Quantification of the affinities and kinetics of protein interactions using silicon nanowire biosensors

Abstract

Monitoring the binding affinities and kinetics of protein interactions is important in clinical diagnostics and drug development because such information is used to identify new therapeutic candidates. Surface plasmon resonance is at present the standard method used for such analysis, but this is limited by low sensitivity and low-throughput analysis. Here, we show that silicon nanowire field-effect transistors can be used as biosensors to measure protein–ligand binding affinities and kinetics with sensitivities down to femtomolar concentrations. Based on this sensing mechanism, we develop an analytical model to calibrate the sensor response and quantify the molecular binding affinities of two representative protein–ligand binding pairs. The rate constant of the association and dissociation of the protein–ligand pair is determined by monitoring the reaction kinetics, demonstrating that silicon nanowire field-effect transistors can be readily used as high-throughput biosensors to quantify protein interactions.

Low-cost top-down zinc oxide nanowire sensors through a highly transferable ion beam etching for healthcare applications

“…Over the past decades, Ion Sensitive Field Effect Transistors (ISFETs) have been intensively researched for a wide range of sensing applications, such as ion [1], pH [2], DNA [3] and protein [4] sensing. Siliconbased nanowires have been of particular interest as their large surface-to-volume ratio offers a high sensitivity [4,5].…”

“…Siliconbased nanowires have been of particular interest as their large surface-to-volume ratio offers a high sensitivity [4,5]. Nanowires fabricated in a top-down process are the preferred solution for commercialization of the technology by the semiconductor industry due to precise dimension and position control.…”

Silicon nanowire-transistor biosensor for study of molecule-molecule interactions

“…For example, Cui et al (2001) developed a boron-doped SiNW-FET sensor functionalized with small molecule-biotin, which is able to probe streptavidin down to a picomolar level. Another group also employed this molecule pair to measure protein-ligand binding affinities and kinetics via an SiNW biosensor and further determined the rate constant of the association and dissociation of the molecule pair (Duan et al 2012b). …”

“…This demonstrated the capability of the SiNW biosensor for the direct detection of protein-DNA interactions in the complex environment of real samples. Next, Duan et al (2012b) showed that SiNW FETs can be used to measure the affinities and kinetics of protein-DNA interactions with sensitivity down to femtomolar range. A representative protein-DNA binding pair, high mobility group box 1 (HMGB1) proteins and DNA that shows slow association/dissociation kinetics, was selected as an analytical model to investigate the binding affinities and kinetics based on an SiNW biosensing platform ( Figure 4B).…”

“…Recently, silicon nanowire field-effect transistors (SiNWFETs) have proven to be a promising tool in the investigation of molecular interactions due to their capability of ultrasensitive probing, real-time recording, and label-free detection (Duan et al 2012b). Molecular interactions, such as protein-protein binding and nucleic acid-nucleic acid hybridization, are essential in extracellular and intracellular signaling (Pawson andNash 2000, Sancar et al 2004).…”