Miniaturized devices for DNA amplification and fluorescence based detection

Journal of the Indian Institute of Science

Volumn 87, Issue 3, 2007, Pages 309-332

  Mondai, Sudip ^a   Venkataraman, V ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCOMPATIBILITY; BIOMOLECULES; DNA SEQUENCES; FLUORESCENCE; MEMS; PATHOGENS;

DNA AMPLIFICATION; MINIATURIZED CHIPS; MINIATURIZED DEVICES;

MINIATURE INSTRUMENTS;

EID: 36949004322     PISSN: 09704140     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (107)

1. L.J. Kricka and P. Wilding. Microchip PCR. Anal. Bioanal. Chem., 377: 820-825, 2003.
2. E.T. Lagally, J.R. Scherer, R.G. Blazej, N.M. Toriello, B.A. Diep, M. Ramchandrani, G.F. Sensabaugh, L.W. Riley, and R.A. Mathies. Integrated portable genetic analysis microsystem for pathogen/infectious disease detection. Anal. Chem., 76, 3162-3170, 2004.
3. P.A. Auroux, Y. Koc, A. deMello, A. Manz, and P.J.R. Day. Miniaturised nucleic acid analysis. Lab Chip, 4, 534-546, 2004.
4. C. Zhang, J. Xu, W. Ma, and W. Zheng. PCR microfluidic devices for DNA amplification. Biotechnol. Adv., 24, 243-284, 2006.
5. K.B. Mullis. The unusual origin of the polymerase chain reaction. Sci. Am., 262, 36-43, 1990.
6. R.K. Saiki, S. Scharf, F. Faloona, K.B. Mullis, G.T. Horn, H.A. Erlich, and N. Arnheim. Enzymatic amplification of β-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science, 230, 1350-1354, 1985.
7. C.T. Wittwer, G.C. Fillmore, and D.J. Garling. Minimizing the time required for DNA amplification by efficient heat transfer to small samples. Anal. Biochem., 186, 328-331, 1990.
8. M.A. Northrup, M.T. Ching, R.M. White, and R.T. Watson. DNA amplification with a microfabricated reaction chamber. In Transducers'93, seventh international conference on solid state Sens Actuators, Yokohama, Japan, pages 924-926, 1993.
9. P. Neuzil, J. Pipper, and T.M. Hsieh. Disposable real-time microPCR device: lab-on-a-chip at a low cost. Mol. Biosyst., 2, 292-298, 2006.
10. A.T. Woolley, D. Hadley, P. Landre, A.J. deMellow, R.A. Mathies, and M.A. Northrup. Functional integration of PCR amplification and capillary electrophoresis in a microfabricated DNA analysis device. Anal. Chem., 68, 4081-4086, 1996.
11. J.H. Daniel, S. Iqbal, R.B. Millington, D.F. Moore, C.R. Lowe, D.L. Leslie, M.A. Lee, and M.J. Pearce. Silicon microchambers for DNA amplification. Sens. Actuators A, 71, 81-88, 1998.
12. Y.C. Lin, C.C. Yang, and M.Y. Huang. Simulation and experimental validation of micro polymerase chain reaction chips. Sens. Actuators B, 71, 127-133, 2000.
13. D.S. Yoon, Y.S. Lee, Y. Lee, H.J. Cho, S.W. Sung, K.W. Oh, J. Cha, and G. Lim. Precise temperature control and rapid thermal cycling in a micromachined DNA polymerase chain reaction chip. J. Micromech. Microeng., 12, 813-823, 2002.
14. Q. Zou, Y. Miao, Y. Chen, U. Sridhar, C.S. Chong, T. Chai, Y. Tie, C.H.X. Teh, T.M. Lim, and C.K. Heng. Microassembled multi-chamber thermal cycler for low-cost reaction chip thermal multiplexing. Sens. Actuators A, 102, 114-121, 2002.
15. Y.S. Shin, K. Cho, S.H. Lim, S. Chung, S.J. Park, C. Chung, D.C. Han, and J.K. Chang. PDMS-based micro PCR chip with Parylene coating. J. Micromech. Microeng., 13, 768-774, 2003.
