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Rapid DNA amplification in a capillary tube by natural convection with a single isothermal heater
 
Wen Pin Chou1, Ping Hei Chen1, Ming Miao2, Long Sheng Kuo1, Shiou Hwei Yeh3, and Pei Jer Chen4
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Supplementary Material





In recent years, a growing number of studies have focused on developing a fast and portable PCR platform for nucleic acid testing. However, thermocyclers based on thermal conductivity for their heating mechanism still require a delicate digital controller to rapidly heat and cool the sample. Natural convection, another mode of heat transfer, promotes spontaneous and repeated liquid circulation to provide working temperatures for denaturation, annealing and extension. Here, we have described CCPCR, a simple platform for DNA amplification in a capillary tube using natural convection. Our study indicates that such a simple amplification method does necessitate the redesign and optimization of both amplicons and primers (high-Tm primers and low-Td amplicons) for the best performance to make it equivalent to traditional PCR. Such optimization increases the relative temperature differences for Th–Td and Tm–Tl, thereby extending the space and time for effective denaturing/annealing/extension reactions.

One major concern is the possible effect of ambient temperature on CCPCR since the platform uses ambient temperature as the cooling mechanism. In our test, CCPCR was effective both at 4°C in a refrigerator and at 33°C in an incubator, although it failed when the ambient temperature was >38°C (Supplementary Figure S4). Thus, CCPCR is compatible with general indoor operations except in extremely hot locations.

Because of the simplicity of CCPCR, it offers operators great convenience without any complicated hardware settings. Furthermore, the dry bath in this platform can be replaced easily by any heating source as long as it can provide the required denaturation temperature at the bottom of capillary tubes—for example, a hot-water bath or the heating plate of a commercial portable scent-based mosquito repellent device. We found that such simple heating sources could amplify HBV DNA successfully in 30 min (Supplementary Figure S5). With its advantages of low cost and ease of operation, CCPCR would be well suited for less developed countries to improve surveillance systems for disease outbreaks. We also hope that CCPCR can make nucleic acid testing more accessible beyond laboratories by facilitating point-of-care applications.

Acknowledgments

We thank L.-M. Huang for providing HIV vector pNL4-3; I.-F. Shieh, H.-H. Chen and H.-H. S. for technical assistance. This work was supported by the Research Program of Department of health (DOH97-TD-I-111-TM008) and the NSC sponsored research grants (98-2622-E-002-031-CC2).

Competing interests

The authors declare no competing interests.

Correspondence
Address correspondence to Ping Hei Chen, Department of Mechanical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan, e-mail: [email protected] or Pei Jer Chen, Graduate Institute of Clinical Medicine, National Taiwan University, No.2, Syu-jhou Road, Taipei, 10055, Taiwan, e-mail: [email protected]

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