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).
Highlights
Microfluidic biochips are widely used for high-throughput analysis of mutations, expression profiles, and in identification of microorganisms [1] and are based on highly selective solid-phase nucleic acid hybridization [2]
Flow rate is one of the key parameters that determines whether the kinetics of DNA hybridization hybridization in the microfluidic biochip is transport‐limited or reaction‐limited [31]
The developed three-dimensional mathematical model identified sample concentration, flow rate, binding constants, and temperature as crucial parameters affecting the rate of DNA hybridization for vancomycin resistance genes (VRGs)
Summary
Microfluidic biochips are widely used for high-throughput analysis of mutations, expression profiles, and in identification of microorganisms [1] and are based on highly selective solid-phase nucleic acid hybridization [2]. The biochip used was developed by Xeotron, owned by Invitrogen (Carlsbad, flow rate and rate constants on the hybridization kinetics, with target concentration, rate constants, and CA, USA) and has been previously described [13]. The20‐mer predictive capability andresistant performance of the kinetics of eighteen probes targeting vancomycin genes This gene was model and its chosen as a model because emergence of antibiotic resistance associated with pathogenic bacteriawere is potential for application in optimizing hybridization protocols and chip geometry considered an alarming global issue [14,15] and numerous hybridization‐based biochip platforms are being adequate with some exceptions. A three-dimensional mathematical model implemented to describe the hybridization of capability and performance of the model and its potential for application in optimizing hybridization a DNA target to a surface-immobilized probe in a glass wafer microfluidic biochip Both the association and dissociation events are modeled here using a differential kinetic equation
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