16. J.E. Ali, I.R.P. Nielsen, C.R. Poulsen, D.D. Bang, P.Telleman, and A. Wolff. Simulation and experimental validation of a SU-8 based PCR thermocycler chip with integrated heaters and temperature sensor. Sens. Actuators A, 110, 3-10, 2004.
17. Z.Q. Zou, X. Chen, Q.H. Jin, M.S. Yang, and J.X. Zhao. A novel miniaturized PCR multi-reactor array fabricated using flip-chip bonding techniques. J. Micromech. Microeng., 15, 1476-1481, 2005.
18. C. Ke, A.M. Kelleher, H. Berney, M. Sheehan, and A. Mathewson. Single step cell lysis/PCR detection of Escherichia coli in an independently controllable silicon microreactor. Sens. Actuators B, 120, 538-544, 2007.
19. Y.K. Cho, J. Kim, Y. Lee, Y.A. Kim, K. Namkoong, H. Lim, K.W. Oh, S. Kim, J. Han, C. Park, Y.E. Pak, C.S. Ki, J.R. Choi, H.K. Myeong, and C. Ko. Clinical evaluation of micro-scale chip-based PCR system for rapid detection of hepatitis B virus. Biosens. Bioelectron., 21, 2161-2169, 2006.
20. Z.Q. Niu, W.Y. Chen, S.Y. Shao, X.Y. Jia, and W.P. Zhang. DNA amplification on a PDMS-glass hybrid microchip. J. Micromech. Microeng., 16, 425-433, 2006.
21. J. Xiaoyu, N. Zhiqiang, C. Wenyuan, and Z. Weiping. Polydimethylsiloxane (PDMS)-based spiral channel PCR chip. Electron. Lett., 41:no. 16, 2005.
22. M.U. Kopp, A.J. deMello, and A. Manz. Chemical amplification: continuous-flow PCR on a chip. Science, 280, 1046-1048, 1998.
23. Y. Zhang, D.J. Isaacman, R.M. Wadowsky, J.R. White, J.C. Post, and G.D. Ehrlich. Detection of Streptococcus pneumoniae in whole blood by PCR. J. Clin. Microbiol., 33, 596-601, 1995.
24. R. Higuchi, C.H.V. Beroldingen, G.F. Sensabaugh, and H.A. Erlich. DNA typing from single hairs. Nature, 332, 543-546, 1988.
25. S.A. Ansari, S.R. Farrah, and G.R. Chaudhry. Presence of human immunodeficiency virus nucleic acids in wastewater and their detection by polymerase chain reaction. Appl. Environ. Microbiol., 58, 3984-3990, 1992.
26. S.Y. Lee, J. Bollinger, D. Bezdicek, and A. Ogram. Estimation of the abundance of an uncultured soil bacterial strain by a competitive quantitative PCR method. Appl Environ. Microbiol., 62, 3787-3793, 1996.
27. C.T. Wittwer, G.C. Fillmore, and D.R. Hillyard. Automated polymerase chain reaction in capillary tubes with hot air. Nucleic Acids Res., 17, 4353-4357, 1989.
28. A.F.R. Hühmer and J.P. Landers. Noncontact infraredmediated thermocycling for effective polymerase chain reaction amplification of DNA in nanoliter volumes. Anal. Chem., 72, 5507-5512, 2000.
29. B.C. Giordano, J. Ferrance, S. Swedberg, A.F.R. Hühmer, and J.P. Landers. Polymerase chain reaction in polymeric microchips: DNA amplification in less than 240 seconds. Anal. Biochem., 291, 124-132, 2001.
30. J. Liu, M. Enzelberger, and S. Quake. A nanoliter rotary device for polymerase chain reaction. Electrophoresis, 23, 1531-1536, 2002.
31. N.J. Panaro, X.J. Lou, P. Fortina, L.J. Kricka, and P. Wilding. Surface effects on PCR reactions in multichip microfluidic platforms. Biomed. Microdevices, 6, 75-80, 2004.
