Design and Microfabrication of a High Throughput Thermal Cycling Platform with Various Annealing Temperatures
This study describes a micro device integrated with
multi-chamber for polymerase chain reaction (PCR) with different
annealing temperatures. The device consists of the reaction
polydimethylsiloxane (PDMS) chip, a cover glass chip, and is
equipped with cartridge heaters, fans, and thermocouples for
temperature control. In this prototype, commercial software is utilized
to determine the geometric and operational parameters those are
responsible for creating the denaturation, annealing, and extension
temperatures within the chip. Two cartridge heaters are placed at two
sides of the chip and maintained at two different temperatures to
achieve a thermal gradient on the chip during the annealing step. The
temperatures on the chip surface are measured via an infrared imager.
Some thermocouples inserted into the reaction chambers are used to
obtain the transient temperature profiles of the reaction chambers
during several thermal cycles. The experimental temperatures
compared to the simulated results show a similar trend. This work
should be interesting to persons involved in the high-temperature
based reactions and genomics or cell analysis.
[1] R. K. Saiki, S. Scharf, F. Faloona, K.B. Mullis, G. T. Horn, H. A. Erlich,
and N. Arnheim, "Enzymatic amplification of beta-globin genomic
sequences and restriction site analysis for diagnosis of sickle cell anemia,"
Science, vol. 230, pp. 1950-1954, 1985.
[2] M. A. Northrup, M. T. Ching, R. M. White, and R. T. Wltson, "DNA
amplification in a microfabricated reaction chamber," in Proceeding of
the 7th international conference of solid state sensors and actuators, pp
924-926, 1993.
[3] Q. Xiang, B. Xu, R. Fu, and D. Li, "Real time PCR on disposable PDMS
chip with a miniaturized thermal cycler," Biomed. Microdevices, vol. 7,
pp. 273-279, 2005.
[4] T. Ohashi, H. Kuyama, N. Hanafusa, and Y. Togawa, "A simple device
using magnetic transportation for droplet-based PCR," Biomed.
Microdevices, vol. 9, pp. 695-702, 2007.
[5] Y. Sun, N. T. Nguyen, and Y. C. Kwok, "High-throughput polymerase
chain reaction in parallel circular loops using magnetic actuation," Anal.
Chem., vol. 80, pp. 6127-6130, 2008.
[6] N. Ramalingam, Z. Rui, H. B. Liu, C. C. Dai, R. Kaushik, B. Ratnaharika,
and H. Q. Gong, "Real-time PCR-based microfluidic array chip for
simultaneous detection of multiple waterborne pathogens," Sensor.
Actuat. B-Chem., vol. 145, pp. 543-552, 2010.
[7] C. Zhang, and D. Xing, "Microfluidic gradient PCR (MG-PCR): a new
method for microfluidic DNA amplification," Biomed. Microdevices, vol.
12, pp. 1-12, 2010.
[8] E. Wulff-Burchfield, W. A. Schell, A. E. Eckhardt, M. G. Pollack, Z. Hua,
J. L. Rouse, V. K. Pamula, V. Srinivasan, J. L. Benton, B. D. Alexander, D.
A. Wilfret, M. Kraft, C. B. Cairns, J. R. Perfect, and T. G. Mitchell,
"Microfluidic platform versus conventional real-time polymerase chain
reaction for the detection of Mycoplasma pneumoniae in respiratory
specimens," Diag. Micr. Infec. Dis., vol. 67, pp. 22-29, 2010.
[9] D. Sugumar, L. X. Kong, A. Ismail, M. Ravichandran, and L. S. Yin,
"Rapid multi sample DNA amplification using rotary-linear polymerase
chain reaction device (PCRDisc)," Biomicrofluidics, vol. 6, 014119,
2012.
[10] D. Liu, G. Liang, X. Lei, B. Chen, W. Wang, and X. Zhou, "Highly
efficient capillary polymerase chain reaction using an oscillation droplet
microreactor," Anal. Chim. Acta, vol. 718, pp. 58-63, 2012.
[11] J. P. Holman, Heat Transfer, 10th ed. McGraw-Hill, New York, 2009.
[12] T. J. Barth, and D. C. Jespersen, "The design and application of upwind
schemes on unstructured meshes," in 27th Aerospace Sciences Meeting
and Exhibit, AIAA-89-0366, 1989.
[13] L. H. Howell, R. B. Pember, P. Colella, J. P. Jessee, and W. A. Fiveland,
"A conservative adaptive-mesh algorithm for unsteady, combined-mode
heat transfer using the discrete ordinates method," Numer. Heat Tr.
B-Fund., vol. 35, pp. 407-430, 1999.
[14] J. J. Chen, C. H. Chen, and S. R. Shie, "Optimal designs of staggered
Dean vortex micromixers," Int. J. Mol. Sci., vol. 12, pp. 3500-3524, 2011.
