Stanford Advisors

All Publications

  • Comparing assays via the resolution of molecular concentration. Nature biomedical engineering Wilson, B. D., Eisenstein, M., Soh, H. T. 1800

    View details for DOI 10.1038/s41551-021-00832-8

    View details for PubMedID 34934175

  • Accelerated Electron Transfer in Nanostructured Electrodes Improves the Sensitivity of Electrochemical Biosensors. Advanced science (Weinheim, Baden-Wurttemberg, Germany) Fu, K., Seo, J., Kesler, V., Maganzini, N., Wilson, B. D., Eisenstein, M., Murmann, B., Soh, H. T. 2021: e2102495


    Electrochemical biosensors hold the exciting potential to integrate molecular detection with signal processing and wireless communication in a miniaturized, low-cost system. However, as electrochemical biosensors are miniaturized to the micrometer scale, their signal-to-noise ratio degrades and reduces their utility for molecular diagnostics. Studies have reported that nanostructured electrodes can improve electrochemical biosensor signals, but since the underlying mechanism remains poorly understood, it remains difficult to fully exploit this phenomenon to improve biosensor performance. In this work, electrochemical aptamer biosensors on nanoporous electrode are optimized to achieve improved sensitivity by tuning pore size, probe density, and electrochemical measurement parameters. Further, a novel mechanism in which electron transfer is physically accelerated within nanostructured electrodes due to reduced charge screening, resulting in enhanced sensitivity is proposed and experimentally validated. In concert with the increased surface areas achieved with this platform, this newly identified effect can yield an up to 24-fold increase in signal level and nearly fourfold lower limit of detection relative to planar electrodes with the same footprint. Importantly, this strategy can be generalized to virtually any electrochemical aptamer sensor, enabling sensitive detection in applications where miniaturization is a necessity, and should likewise prove broadly applicable for improving electrochemical biosensor performance in general.

    View details for DOI 10.1002/advs.202102495

    View details for PubMedID 34668339

  • Re-Evaluating the Conventional Wisdom about Binding Assays. Trends in biochemical sciences Wilson, B. D., Soh, H. T. 2020


    Analytical technologies based on binding assays have evolved substantially since their inception nearly 60 years ago, but our conceptual understanding of molecular recognition has not kept pace. Contemporary technologies, such as single-molecule and digital measurements, have challenged, or even rendered obsolete, core concepts behind conventional binding assay design. Here, we explore the fundamental principles underlying molecular recognition systems, which we consider in terms of signals generated through concentration-dependent shifts in equilibrium. We challenge certain orthodoxies related to binding-based detection assays, including the primary importance of a low dissociation constant (KD) and the extent to which this parameter constrains dynamic range and limit of detection. Lastly, we identify key principles for designing binding assays that are optimally suited for a given detection application.

    View details for DOI 10.1016/j.tibs.2020.04.005

    View details for PubMedID 32402748

  • High-Fidelity Nanopore Sequencing of Ultra-Short DNA Targets. Analytical chemistry Wilson, B. D., Eisenstein, M. n., Soh, H. T. 2019


    Nanopore sequencing offers a portable and affordable alternative to sequencing-by-synthesis methods but suffers from lower accuracy and cannot sequence ultrashort DNA. This puts applications such as molecular diagnostics based on the analysis of cell-free DNA or single-nucleotide variants (SNVs) out of reach. To overcome these limitations, we report a nanopore-based sequencing strategy in which short target sequences are first circularized and then amplified via rolling-circle amplification to produce long stretches of concatemeric repeats. After sequencing on the Oxford Nanopore Technologies MinION platform, the resulting repeat sequences can be aligned to produce a highly accurate consensus that reduces the high error-rate present in the individual repeats. Using this approach, we demonstrate for the first time the ability to obtain unbiased and accurate nanopore data for target DNA sequences <100 bp. Critically, this approach is sensitive enough to achieve SNV discrimination in mixtures of sequences and even enables quantitative detection of specific variants present at ratios of <10%. Our method is simple, cost-effective, and only requires well-established processes. It therefore expands the utility of nanopore sequencing for molecular diagnostics and other applications, especially in resource-limited settings.

    View details for PubMedID 31038923

  • Independent control of the thermodynamic and kinetic properties of aptamer switches. Nature communications Wilson, B. D., Hariri, A. A., Thompson, I. A., Eisenstein, M. n., Soh, H. T. 2019; 10 (1): 5079


    Molecular switches that change their conformation upon target binding offer powerful capabilities for biotechnology and synthetic biology. Aptamers are useful as molecular switches because they offer excellent binding properties, undergo reversible folding, and can be engineered into many nanostructures. Unfortunately, the thermodynamic and kinetic properties of the aptamer switches developed to date are intrinsically coupled, such that high temporal resolution can only be achieved at the cost of lower sensitivity or high background. Here, we describe a design strategy that decouples and enables independent control over the thermodynamics and kinetics of aptamer switches. Starting from a single aptamer, we create an array of aptamer switches with effective dissociation constants ranging from 10 μM to 40 mM and binding kinetics ranging from 170 ms to 3 s. Our strategy is broadly applicable to other aptamers, enabling the development of switches suitable for a diverse range of biotechnology applications.

    View details for DOI 10.1038/s41467-019-13137-x

    View details for PubMedID 31699984