32. M.J. Madou. Fundamentals of microfabrication. CRC Press, 1997.
33. J.E. Mark. Polymer data handbook. Oxford Univ. Press, 1999.
34. M.A. Shoffner, J. Cheng, G.E. Hvichia, L.J. Kricka, and P. Wilding. Chip PCR.I. Surface passivation of microfabricated silicon-glass chips for PCR. Nucleic Acids Res., 24, 375-379, 1996.
35. R.P. Oda, M.A. Strausbauch, A.F.R. Hühmer, N. Borson, S.R. Jurrens, J. Craighead, P.J. Wettstein, B. Eckloff, B. Kline, and J.P. Landers. Infrared-mediated thermocycling for ultrafast polymerase chain reaction amplification of DNA. Anal. Chem., 70, 4361-4368, 1998.
36. I. Erill, S. Campoy, J. Rus, L. Fonseca, A. Ivorra, Z. Navarro, J.A. Plaza, J. Aguiló, and J. Barbé. Development of a CMOScompatible PCR chip: comparison of design and system strategies. J. Micromech. Microeng., 14, 1558-1568, 2004.
37. R.C. Anderson, X. Su, G.J. Bogdan, and J. Fenton. A miniature integrated device for automated multistep genetic assays. Nucleic Acids Res., 28:e60, 2000.
38. I. Schneegaß, R. Bräutigam, and J.M. Köhler. Miniaturized flow-through PCR with different template types in a silicon chip thermocyder. Lab Chip, 1, 42-49, 2001.
39. T.B. Taylor, E.S.W. Deen, E. Picozza, T.M. Woudenberg, and M. Albin. Optimization of the performance of the polymerase chain reaction in silicon-based microstructures. Nucleic Acids Res., 25, 3164-3168, 1997.
40. I. Erill, S. Campoy, N. Erill, J. Barbé, and J. Aguiló. Biochemical analysis and optimization of inhibition and adsorption phenomena in glass-silicon PCR-chips. Sens. Actuators B, 96, 685-692, 2003.
41. D.B. Lee. Anisotropic etching of silicon. J. Appl. Phys., 40, 4569-4574, 1969.
42. K.E. Bean. Anisotropic etching of silicon. IEEE Trans. Electron. Devices, ED-25, 1185-1193, 1978.
43. Y. Xia and G. M. Whitesides. Soft lithography. Annu. Rev. Mater. Sci., 28, 153-184, 1998.
44. J.C. McDonald, D.C. Duffy, J.R. Anderson, D.T. Chiu, H. Wu, O.J.A. Schueller, and G.M. Whitesides. Fabrication of microfluidic systems in poly(dimethylsiloxane). Electrophoresis, 21, 27-40, 2000.
45. J.C. McDonald and G.M. Whitesides. Poly(dimethylsiloxane) as a material for fabricating microfluidic devices. Acc. Chem. Res., 35, 491-499, 2002.
46. G.S. Fiorini and D.T. Chiu. Disposable microfluidic devices: fabrication, function, and application. BioTechniques, 38, 429-446, 2005.
47. C. Yamahata, F. Lacharme, and M.A.M. Gijs. Glass valveless micropump using electromagnetic actuation. Microelectron. Eng., 78-79, 132-137, 2005.
48. C.W. Li, C.N. Cheung, J. Yang, C.H. Tzang, and M. Yang. PDMS-based microfluidic device with multi-height structures fabricated by single-step photolithography using printed circuit board as masters. Analyst, 128, 1137-1142, 2003.
49. A.P. Sudarsan and V.M. Ugaz. Printed circuit technology for fabrication of plastic-based microfluidic devices. Anal. Chem., 76, 3229-3235, 2004.
50. D.C. Duffy, J.C. McDonald, O.J.A. Schueller, and G.M. Whitesides. Rapid prototyping of microfluidic systems in poly(dimethylsiloxane). Anal. Chem., 70, 4974-4984, 1998.
51. Q. Xiang, B. Xu, R. Fu, and D. Li. Real time PCR on disposable PDMS chip with a miniaturized thermal cycler. Biomed. Microdevices, 7, 273-279, 2005.
