Nanopore biphasic-pulse biosensor

Single-molecule lipopolysaccharides identification and the interplay with biomolecules via nanopore readout

Lipopolysaccharides (LPS) are the major constituent on the cell envelope of all gram-negative bacteria. They are ubiquitous in air, and are toxic inflammatory stimulators for urinary disorders and sepsis. The reported optical, thermal, and electrochemical sensors via the intermolecular interplay of LPS with proteins and aptamers are generally complicated methods. We demonstrate the single-molecule nanopore approach for LPS identification in distinct bacteria as well as the serotypes discrimination. With a 4 nm nanopore, we achieve a detection limit of 10 ng/mL. Both the antibiotic polymyxin B (PMB) and DNA aptamer display specific binding to LPS. The identification of LPS in both human serum and tap water show good performance with nanopore platforms. Our work shows a highly-sensitive and easy-to-handle scheme for clinical and environmental biomarkers determination and provides a promising screening tool for early warning of contamination in water and medical supplies.

Tunable nanochannel resistive pulse sensing device using a novel multi-module self-assembly

Nanochannel-based resistive pulse sensing (nano-RPS) system is widely used for the high-sensitive measurement and characterization of nanoscale biological particles and biomolecules due to its high surface to volume ratio. However, the geometric dimensions and surface properties of nanochannel are usually fixed, which limit the detections within particular ranges or types of nanoparticles. In order to improve the flexibility of nano-RPS system, it is of great significance to develop nanochannels with tunable dimensions and surface properties. In this work, we proposed a novel multi-module self-assembly (MS) strategy which allows to shrink the geometric dimensions and tune surface properties of the nanochannels simultaneously. The MS-tuned nano-RPS device exhibits an enhanced signal-to-noise ratio (SNR) for nanoparticle detections after shrunk the geometric dimensions by MS strategy. Meanwhile, by tuning the surface charge, an enhanced resolution for viral particles detection was achieved with the MS-tuned nano-RPS devices by analyzing the variation of pulse width due the tuned surface charge. The proposed MS strategy is versatile for various types of surface materials and can be potentially applied for nanoscale surface reconfiguration in various nanofluidic devices.

Nanopore discrimination and sensitive plasma detection of multiple natriuretic peptides: The representative biomarker of human heart failure

Natriuretic peptides can relieve cardiovascular stress and closely related to heart failure. Besides, these peptides also have preferable interactions of binding to cellular protein receptors, and subsequently mediate various physiology actions. Hence, detection of these circulating biomarkers could be evaluated as a predictor ("Gold standard") for rapid, early diagnosis and risk stratification in heart failure. Herein, we proposed a measurement to discriminate multiple natriuretic peptides via the peptide-protein nanopore interaction. The nanopore single-molecular kinetics revealed that the strength of peptide-protein interactions was in the order of ANP > CNP > BNP, which was demonstrated by the simulated peptide structures using SWISS-MODEL. More importantly, the peptide-protein interaction analyzing also allowed us to measure the peptide linear analogs and structure damage in peptide by single-chemical bond breakup. Finally, we presented an ultra-sensitive detection of plasma natriuretic peptide using asymmetric electrolyte assay, obtaining a detection limit of ∼770 fM for BNP. At approximately, it is 1597 times lower than that of using symmetric assay (∼1.23 nM), 8 times lower than normal human level (∼6 pM), and 13 times lower than the diagnostic values (∼10.09 pM) complied in the guideline of European Society of Cardiology. That said, the designed nanopore sensor is benefit for natriuretic peptides measurement at single molecule level and demonstrates its potential for heart failure diagnosis.

Nanopore single-molecule biosensor in protein denaturation analysis

Unclear issues in protein studies include but not limited to the stability and denaturation mechanism in the presence of denaturants. Herein, we report a dynamic monitoring approach based on nanopore single-molecule biosensor, which can detect the protein's folding and unfolding transitions by recording a nanopore ionic current. When gradually increasing the concentration of denaturant guanidine hydrochloride (GdmCl), sensitive responses were observed with lysozyme unfolding. The emergence of the featured biphasic-pulse demonstrated the existence of a stable intermediate. It was the first time to experimentally confirm the dynamic equilibrium between the intermediate and the native states at single molecule level, therefore consolidating the standpoint of lysozyme denaturation process following the three-state model. Additionally, we got more insights into the conformation about the intermediate as globular-like structure, larger gyration radius, and enhanced positive charge density. We considered that the manner of denaturant toward lysozyme adopts the "direct" model based on stronger electrostatic and van der Waals forces. Nanopore biosensor exhibited excellent sensitivity with a low detection concentration of 280 pM and reproducibility in analysing the folding intermediate of lysozyme.

Resistive amplitude fingerprints during translocation of linear molecules through charged solid-state nanopores

We report the first analytical theory on the amplitude of resistive signals during molecular translocation through charged solid-state nanopores with variable cross-sectional area and piecewise-constant surface charge densities. By providing closed-form explicit algebraic expressions for the concentration profiles inside charged nanopores, this theory allows the prediction of baseline and translocation resistive signals without the need for numerical simulation of the electrokinetic phenomena. A transversely homogenized theory and an asymptotic expansion for weakly charged pores capture DC or quasi-static rectification due to field-induced intrapore concentration polarization (as a result of pore charge inhomogeneity or a translocating molecule). This theory, validated by simulations and experiments, is then used to explain why the amplitude of a single stranded DNA molecule can be twice as high as the amplitude of its double stranded counterpart. It also suggests designs for intrapore concentration polarization and volume exclusion effects that can produce biphasic and other amplitude fingerprints for high-throughput and yet discriminating molecular identification.