Single-molecule fingerprinting of protein-drug interaction using a funneled biological nanopore.

In drug discovery, efficient screening of protein-drug interactions (PDIs) is hampered by the limitations of current biophysical approaches. Here, we develop a biological nanopore sensor for single-molecule detection of proteins and PDIs using the pore-forming toxin YaxAB. Using this YaxAB nanopore, we demonstrate label-free, single-molecule detection of interactions between the anticancer Bcl-xL protein and small-molecule drugs as well as the Bak-BH3 peptide. The long funnel-shaped structure and nanofluidic characteristics of the YaxAB nanopore enable the electro-osmotic trapping of diverse folded proteins and high-resolution monitoring of PDIs. Distinctive nanopore event distributions observed in the two-dimensional (ΔI/Io-versus-IN) plot illustrate the ability of the YaxAB nanopore to discriminate individual small-molecule drugs bound to Bcl-xL from non-binders. Taken together, our results present the YaxAB nanopore as a robust platform for label-free, ultrasensitive, single-molecule detection of PDIs, opening up a possibility for low-cost, highly efficient drug discovery against diverse drug targets.

Application of Nanopore Sensors for Biomolecular Interactions and Drug Discovery.

Biomolecular interactions, such as protein-protein, protein-nucleic acid, and protein/nucleic acid-ligand interactions, play crucial roles in various cellular signaling and biological processes, and offer attractive therapeutic targets in numerous human diseases. Currently, drug discovery is limited by the low efficiency and high cost of conventional ensemble-averaging-based techniques for biomolecular interaction analysis and high-throughput drug screening. Nanopores are an emerging technology for single-molecule sensing of biomolecules. Owing to the notable merits of single-molecule sensing, nanopore sensors have contributed tremendously to nucleic acid sequencing and disease diagnostics. In this minireview, we summarize the recent developments and outlooks in single-molecule sensing of various biomolecular interactions for drug discovery applications using biological and solid-state nanopore sensors.

Single-Molecule Sensing of an Anticancer Therapeutic Protein-Protein Interaction Using the Chemically Modified OmpG Nanopore.

Nanopore sensors are a highly attractive platform for single-molecule sensing for sequencing, disease diagnostics, and drug screening. Outer membrane protein G (OmpG) nanopores have advantages for single-molecule sensing owing to their rigid monomeric structure, which comprises seven flexible loops, providing distinct gating patterns upon analyte binding. Blocking of the protein-protein interaction between B-cell lymphoma-extra-large (Bcl-xL) and the BH3 domain of Bcl-2 homologous antagonist/killer (Bak-BH3) has been reported as a promising strategy for anticancer therapy. Here, we characterized the interaction between Bcl-xL and Bak-BH3 as well as its inhibition by a small-molecule inhibitor using click chemistry-based Bak-BH3 peptide-conjugated OmpG nanopores. The binding of Bcl-xL to Bak-BH3 generated characteristic gating signals involving significant changes in the amplitudes of noise and gating parameters such as gating frequency, open probability, and durations of open and closed states. Notably, specific inhibition of Bcl-xL by the small-molecule antagonist, ABT-737, led to the recovery of the noise and gating parameters. Collectively, these results revealed that the chemically modified OmpG nanopore can serve as a valuable sensor platform for ultrasensitive, rapid, and single-molecule-based drug screening against protein-protein interactions, which are therapeutic targets for various diseases.

Modulation of the peroxidase-like activity of iron oxide nanoparticles by surface functionalization with polysaccharides and its application for the detection of glutathione.

Here, we employed three polysaccharides, such as dextran, hyaluronic acid, and chitosan, for surface modification of iron oxide nanoparticles (IONPs) and carried out in-depth investigation to elucidate the effect of surface functionalities on the peroxidase (POD) like activity of IONPs. The affinity of substrates to the catalytic site of IONPs was found to be determined by the surface functional groups and hydration layer of polysaccharide coating on the surface of IONPs. The role of hydration layer was further confirmed by the results that the POD-like activity of IONPs coated with a certain polysaccharide having higher water holding capacity was significantly enhanced by salting-out reagent, such as ammonium chloride that is known to reduce the thickness of hydration layer. Moreover, the excellent catalytic activity of dextran-coated IONPs was successfully applied to develop a highly sensitive sensing system for the detection of glutathione (GSH) with a limit of detection of 2.3 nM.

