Biology subjects

Chau, C. C.

Publications and source records attributed to Chau, C. C..

7 recordsLinked to original sources

bioRxiv2026

Empirical Validation of Composite Fractional Noise Models in Nanopore Signals

Nanopore sensors have transformed single-molecule analysis, enabling real-time detection of biomolecules with unprecedented resolution. Understanding and modelling noise in nanopore sensing is essential to unlocking their full analytical potential. Although mechanistic models of nanopore noise exist, a rigorous statistical framework that characterises noise structure across diverse experimental conditions is still lacking. Here, we present a comprehensive empirical analysis of nanopore noise using twelve diverse experimental conditions acquired with different nanopores, analytes, and electronic recording systems. By employing multiple, mutually reinforcing statistical methods, we establish that nanopore noise is well described by a composite fractional model comprising multiple fractional Gaussian noise and fractional Brownian motion components. This finding is supported by confirmation of Gaussianity, rigorous interpretation of second-order exponents, multifractal analysis, and evidence that transient deviations are attributable to deterministic or experimental artefacts rather than alternative stochastic mechanisms. We further resolve quasi-deterministic structures, such as baseline trends and structural breaks, and demonstrate their separability from the underlying stochastic profile. Collectively, these results provide the first formal statistical validation of a composite fractional model for nanopore noise and establish a principled basis for noise reconstruction, realistic simulation, and statistically grounded algorithm design for nanopore sensing applications. This study provides the foundation for the creation of high-fidelity performance evaluation datasets for signal processing, and the controlled generation and augmentation of data for machine learning while maintaining statistical fidelity to experimental conditions.

biophysics↗

bioRxiv2025

Buffer-dependent conformational dynamics of α-synuclein revealed by nanopipette electrospray ionisation ion mobility mass spectrometry

Electrolyte conditions in vivo and in vitro are known to influence protein structure and function. Intrinsically disordered proteins (IDPs) are particularly sensitive to their solution conditions such as ionic strength and molecular crowding, and their dynamic structural ensembles rapidly respond to the cellular environment. While structural mass spectrometry (MS) techniques are uniquely able to capture aspects of this structural diversity, technical limitations have largely precluded the use of native MS approaches to interrogate the conformational rearrangements of IDPs in response to high concentrations of non-volatile salts. Here, we overcome this challenge by employing sub 100-nm nanopipette electrospray emitters for more gentle and salt-tolerant analysis to study the conformational distribution of -Synuclein (S) using native MS and ion mobility-MS in varied solution conditions, including in phosphate buffered saline. We show using native MS that it is possible to capture salt and buffer induced changes in the S conformational ensemble when using traditional biochemical buffers, which reflect structural changes from in silico predictions and in-solution measurements. This work demonstrates the power of nanopipette emitters for the study of IDPs, and establishes native MS as a method that can be routinely used to determine how solution conditions tune the conformational landscape of IDPs. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/671163v2_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@35ff69org.highwire.dtl.DTLVardef@113821aorg.highwire.dtl.DTLVardef@1c27b90org.highwire.dtl.DTLVardef@13e4db1_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

High-speed AFM imaging of the Entropic Disassembly of DNA Origami for Single-Molecule Biosensing

Circulating microRNAs (miRNAs) are promising biomarkers for disease diagnosis, but their small size and instability hinder direct detection. The detection of small RNA, such as miRNA, using solid-state nanopores typically involves the binding of miRNA to a larger carrier molecule to generate detectable signals. However, this approach is prone to RNAse degradation in the environment leading to accidental digestion of miRNA prior to analysis. Here, we present an alternative approach based on DNA origami disassembly driven by toehold-mediated strand displacement (TMSD). Specifically, we designed a symmetric DNA origami dimer that undergoes TMSD-driven separation into monomers using miRNAs as invading strands. We visualized the real-time dynamics of dimer separation at high resolution using high-speed atomic force microscopy (HS-AFM), directly capturing nanoscale mechanical dynamics of the TMSD process that are inaccessible to ensemble or fluorescence-based measurements. Following the TMSD, single molecule nanopore sensing enables quantitative endpoint analysis of dimer separation by measuring the ratio of dimers to monomers. This direct read-out method enabled the multiplexed detection of miRNAs. Due to the near irreversible process of the TMSD, we performed the detection of miRNA in crude RNA tissue extracts under the presence of RNAse and showed that our approach allowed the robust detection of small RNA that is unaffected by the complex degrading environment.