[1] R. K. Saiki, S. Scharf, F. Faloona, K.B. Mullis, G. T. Horn, H. A. Erlich,
and N. Arnheim, "Enzymatic amplification of beta-globin genomic
sequences and restriction site analysis for diagnosis of sickle cell anemia,"
Science, vol. 230, pp. 1950-1954, 1985.
[2] M. A. Northrup, M. T. Ching, R. M. White, and R. T. Wltson, "DNA
amplification in a microfabricated reaction chamber," in Proceeding of
the 7th international conference of solid state sensors and actuators, pp
924-926, 1993.
[3] Q. Xiang, B. Xu, R. Fu, and D. Li, "Real time PCR on disposable PDMS
chip with a miniaturized thermal cycler," Biomed. Microdevices, vol. 7,
pp. 273-279, 2005.
[4] T. Ohashi, H. Kuyama, N. Hanafusa, and Y. Togawa, "A simple device
using magnetic transportation for droplet-based PCR," Biomed.
Microdevices, vol. 9, pp. 695-702, 2007.
[5] Y. Sun, N. T. Nguyen, and Y. C. Kwok, "High-throughput polymerase
chain reaction in parallel circular loops using magnetic actuation," Anal.
Chem., vol. 80, pp. 6127-6130, 2008.
[6] N. Ramalingam, Z. Rui, H. B. Liu, C. C. Dai, R. Kaushik, B. Ratnaharika,
and H. Q. Gong, "Real-time PCR-based microfluidic array chip for
simultaneous detection of multiple waterborne pathogens," Sensor.
Actuat. B-Chem., vol. 145, pp. 543-552, 2010.
[7] C. Zhang, and D. Xing, "Microfluidic gradient PCR (MG-PCR): a new
method for microfluidic DNA amplification," Biomed. Microdevices, vol.
12, pp. 1-12, 2010.
[8] E. Wulff-Burchfield, W. A. Schell, A. E. Eckhardt, M. G. Pollack, Z. Hua,
J. L. Rouse, V. K. Pamula, V. Srinivasan, J. L. Benton, B. D. Alexander, D.
A. Wilfret, M. Kraft, C. B. Cairns, J. R. Perfect, and T. G. Mitchell,
"Microfluidic platform versus conventional real-time polymerase chain
reaction for the detection of Mycoplasma pneumoniae in respiratory
specimens," Diag. Micr. Infec. Dis., vol. 67, pp. 22-29, 2010.
[9] D. Sugumar, L. X. Kong, A. Ismail, M. Ravichandran, and L. S. Yin,
"Rapid multi sample DNA amplification using rotary-linear polymerase
chain reaction device (PCRDisc)," Biomicrofluidics, vol. 6, 014119,
2012.
[10] D. Liu, G. Liang, X. Lei, B. Chen, W. Wang, and X. Zhou, "Highly
efficient capillary polymerase chain reaction using an oscillation droplet
microreactor," Anal. Chim. Acta, vol. 718, pp. 58-63, 2012.
[11] J. P. Holman, Heat Transfer, 10th ed. McGraw-Hill, New York, 2009.
[12] T. J. Barth, and D. C. Jespersen, "The design and application of upwind
schemes on unstructured meshes," in 27th Aerospace Sciences Meeting
and Exhibit, AIAA-89-0366, 1989.
[13] L. H. Howell, R. B. Pember, P. Colella, J. P. Jessee, and W. A. Fiveland,
"A conservative adaptive-mesh algorithm for unsteady, combined-mode
heat transfer using the discrete ordinates method," Numer. Heat Tr.
B-Fund., vol. 35, pp. 407-430, 1999.
[14] J. J. Chen, C. H. Chen, and S. R. Shie, "Optimal designs of staggered
Dean vortex micromixers," Int. J. Mol. Sci., vol. 12, pp. 3500-3524, 2011.
@article{"International Journal of Mechanical, Industrial and Aerospace Sciences:60635", author = "Sin J. Chen and Jyh J. Chen", title = "Design and Microfabrication of a High Throughput Thermal Cycling Platform with Various Annealing Temperatures", abstract = "This study describes a micro device integrated with
multi-chamber for polymerase chain reaction (PCR) with different
annealing temperatures. The device consists of the reaction
polydimethylsiloxane (PDMS) chip, a cover glass chip, and is
equipped with cartridge heaters, fans, and thermocouples for
temperature control. In this prototype, commercial software is utilized
to determine the geometric and operational parameters those are
responsible for creating the denaturation, annealing, and extension
temperatures within the chip. Two cartridge heaters are placed at two
sides of the chip and maintained at two different temperatures to
achieve a thermal gradient on the chip during the annealing step. The
temperatures on the chip surface are measured via an infrared imager.
Some thermocouples inserted into the reaction chambers are used to
obtain the transient temperature profiles of the reaction chambers
during several thermal cycles. The experimental temperatures
compared to the simulated results show a similar trend. This work
should be interesting to persons involved in the high-temperature
based reactions and genomics or cell analysis.", keywords = "Polymerase chain reaction, thermal cycles,
temperature gradient, micro-fabrication.", volume = "7", number = "3", pages = "433-9", }