Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB

Abstract

Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics) to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs). Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R2 = 0.8131).

Circulating microRNA detection using electrochemical biosensor for rapid diagnosis of liver disease in dogs

“…4A). Although, our binding kinetics studies with P-S3 10 exhibited an overall similar behaviour to our previous observation with P-FL 22 and miR-122 target hybridisation, 24 and other binding kinetics studies with surface bound PNA/DNA probes, 43,44 with a steadier increase and close to faster saturation at higher concentrations. At elevated concentrations, we anticipate more targets are available for binding, potentially leading to higher signals.…”

Amplification-free electrochemical biosensor detection of circulating microRNA to identify drug-induced liver injury

“…Although, the kinetics curves (Figure 3A) indicate signal saturation for 10 nM or at higher concentrations with a faster saturation with the increasing concentrations. Previous studies on binding kinetics of surface bound PNA/DNA probes with their complementary targets also showed target concentration dependent hybridisation signals with a faster saturation with the increasing concentrations (Jensen et al 1997;Munir et al 2017). Our observation suggests that all the available probe binding sites on the electrode surface were saturated with ≥ 10 nM concentrations within 60 min in the closed-loop continuous flow measurements.…”

Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review

“…Tremendous amount of work has been published regarding the use of conventional hybridization array technology in the field of antimicrobial resistance [26,27,28,29]. The major advantage of microarray technology over HT-qPCR is the number of ARGs (~1000′s) which can be profiled in one run.…”