biophysics↗

bioRxiv2024

Solid-State Nanopore Real Time Assay for Monitoring Cas9 Endonuclease Reactivity

The field of nanopore sensing is now moving beyond nucleic acid sequencing. An exciting new avenue is the use of nanopore platforms for the monitoring of biochemical reactions. Biological nanopores have been used to investigate the dynamics of enzymatic reactions but solid-state nanopore approaches have lagged. This is partially due to the necessity of using higher salt conditions (e.g. 4M LiCl) to improve the signal-to-noise ratio. These conditions are often incompatible with monitoring biological activities such as restriction enzyme and CRISPR-Cas9 endonuclease activities, as their abilities to digest DNA are largely abolished under high salt conditions. We pioneered a polymer electrolyte based solid-state nanopore approach that can maintain a high signal-to-noise ratio even at a physiologically relevant salt concentration. Based on this, we report monitoring the endonuclease activities at physiological salt conditions in real time with a polymer electrolyte nanopore. We successfully monitor the dsDNA cleavage activity of the restriction enzyme SwaI in in a range of digestion buffers and the off-target activity of CRISPR-Cas9 RNP endonuclease in the presence of single base pair mismatches. This approach enables solid-state nanopore technology for the dynamic monitoring of biochemical reactions at single molecule resolution.

biophysics↗

bioRxiv2023

Single Cell Track and Trace: live cell labelling and temporal transcriptomics via nanobiopsy.

Single-cell RNA sequencing has revolutionised our understanding of cellular heterogeneity, but whether using isolated cells or more recent spatial transcriptomics approaches, these methods require isolation and lysis of the cell under investigation. This provides a snapshot of the cell transcriptome from which dynamic trajectories, such as those that trigger cell state transitions, can only be inferred. Here, we present cellular nanobiopsy: a platform that enables simultaneous labelling and sampling from a single cell without killing it. The technique is based on scanning ion conductance microscopy (SICM) and uses a double-barrel nanopipette to inject a fluorescent dye and to extract femtolitre-volumes of cytosol. We used the nanobiopsy to longitudinally profile the transcriptome of single glioblastoma (GBM) brain tumour cells in vitro over 72hrs with and without standard treatment. Our results suggest that treatment either induces or selects for more transcriptionally stable cells. We envision the nanobiopsy will transform standard single-cell transcriptomics from a static analysis into a dynamic and temporal assay.

genomics↗

bioRxiv2022

Asymmetric Ion Mobility and Interface Displacement Drive the Signal Enhancement in a Polymer-electrolyte Nanopore

Solid-state nanopores have been widely employed in the detection of biomolecules, but low signal-to-noise ratios still represent a major obstacle to enable the discrimination of short nucleic acid and protein sequences. The addition of 50% polyethylene glycol (PEG) to the bath solution was recently demonstrated as a simple way to enhance the detection of such biomolecules translocating through a model solid-state nanopore. Here, we provide a comprehensive description of the physics describing a nanopore measurement carried out in 50% PEG that is supported by finite-element modelling and experiments. We demonstrate that the addition of PEG to the external solution introduces a strong imbalance in the transport properties of cations and anions, drastically affecting the characteristic current response of the nanopore. We further show that the strong asymmetric current response is due to a polarity-dependent ion distribution and transport at the nanopipette tip region, leading to either ion depletion or enrichment for few tens of nanometers across the aperture. Under negative potential, when double-stranded DNA molecules translocate, the depleted region (sensing region) significantly improves the sensitivity compared to systems without PEG. We then introduce a displacement of the interface between pore and external solution to simulate the mechanical interactions between analyte and PEG molecules. We found that this displacement affects the ion distribution in the sensing region, enhancing the detection current during the translocation of biomolecules.

biophysics↗

bioRxiv2021

Cooperative electrolyte-PEG interactions drive the signal amplification in a solid-state nanopore

Nanopore systems have emerged as a leading platform for the analysis of biomolecular complexes with single molecule resolution. However, the analysis of several analytes like short nucleic acids or proteins with nanopores represents a sensitivity challenge, because their translocation lead to small signals difficult to distinguish from the noise. Here, we report a simple method to enhance the signal to noise ratio in nanopore experiments by a simple modification of the solution used in nanopore sensing. The addition of poly-ethylene glycol (PEG) and the careful selection of the supporting electrolyte leads to large signal enhancement. We observed that the translocation dynamics are in good agreement with an established method that uses the lattice energy of an electrolyte to approximate the affinity of an ion to PEG. We identified CsBr as the optimal supporting electrolyte to complement PEG to enable the analysis of dsDNA at 500 kHz bandwidth, and the detection of dsDNA as short as 75 bp.

biophysics↗