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Nucleic Acids Research 2005 33(8):e78; doi:10.1093/nar/gni078
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Published online 12 May 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Methods Online

Using a microfluidic device for 1 µl DNA microarray hybridization in 500 s

Cheng-Wey Wei1,2, Ji-Yen Cheng1,*, Chih-Ting Huang1, Meng-Hua Yen1,2 and Tai-Horng Young2

1Research Center for Applied Sciences, Academia Sinica Taipei 11529, Taiwan 2Institute of Biomedical Engineering, National Taiwan University Taipei 10051, Taiwan

*To whom correspondence should be addressed at 128 Sec. 2 Academia Road, Taipei 11529, Taiwan. Tel: +886 2 2789 8000; Fax: +886 2 2782 6680; Email: jycheng{at}gate.sinica.edu.tw

Received December 17, 2004. Revised March 25, 2005. Accepted April 20, 2005.

This work describes a novel and simple modification of the current microarray format. It reduces the sample/reagent volume to 1 µl and the hybridization time to 500 s. Both 20mer and 80mer oligonucleotide probes and singly labeled 20mer and 80mer targets, representative of the T-cell acute lymphocytic leukemia 1 (TAL1) gene, have been used to elucidate the performance of this hybridization approach. In this format, called shuttle hybridization, a conventional flat glass DNA microarray is integrated with a PMMA microfluidic chip to reduce the sample and reagent consumption to 1/100 of that associated with the conventional format. A serpentine microtrench is designed and fabricated on a PMMA chip using a widely available CO2 laser scriber. The trench spacing is compatible with the inter-spot distance in standard microarrays. The microtrench chip and microarray chip are easily aligned and assembled manually so that the microarray is integrated with a microfluidic channel. Discrete sample plugs are employed in the microchannel for hybridization. Flowing through the microchannel with alternating depths and widths scrambles continuous sample plug into discrete short plugs. These plugs are shuttled back and forth along the channel, sweeping over microarray probes while re-circulation mixing occurs inside the plugs. Integrating the microarrays into the microfluidic channel reduces the DNA–DNA hybridization time from 18 h to 500 s. Additionally, the enhancement of DNA hybridization reaction by the microfluidic device is investigated by determining the coefficient of variation (CV), the growth rate of the hybridization signal and the ability to discriminate single-base mismatch. Detection limit of 19 amol was obtained for shuttle hybridization. A 1 µl target was used to hybridize with an array that can hold 5000 probes.


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