Munir Ahsan, Waseem Hassan, Williams Maggie R, Stedtfeld Robert D, Gulari Erdogan, Tiedje James M, Hashsham Syed A
Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48823,USA.
Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
Microarrays (Basel). 2017 May 29;6(2):9. doi: 10.3390/microarrays6020009.
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).
能够检测特定DNA序列的微流控DNA生物芯片在医学诊断、药物研发、食品安全监测和农业领域都很有用。它们被用作基于核酸的生物标志物分析的小型化平台。固定在表面的单链DNA与其样品中存在的互补链之间的结合动力学备受关注。为了以最小的样本量和快速杂交实现最佳灵敏度，基于探针的热力学特性预测杂交动力学的能力至关重要。在本研究中，使用有限元技术打包软件工具（FEMLAB；COMSOL Multiphysics中包含的软件包）开发了一种用于设计和优化流通式生物芯片的计算机辅助数值模型，以模拟DNA通过微流控腔室传输到反应表面的过程。该模型考虑了通道和反应表面中的流体流动、对流和扩散。浓度、缔合速率常数、解离速率常数、再循环流速和温度是影响杂交速率的关键参数。该模型预测了针对万古霉素抗性基因（VRGs）的18个20聚体探针的动力学曲线和信号强度。预测的信号强度和杂交动力学与生物芯片中的实验数据高度相关（R² = 0.8131）。
