importance to developing functional materials for clinical use. However, the site-specific immobilization of growth factors to endow materials with bioactivities has been a challenge to date. Considering the wide existence of glycosylation in mammalian proteins or recombinant proteins, we establish a bioaffinity-based protein immobilization strategy (bioanchoring method) utilizing the native sugar-lectin interaction between concanavalin A (Con A) and the oligosaccharide chain on glycosylated bone morphogenetic protein-2 (GBMP-2). The interaction realizes the site-specific immobilization of GBMP-2 to a substrate modified with Con A while preserving its bioactivity in a sustained and highly efficient way, as evidenced by its enhanced ability to induce osteodifferentiation compared with that of the soluble GBMP-2. Moreover, the surface with Con A-bioanchored GBMP-2 can be reused to stimulate multiple batches of C2C12 cells to differentiate almost to the same degree. Even after 4 month storage at 4 °C in phosphate-buffered saline (PBS), the Con A-bioanchored GBMP-2 still maintains the bioactivity to stimulate the differentiation of C2C12 cells. Furthermore, the ectopic ossification test proves the in vivo bioactivity of bioanchored GBMP-2. Overall, our results demonstrate that the tag-free and site (i.e., sugar chain)-specific protein immobilization strategy represents a simple and generic alternative, which is promising to apply for other glycoprotein immobilization and application. It should be noted that although the lectin we utilized can only bind to d-mannose/d-glucose, the diversity of the lectin family assures that a specific lectin could be offered for other sugar types, thus expanding the applicable scope further.

A mechanistic examination of salting out in protein-polymer membrane interactions

Developing a mechanistic understanding of protein dynamics and conformational changes at polymer interfaces is critical for a range of processes including industrial protein separations. Salting out is one example of a procedure that is ubiquitous in protein separations yet is optimized empirically because there is no mechanistic description of the underlying interactions that would allow predictive modeling. Here, we investigate peak narrowing in a model transferrin-nylon system under salting out conditions using a combination of single-molecule tracking and ensemble separations. Distinct surface transport modes and protein conformational changes at the negatively charged nylon interface are quantified as a function of salt concentration. Single-molecule kinetics relate macroscale improvements in chromatographic peak broadening with microscale distributions of surface interaction mechanisms such as continuous-time random walks and simple adsorption-desorption. Monte Carlo simulations underpinned by the stochastic theory of chromatography are performed using kinetic data extracted from single-molecule observations. Simulations agree with experiment, revealing a decrease in peak broadening as the salt concentration increases. The results suggest that chemical modifications to membranes that decrease the probability of surface random walks could reduce peak broadening in full-scale protein separations. More broadly, this work represents a proof of concept for combining single-molecule experiments and a mechanistic theory to improve costly and time-consuming empirical methods of optimization.

Highly sensitive detection of antibodies in a soft bioactive three-dimensional bioorthogonal hydrogel

This three-dimensional detection method of antibodies offers a high sensitivity and good biomolecule stability for new biosensing devices.

FoldX as Protein Engineering Tool: Better Than Random Based Approaches?

Improving protein stability is an important goal for basic research as well as for clinical and industrial applications but no commonly accepted and widely used strategy for efficient engineering is known. Beside random approaches like error prone PCR or physical techniques to stabilize proteins, e.g. by immobilization, in silico approaches are gaining more attention to apply target-oriented mutagenesis. In this review different algorithms for the prediction of beneficial mutation sites to enhance protein stability are summarized and the advantages and disadvantages of FoldX are highlighted. The question whether the prediction of mutation sites by the algorithm FoldX is more accurate than random based approaches is addressed.

Conductive polycrystalline diamond probes for local anodic oxidation lithography

This is the first report characterizing local anodic oxidation (LAO) lithography performed using conductive monolithic polycrystalline diamond (MD) and conductive polycrystalline diamond-coated (DC) tips and comparing it to the diamond-like carbon-coated and metal-coated silicon tips. The range and the rate of increase in the lithographic linewidth and height with tip bias (dw/dV and dh/dV) differed based on the tip material. The DC tips resulted in wider and taller lines and a higher dw/dV and dh/dV compared to metal-coated tips with a similar force constant (k(Avg)). The metal-coated and the DC tips with comparable k(Avg) showed comparable threshold voltages, whereas the MD tips with similar k(Avg) showed a higher threshold voltage. The MD tips exhibited less than half the height and nearly half the dw/dV and dh/dV obtained with the metal-coated tips with similar k Avg, thus also resulting in a smaller width at -10 V. The linewidths were found to be proportional to the inverse of the log of write speed(v) for all the tips; however, the proportionality constant varied with tip material; the DC tips had larger values, and the MD and the metal-coated tips had comparable values. When varying the speed, the height was found to be a sigmoidal function of width, with the MD probes achieving lower height compared to the metal-coated and the DC tips with comparable k(Avg). This study expands the application of monolithic conductive polycrystalline diamond (PCD) probes with outstanding wear resistance to fine LAO lithography.