Paper-based colorimetric detection of pathogenic bacteria in food through magnetic separation and enzyme-mediated signal amplification on paper disc.

Herein, we report a colorimetric sensing system for the detection of highly virulent bacteria, Escherichiacoli O157:H7, in sausage by utilizing magnetic separation and enzyme-mediated signal amplification on paper disc. For magnetic separation, Poly-l-lysine coated starch magnetic particles (PLL@SMPs) were synthesized and utilized for the separation and concentration of the bacteria in sample suspension. Horseradish peroxidase-conjugated antibody (HRP-Antibody) and 3,3',5,5'- tetramethylbenzidine (TMB) were employed for the specific signal amplification in the presence of target bacteria. The synthesized PLL@SMPs showed an excellent capture efficiency (>90%) for the pathogenic bacteria in large volume sample suspension. The intrinsic problems associated with the non-specific binding of sensing components that lead to the high background signal and low sensitivity in colorimetric detection was successfully resolved by employing hyaluronic acid as a blocking agent. The effective separation and concentration of target bacteria by PLL@SMPs and target-specific signal amplification with exceptionally high signal to noise ratio enabled the detection of target bacteria with a detection limit in the single digit regime. The sensing system proposed in this study was successfully used for the detection of the target pathogenic bacteria, E. coli O157:H7, in sausage sample with the limit of detection (LOD) as low as 30.8 CFU/mL with 95% probability. The simple nature of paper-based detection system with a great sensitivity and specificity would provide an effective means of evaluating the safety of food and environmental samples.

Topological analysis of single-stranded DNA with an alpha-hederin nanopore.

Nanopores have been emerged as a powerful tool for analyzing the structural information and interactional properties of a range of biomolecules. The spatial resolution of nanopore is determined by the diameter and effective thickness of its constriction region, but the presence of vestibule or stem structure in protein-based nanopore could negatively affect the sensitivity of the nanopore when applied for genome sequencing and topological analysis of DNA. Recently, alpha-hederin (Ah) has been reported to form a sub-nanometer scale pore structure in lipid membrane. With the simple structure and extremely small effective thickness, the Ah nanopore was shown to discriminate four different types of nucleotides. However, identification of a certain nucleotide in a strand of DNA, which is essential for genome sequencing, remains challenging. Here, we investigated the resolving capability of Ah nanopore to discriminate few nucleotides in a strand of single-stranded DNA, and the factors determining the sensitivity of Ah nanopore. The Ah nanopore was shown to be able to identify as few as three adenosine nucleotides in a strand of poly cytidine, in which the dwell time of the additional current blockade that represents the adenosine residue was in good agreement with their physical length. We also found that the lateral tension and chain pressure generated around the nanopore were influenced by pore's diameter and played as a dependent variables to determine the geometry of nanopore's constriction as well as the spatial resolution of the Ah nanopore.

Colorimetric assay for the determination of molecular weight distribution and branching characteristics of starch hydrolysates.

Here, we present a gold nanoparticle-based colorimetric assay for the determination of molecular weight distribution and branching characteristics of enzymatically hydrolyzed starch. The steric stabilization effect of starch hydrolysate on the colloidal stability of AuNPs was found to be proportional to the ratio of high molecular weight amylopectins, which was clearly reflected by the intensity of the characteristic surface plasmonic resonance (SPR) absorbance peak of the AuNPs. The fractional change of high molecular weight amylopectin over the course of enzymatic hydrolysis reaction could be measured based on the intensity of SPR peak, in which the results correlated well with those obtained by conventional gel permeation chromatography. With the proper calibration of a specific set of enzyme and starch type, this method would provide a fairly simple and fast means of analyzing the molecular weight distribution of starch hydrolysate on site as well as the amylose content in native starch.