52. S. Li and S. Chen. Polydimethylsioxane fluidic interconnects for microfluidic systems. IEEE Trans. Adv. Pack., 26, 242-247, 2003.
53. M.A. Unger, H.P. Chou, T. Thorsen, A. Scherer, and S.R. Quake. Monolithic microfabricated valves and pumps by multilayer soft lithography. Science, 288, 113-116, 2000.
54. J.R. Anderson, D.T. Chiu, R.J. Jackman, O. Cherniavskaya, J.C. McDonald, H. Wu, S.H. Whitesides, and G.M. Whitesides. Fabrication of topologically complex three-dimensional microfluidic systems in PDMS by rapid prototyping. Anal. Chem., 72, 3158-3164, 2000.
55. S. Poser, T. Schulz, U. Dillner, V. Baier, J.M. Köhler, D. Schimkat, G. Mayer, and A. Siebert. Chip elements for fast thermocycling. Sens. Actuators A, 62, 672-675, 1997.
56. Z. Zhao, Z. Cui, D. Cui, and S. Xia. Monolithically integrated PCR biochip for DNA amplification. Sens. Actuators A, 108, 162-167, 2003.
57. K. Sun, A. Yamaguchi, Y. Ishida, S. Matsuo, and H. Misawa. A heater-integrated transparent microchannel chip for continuous-flow PCR. Sens. Actuators B, 84, 283-289, 2002.
58. Y.C. Lin, M.Y. Huang, K.C. Young, T.T. Chang, and C.Y. Wu. A rapid micro-polymerase chain reaction system for hepatitis C virus amplification. Sens. Actuators B, 71, 2-8, 2000.
59. J. Khandurina, T.E. McKnight, S.C. Jacobson, L.C. Waters, R.S. Foote, and J.M. Ramsey. Integrated system for rapid PCR-based DNA analysis in microfluidic devices. Anal. Chem., 72, 2995-3000, 2000.
60. M. Krishnan, V.M. Ugaz, and M.A. Burns. PCR in a RayleighBérnard convection cell. Science, 298, 793, 2002.
61. D. Braun, N.L. Goddard, and A. Libchaber. Exponential DNA replication by laminar convection. Phys. Rev. Lett., 91, 158103, 2003.
62. D.M. Heap, M.G. Herrmann, and C.T. Wittwer. PCR amplification using electrolytic resistance for heating and temperature monitoring. BioTechniques, 29, 1006-1012, 2000.
63. D.S. Lee, M.H. Wu, U. Ramesh, C.W. Lin, T.M. Lee, and P.H. Chen. A novel real-time PCR machine with a miniature spectrometer for fluorescence sensing in a micro liter volume glass capillary. Sens. Actuators B, 100, 401-410, 2004.
64. Y. Tanaka, M.N. Slyadnev, A. Hibara, M. Tokeshi, and T. Kitamori. Non-contact photothermal control of enzyme reactions on a microchip by using a compact diode laser. J. Chromatogr. A, 894, 45-51, 2000.
65. M.N. Slyadnev, Y. Tanaka, M. Tokeshi, and T. Kitamori. Photothermal temperature control of a chemical reaction on a microchip using an infrared diode laser. Anal. Chem., 73, 4037-4044, 2001.
66. D. Pal and V. Venkataraman. A portable battery-operated chip thermocyder based on induction heating. Sens. Actuators A, 102,151-156,2002.
67. C.R. Smith, D.R. Sabatino, and T.J. Praisner. Temperature sensing with thermochromic liquid crystals. Exp. Fluids, 30, 190-201, 2001.
68. J. Noh, S.W. Sung, M.K. Jeon, S.H. Kim, L.P. Lee, and S.I. Woo. In situ thermal diagnostics of the micro-PCR system using liquid crystals. Sens. Actuators A, 122, 196-202, 2005.
69. A.M. Chaudhari, T.M. Woudenberg, M. Albin, and K.E. Goodson. Transient liquid crystal thermometry of microfabricated PCR vessel arrays. J. Microelectromech. Syst., 7, 345-355, 1998.