The effect of electrode size and surface heterogeneity on electrochemical properties of ultrananocrystalline diamond microelectrode

We report here the effect of electrode size on electrochemical properties of boron-doped ultrananocrystalline diamond (UNCD) microelectrodes using electrochemical impedance spectroscopy (EIS). By reducing microelectrode size from 250-μm to 10-μm diameter (D), the shape of impedance spectra changes from linear line to two-arcs. The fitting of experimental data to electrochemical circuit model suggests that each arc likely corresponds to UNCD grains and grain boundary phases. The two phases become separable as a result of microelectrode size reduction. In addition, for D ≤ 100-μm, microstructural and morphological defects/heterogeneities of grain boundaries and the presence of surface oxygen are also revealed in the spectra. The microelectrode size reduction specifically affect the impedance of the grain boundaries, e.g. for ultramicroelectrodes, UMEs (D ≤ 25-μm), as the grain boundary impedance increases by ~30-fold. Thus, at UMEs, the grain-grain boundary properties are revealed more sensitively in the spectra. Atomic force microscopy, scanning electron microscopy, Raman spectroscopy and surface profilometry measurements were performed to study the influence of microfabrication on surface properties. A significant increase in surface roughness after microfabrication shows that heterogeneities as observed in the spectra are not only due to intrinsic UNCD properties but also arises from microfabrication.

The effect of electrode size and surface heterogeneity on electrochemical properties of ultrananocrystalline diamond microelectrode

We report here the effect of electrode size on electrochemical properties of boron-doped ultrananocrystalline diamond (UNCD) microelectrodes using electrochemical impedance spectroscopy (EIS). By reducing microelectrode size from 250-μm to 10-μm diameter (D), the shape of impedance spectra changes from linear line to two-arcs. The fitting of experimental data to electrochemical circuit model suggests that each arc likely corresponds to UNCD grains and grain boundary phases. The two phases become separable as a result of microelectrode size reduction. In addition, for D ≤ 100-μm, microstructural and morphological defects/heterogeneities of grain boundaries and the presence of surface oxygen are also revealed in the spectra. The microelectrode size reduction specifically affect the impedance of the grain boundaries, e.g. for ultramicroelectrodes, UMEs (D ≤ 25-μm), as the grain boundary impedance increases by ~30-fold. Thus, at UMEs, the grain-grain boundary properties are revealed more sensitively in the spectra. Atomic force microscopy, scanning electron microscopy, Raman spectroscopy and surface profilometry measurements were performed to study the influence of microfabrication on surface properties. A significant increase in surface roughness after microfabrication shows that heterogeneities as observed in the spectra are not only due to intrinsic UNCD properties but also arises from microfabrication.

Carbon Substrates: A Stable Foundation for Biomolecular Arrays

Since their advent in the early 1990s, microarray technologies have developed into a powerful and ubiquitous platform for biomolecular analysis. Microarrays consist of three major elements: the substrate upon which they are constructed, the chemistry employed to attach biomolecules, and the biomolecules themselves. Although glass substrates and silane-based attachment chemistries are used for the vast majority of current microarray platforms, these materials suffer from severe limitations in stability, due to hydrolysis of both the substrate material itself and of the silyl ether linkages employed for attachment. These limitations in stability compromise assay performance and render impossible many potential microarray applications. We describe here a suite of alternative carbon-based substrates and associated attachment chemistries for microarray fabrication. The substrates themselves, as well as the carbon-carbon bond-based attachment chemistries, offer greatly increased chemical stability, enabling a myriad of novel applications.

Nanostructuring of biosensing electrodes with nanodiamonds for antibody immobilization

While chemical vapor deposition of diamond films is currently cost prohibitive for biosensor construction, in this paper, we show that sonication-assisted nanostructuring of biosensing electrodes with nanodiamonds (NDs) allows harnessing the hydrolytic stability of the diamond biofunctionalization chemistry for real-time continuous sensing, while improving the detector sensitivity and stability. We find that the higher surface coverages were important for improved bacterial capture and can be achieved through proper choice of solvent, ND concentration, and seeding time. A mixture of methanol and dimethyl sulfoxide provides the highest surface coverage (33.6 ± 3.4%) for the NDs with positive zeta-potential, compared to dilutions of dimethyl sulfoxide with acetone, ethanol, isopropyl alcohol, or water. Through impedance spectroscopy of ND-seeded interdigitated electrodes (IDEs), we found that the ND seeds serve as electrically conductive islands only a few nanometers apart. Also we show that the seeded NDs are amply hydrogenated to be decorated with antibodies using the UV-alkene chemistry, and higher bacterial captures can be obtained compared to our previously reported work with diamond films. When sensing bacteria from 10(6) cfu/mL E. coli O157:H7, the resistance to charge transfer at the IDEs decreased by ∼ 38.8%, which is nearly 1.5 times better than that reported previously using redox probes. Further in the case of 10(8) cfu/mL E. coli O157:H7, the charge transfer resistance changed by ∼ 46%, which is similar to the magnitude of improvement reported using magnetic nanoparticle-based sample enrichment prior to impedance detection. Thus ND seeding allows impedance biosensing in low conductivity solutions with competitive sensitivity.

