TRANSCRIPTOME 2002: From Functional Genomics to Systems Biology
March 10-13, 2002
Seattle, Washington, USA


Microarray Hybridization by Shear-Driven Flows, a New Approach to Enhance Both Sensitivity and Efficiency of Microarray Analysis

Paul Van Hummelen, Kris Pappaert, Johan Vanderhoeven, Danny Clicq, Gino V Baron and Gert Desmet, MicroArray Facility, Flanders Interuniversity Institute (VIB), Leuven, BELGIUM and Department of Chemical Engineering, Brussel, BELGIUM

Traditional diffusion driven hybridization takes at least 15 hours with an efficiency of less than 1%. Therefore, it is highly unlikely that labeled molecules from low expressed genes will reach the corresponding spot to hybridize. To elevate diffusion limitation we used Shear-Driven flows to generate a rapid lateral convective transport across the microarray surface and compared this to traditional overnight hybridizations. Shear-Driven flows relies on the dragging action exerted by a moving surface on an adjacent fluid layer and can transport extremely thin fluid layers at high velocities. We built two prototype modules, one excerting linear and one excerting rotating driving flows onto regular microarray slides. Hybridization tests were done with fluorescent cDNA pools, labeled by nick-translation. We could demonstrate that in 1 hour fluorescent intensities were achieved comparable to conventional overnight hybridization. Using the rotating module, the hybridization rate was increased by increasing the fluid velocity. However, using the linear module opposite observations were made. This unexpected result of the linear module may be caused by the striking lack of flatness of the microarray slides used. Future experiments will focus on studying hybridizations of low copy number genes, once a second generation shear-driven flow chambers is build.

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