Abstract
Due to the progress of Human Genome Project, microfluidic microarray has become an effective tool for genomic analysis applications such as gene expression profiling in recent years. In this setting, each single strand oligonucleotide (oDNA) that serves as a probe attached on the microarray surface can bind with its genomic counterpart with specific designed sequences in solution phase. The binding mechanism between single strand DNA probe and its target known as DNA hybridization reaction usually takes from 6 to 24 hours depending upon the testing biological samples of interest as well as the experimental conditions. In addition, hybridization efficiency is linked to binding energy barrier that is hindered by the sequence affinity. Hence, overcoming the duration and efficiency issues of DNA hybridization presents a great challenge to microarray experiments. In this study, a computational model which consists of an inlet channel, outlet channel and single reaction cell is constructed to characterize the effects of vital experimental parameters such as infusion sample flow rate, sample size and reaction kinetic constants on the efficiency and duration of oDNA hybridization. Simulation results reveal that higher infusion flow rate as well as smaller sample fragment can accelerate the hybridization process. And the reaction kinetic constants determine the binding affinity under the equilibrium condition.
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© 2007 International Federation for Medical and Biological Engineering
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Kan, HC. (2007). Numerical Analysis of Deoxynucleotide Hybridization Characteristics using Single Reaction Cell Model. In: Magjarevic, R., Nagel, J.H. (eds) World Congress on Medical Physics and Biomedical Engineering 2006. IFMBE Proceedings, vol 14. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-36841-0_81
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DOI: https://doi.org/10.1007/978-3-540-36841-0_81
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-36839-7
Online ISBN: 978-3-540-36841-0
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