Identifying specific protein residues that guide surface interactions and orientation on silica nanoparticles

We identify specific acylphosphatase (AcP) residues that interact with silica nanoparticles (SNPs) using a combined NMR spectroscopy and proteomics-mass spectrometry approach. AcP associated with 4- and 15-nm diameter SNPs through a common and specific interaction surface formed by amino acids from the two α-helices of the protein. Greater retention of native protein structure was obtained on 4-nm SNPs than on 15-nm particles, presumably due to greater surface curvature-induced protein stabilization with the smaller SNPs. These results demonstrate that proteins may undergo specific and size-dependent orientation on nanoparticle surfaces. Our approach can be broadly applied to various protein-material systems to help understand in much greater detail the protein-nanomaterial interface; it would also encourage better modeling, and thus prediction and design, of the behavior of functional proteins adsorbed onto different surfaces.

A quantitative study of detection mechanism of a label-free impedance biosensor using ultrananocrystalline diamond microelectrode array

It is well recognized that label-free biosensors are the only class of sensors that can rapidly detect antigens in real-time and provide remote environmental monitoring and point-of-care diagnosis that is low-cost, specific, and sensitive. Electrical impedance spectroscopy (EIS) based label-free biosensors have been used to detect a wide variety of antigens including bacteria, viruses, DNA, and proteins due to the simplicity of their detection technique. However, their commercial development has been hindered due to difficulty in interpreting the change in impedance upon antigen binding and poor signal reproducibility as a result of surface fouling and non-specific binding. In this study, we develop a circuit model to adequately describe the physical changes at bio functionalized surface and provide an understanding of the detection mechanism based on electron exchange between electrolyte and surface through pores surrounding antibody-antigen. The model was successfully applied to extract quantitative information about the bio surface at different stages of surface functionalization. Further, we demonstrate boron-doped ultrananocrystalline diamond (UNCD) microelectrode array (3 × 3 format, 200 μm diameter) improves signal reproducibility significantly and increases sensitivity by four orders of magnitude. This study marks the first demonstration of UNCD array based biosensor that can reliably detect a model Escherichia coli K12 bacterium using EIS, positioning this technology for rapid adoption in point-of-use applications.

Atoms-to-microns model for small solute transport through sticky nanochannels

Modeling the transport of solutes through fluidic systems that have adsorbing surfaces is challenging due to the range of length and time scales involved. The components of such systems typically have dimensions from hundreds of nanometres to microns, whereas adsorption of solutes is sensitive to the atomic-scale structure of the solutes and surfaces. Here, we describe an atomic-resolution Brownian dynamics method for modeling the transport of solutes through sticky nanofluidic channels. Our method can fully recreate the results of all-atom molecular dynamics simulations at a fraction of the computational cost of the latter, which makes simulations of micron-size channels at a millisecond time scale possible without losing information about the atomic-scale features of the system. We demonstrate the capability of our method by simulating the rise and fall of solute concentration in sub-micron-long sticky nanochannels, showing that the atomic-scale features of the channels' surfaces have a dramatic effect on the kinetics of solute transport in and out of the channels. We expect our method to find applications in design and optimization of micro and nanofluidic systems for solute-specific transport and to complement existing approaches to modeling lab-on-a-chip devices by providing atomic scale information at a low computational cost.

Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface

Adsorption of dissolved molecules onto solid surfaces can be extremely sensitive to the atomic-scale properties of the solute and surface, causing difficulties for the design of fluidic systems in industrial, medical and technological applications. In this communication, we show that the Langmuir isotherm for adsorption of a small molecule to a realistic, heterogeneous surface can be predicted from atomic structures of the molecule and surface through molecular dynamics (MD) simulations. We highlight the method by studying the adsorption of dimethyl-methylphosphonate (DMMP) to amorphous silica substrates and show that subtle differences in the atomic-scale surface properties can have drastic effects on the Langmuir isotherm. The sensitivity of the method presented is sufficient to permit the optimization of fluidic devices and to determine fundamental design rules for controlling adsorption at the nanoscale.