70. D. Ross, M. Gaitan, and L.E. Locascio. Temperature measurement in microfluidic systems using a temperaturedependent fluorescent dye. Anal. Chem., 73, 4117-4123, 2001.
71. S. Mondal and V. Venkataraman. Novel fluorescence detection technique for non-contact temperature sensing in microchip PCR. J. Biochem. Biophys. Methods, 70, 773-777, 2007.
72. K.L. Davis, K.L.K. Liu, M. Lanan, and M.D. Morris. Spatially resolved temperature measurements in electrophoresis capillaries by Raman thermometry. Anal. Chem., 65, 293-298, 1993.
73. S.H. Kim, J. Noh, M.K. Jeon, K.W. Kim, L.P. Lee, and S.I. Woo. Micro-Raman thermometry for measuring the temperature distribution inside the microchannel of a polymerase chain reaction chip. J. Micromech. Microeng., 16, 526-530, 2006.
74. M.E. Lacey, A.G. Webb, and J.V. Sweedler. Monitoring temperature changes in capillary electrophoresis with nanoliter-volume NMR thermometry. Anal. Chem., 72, 4991-4998, 2000.
75. S. Jeon, J. Turner, and S. Granick. Noncontact temperature measurement in microliter-sized volumes using fluorescentlabeled DNA oligomers. J. Am. Chem. Soc., 125, 9908-9909, 2003.
76. H. Zipper, H. Brunner, J. Bernhagen, and F. Vitzthum. Investigations on DNA intercalation and surface binding by SYBR green I, its structure determination and methodological implications. Nucleic Acids Res., 32:e103, 2004.
77. R. Higuchi, G. Dollinger, P.S. Walsh, and R. Griffith. Simultaneous amplification and detection of specific DNA sequences. Bio/Technology, 10, 413-417, 1992.
78. R. Higuchi, C. Fodder, G. Dollinger, and R. Watson. Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Bio/technology, 11, 1026-1030, 1993.
79. W. Liu and D.A. Saint. Validation of a quantitative method for real time PCR kinetics. Biochem. Biophys. Res. Commun., 294, 347-353, 2002.
80. B. Arezi, W. Xing, J.A. Sorge, and H.H. Hogrefe. Amplification efficiency of thermostable DNA polymerases. Anal. Biochem., 321, 226-235, 2003.
81. C.T. Wittwer, M.G. Herrmann, A.A. Moss, and R.P. Rasmussen. Continuous fluorescence monitoring of rapid cyde DNA amplification. BioTechniques, 22, 130-138, 1997.
82. C.T. Wittwer, K.M. Ririe, R.V. Andrew, D.A. David, R.A. Gundry, and U.J. Balis. The lightcyder: a microvolume multisample fluorimeter with rapid temperature control. BioTechniques, 22, 176-181, 1997.
83. T.B. Morrison, J.J. Weis, and C.T. Wittwer. Quantification of low-copy transcripts by continuous SYBR green I monitoring during amplification. BioTechniques, 24, 954-962, 1998.
84. P. Belgrader, S. Young, B. Yuan, M. Primeau, L.A. Christel, F. Pourahmadi, and M.A. Northrup. A battery-powered notebook thermal cycler for rapid multiplex real-time PCR analysis. Anal. Chem, 73, 286-289, 2001.
85. Y.C. Lin, M. Li, M.T. Chung, C.Y. Wu, and K.C. Young. Realtime microchip polymerase-chain-reaction system. Sens. Mater., 14, 199-208, 2002.
86. A. Gulliksen, L. Solu, F. Karlsen, H. Rogne, E. Hovig, T. Nordstrøm, and R. Sirevȧg. Real-time nucleic acid sequence-based amphfication in nanoliter volumes. Anal. Chem., 76, 9-14, 2004.
87. L. Novak, P. Neuzil, J. Pipper, Y. Zhang, and S. Lee. An integrated fluorescence detection system for lab-on-a-chip applications. Lab Chip, 7, 27-29, 2007.