Gold Nanoparticle-Coated Starch Magnetic Beads for the Separation, Concentration, and SERS-Based Detection of E. coli O157:H7.

Here, we report gold nanoparticle-coated starch magnetic beads (AuNP@SMBs) that were prepared by in situ synthesis of AuNPs on the surface of SMBs. Upon functionalization of the surface with a specific antibody, the immuno-AuNP@SMBs were found to be effective in separating and concentrating the target pathogenic bacteria, Escherichia coli O157:H7, from an aqueous sample as well as providing a hotspot for surface-enhanced Raman scattering (SERS)-based detection. We employed a bifunctional linker protein, 4× gold-binding peptide-tagged Streptococcal protein G (4GS), to immobilize antibodies on AuNP@SMBs and AuNPs in an oriented form. The linker protein also served as a Raman reporter, exhibiting a strong and unique fingerprint signal during the SERS measurement. The amplitude of the SERS signal was shown to have a good correlation with the concentration of target bacteria ranging from 100 to 105 CFU/mL. The detection limit was determined to be as low as a single cell, and the background signals derived from nontarget bacteria were negligible due to the excellent specificity and colloidal stability of the immuno-AuNP@SMBs and SERS tags. The highly sensitive nature of the SERS-based detection system will provide a promising means to detect the pathogenic microorganisms in food or clinical specimen.

Paper-Based Radial Chromatographic Immunoassay for the Detection of Pathogenic Bacteria in Milk.

Here, a paper-based radial flow chromatographic immunoassay (RFCI) employing gold nanoparticles (AuNPs) as chromatic agents was developed for the detection of Escherichia coli O157:H7 in whole milk. A 4-repeated gold-binding peptide-tagged (4GBP) streptococcal protein G (SPG) fusion protein was constructed as a bifunctional linker to immobilize antibodies on the surface of AuNPs with a well-oriented form based on the specific affinity of GBP and SPG to the gold and Fc portion of the antibody, respectively. 4GS@AuNPs prepared with the bifunctional linker protein exhibited excellent colloidal stability even at high salt concentrations of up to 500 mM, which is a critical requirement for its application to a broad range of biological and food samples. The enhanced colloidal stability and excellent binding capability of the immuno-4GS@AuNPs toward target bacteria lowered the detection limit of RFCI for target pathogenic bacteria in whole milk as low as 103 CFU/mL, which is by an order of magnitude lower than that of conventional immuno-AuNPs prepared with physical adsorption of antibodies. The RFCI pattern could also be converted into a grayscale value by simple image processing for quantitative determination of target pathogenic bacteria. This paper-based detection system would provide an effective means of monitoring the presence of food-borne pathogens in real food samples with naked eyes.

Effect of Lecithin on the Spontaneous Crystallization of Enzymatically Synthesized Short-Chain Amylose Molecules into Spherical Microparticles.

Here, we report a facile and effective one-pot approach to prepare uniform amylose-based polymeric microparticles (PMPs) through enzymatic synthesis of short-chain amylose (SCA) followed by spontaneous self-assembly of the SCA in the presence of lecithin. The effect of lecithin on nucleation and growth kinetics of amylose microparticles was investigated by monitoring the turbidity of reaction solution and the size of particles over the course of the self-assembly process. The results suggest that lecithin played a critical role in controlling the self-assembly kinetics to form uniform amylose microparticles through steric stabilization of the growing particles and diffusion-limited growth effect. The crystallinity of amylose microparticles was not affected by lecithin, implying that lecithin did not disrupt the crystal structure within the particle and would mainly be present on the surface of the microparticles. Considering its biodegradable and biocompatible nature, the amylose-based microparticles would find a range of useful applications in the area of food, cosmetics, medicine, chromatography and other related materials sciences.

Alpha-Hederin Nanopore for Single Nucleotide Discrimination.

Various types of biological and synthetic nanopores have been developed and utilized for the high-throughput investigation of individual biomolecules. Biological nanopores made with channel proteins are so far superior to solid-state ones in terms of sensitivity and reproducibility. However, the performance of a biological nanopore is dependent on the protein in the channel structure its dimensions are predetermined and are difficult to modify for broader applications. Here inspired by the cytotoxic mechanisms of a saponin derivative, alpha-hederin, we report a nonproteinaceous nanopore that can be formed spontaneously in a lipid membrane. We propose the pore-forming mechanism of alpha-hederin in a cholesterol-rich lipid membrane and a strategy to control the pore-forming rate by a lipid partitioning method. The small diameter and effective thickness of alpha-hederin nanopores enabled us to discriminate ssDNA homopolymers as well as four types of nucleotides, showing its potential as a DNA sequencing tool.

Reduction of DNA Folding by Ionic Liquids and Its Effects on the Analysis of DNA-Protein Interaction Using Solid-State Nanopore.

DNA folding is not desirable for solid-state nanopore techniques when analyzing the interaction of a biomolecule with its specific binding sites on DNA since the signal derived from the binding site could be buried by a large signal from the folding of DNA nearby. To resolve the problems associated with DNA folding, ionic liquids (ILs), which are known to interact with DNA through charge-charge and hydrophobic interactions are employed. 1-n-butyl-3-methylimidazolium chloride (C4 mim) is found to be the most effective in lowering the incident of DNA folding during its translocation through solid-state nanopores (4-5 nm diameter). The rate of folding signals from the translocation of DNA-C4 mim is decreased by half in comparison to that from the control bare DNA. The conformational changes of DNA upon complexation with C4 mim are further examined using atomic force microscopy, showing that the entanglement of DNA which is common in bare DNA is not observed when treated with C4 mim. The stretching effect of C4 mim on DNA strands improves the detection accuracy of nanopore for identifying the location of zinc finger protein bound to its specific binding site in DNA by lowering the incident of DNA folding.

Molecular Rearrangement of Glucans from Natural Starch To Form Size-Controlled Functional Magnetic Polymer Beads.

Herein, we report a fairly simple and environmentally friendly approach for the fabrication of starch-based magnetic polymer beads (SMPBs) with uniform shape and size through spontaneous rearrangement of short-chain glucan (SCG) produced by enzymatic debranching of waxy maize starch. The paramagnetic materials, dextran-coated iron oxide nanoparticles (Dex@IONPs), were readily incorporated into the starch microstructure and rendered a superparamagnetic property to the SMPBs. The morphology and size of resulting SMPBs turned out to be modulated by Dex@IONPs in a concentration-dependent manner, of which Dex@IONPs was assumed to be acting as a seed inducing the epitaxial crystallization of SCG and further transforming it into homogeneous microparticles. The surface of SMPBs was readily functionalized with an antibody through a one-step reaction using a linker protein. The immuno-SMPBs showed great capture efficiency (>90%) for target bacteria. The colloidal stability and favorable surface environment for biomolecules are believed to be responsible for the high capture efficiency and specificity of the SMPBs. Furthermore, the captured bacteria along with antibody and linker protein were effectively eluted from the surface of SMPBs by adding free maltose, making this new material suitable for various chromatographic applications.

Biosynthesis of superparamagnetic polymer microbeads via simple precipitation of enzymatically synthesized short-chain amylose.

Here, we report a simple and non-emulsion based approach to prepare starch-based magnetic polymer beads with well-defined size, shape and dispersibility in aqueous environment through co-precipitation of enzymatically synthesized short chain amylose (SCA) and dextran-coated iron oxide nanoparticles (Dex@IONPs). The size and morphology of magnetic polymer beads (MPBs) were controlled by employing Dex@IONPs as a seeding agent. The resulting superparamagnetic amylose microbeads (SAMBs) were readily functionalized with antibody through one step reaction using a linker protein, which showed great capture efficiency (>90%) and specificity for target bacteria present in complicated food matrix. The excellent magnetic sensitivity also enabled the SAMBs readily assembled into ordered 1D arrays by external magnetic field whose structure could permanently be fixed by SCA-mediated precipitation process.