88. J.R. Webster, M.A. Burns, D.T. Burke, and C.H. Mastrangelo. Monolithic capillary electrophoresis device with integrated fluorescence detector. Anal. Chem., 73, 1622-1626, 2001.
89. J.A. Higgins, S. Nasarabadi, J.S. Karns, D.R. Shelton, M. Cooper, A. Gbakima, and R.P. Koopman. A handheld real time thermal cycler for bacterial pathogen detection. Biosens. Bioelectron., 18, 1115-1123, 2003.
90. C.T. Wittwer and D.J. Garling. Rapid cycle DNA amplification: time and temperature optimization. BioTechniques, 10, 76-83, 1991.
91. T. Ederhof, N.G. Walter, and A. Schober. On-line polymerase chain reaction (PCR) monitoring. J. Biochem. Biophys. Methods, 37, 99-104, 1998.
92. S. Mondal and V. Venkataraman. In situ monitoring of polymerase extension rate and adaptive feedback control of PCR by using fluorescence measurements. J. Biochem. Biophys. Methods, 65, 97-105, 2005.
93. N.C. Cady, S. Stelick, M.V. Kunnavakkam, and C.A. Batt. Real-time PCR detection of Listeria monocytogenes using an integrated microfluidics platform. Sens. Actuators B, 107, 332-341, 2005.
94. S. Mondal, D. Paul, and V. Venkataraman. Dynamic optimization of on-chip polymerase chain reaction by monitoring intracycle fluorescence using fast synchronous detection. Appl. Phys. Lett., 90, 013902, 2007.
95. K.M. Ririe, R.P. Rasmussen, and C.T. Wittwer. Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal. Biochem., 245, 154-160, 1997.
96. S. Giglio, P.T. Monis, and C.P. Saint. Demonstration of preferential binding of SYBR green I to specific DNA freagments in real-time multiplex PCR Nucleic Acids Res., 31:e136, 2003.
97. W. Li, B. Xi, W. Yang, M. Hawkins, and U.K. Schubart. Complex DNA melting profiles of small PCR products revealed using SYBR green I. BioTechniques, 35, 702-706, 2003.
98. A. Karsai, S. Müller, S. Platz, and M.T. Hauser. Evaluation of a home made SYBR green I reaction mixture for real-time PCR quantification of gene expression. BioTechniques, 32, 790-796, 2002.
99. B.C. Millar, X. Jiru, J.E. Moore, and J.A.P. Earle. A simple and sensitive method to extract bacterial, yeast and fungal DNA from blood culture material. J. Microbiol. Methods, 42, 139-147, 2000.
100. M.C. Breadmore, K.A. Wolfe, I.G. Arcibal, W.K. Leung, D. Dickson, B.C. Giordano, M.E. Power, J.P. Ferrance, S.H. Feldman, P.M. Norris, and J.P. Landers. Microchip-based purification of DNA from biological samples. Anal. Chem., 75, 1880-1886, 2003.
101. P. Wilding, L.J. Kricka, J. Cheng, G. Hvichia, M.A. Shoffner, and P. Fortina. Integrated cell isolation and polymerase chain reaction analysis using silicon microfilter chambers. Anal. Biochem., 257, 95-100, 1998.
102. P.K. Yuen, L.J. Kricka, P. Fortina, N.J. Panaro, T. Sakazume, and P. Wilding. Microchip module for blood sample preparation and nucleic acid amplification reactions. Genome Res., 11, 405-412, 2001.
103. N.C. Cady, S. Stelick, and C.A. Batt. Nucleic acid purification using microfabricated silicon structures. Biosens. Bioelectron., 19, 59-66, 2003.
104. N. Zhang, H. Tan, and E.S. Yeung. Automated and integrated system for high-throughput DNA genotyping directly from blood. Anal. Chem., 71, 1138-1145, 1999.
105. M. Hashimoto, Y. He, and E.S. Yeung. On-line integration of PCR and cycle sequencing in capillaries: from human genomic DNA directly to called bases. Nucleic Acids Res., 31:e41, 2003.
106. C.Y. Lee, G.B. Lee, J.X. Lin, F.C. Huang, and C.S. Liao. Integrated microfluidic systems for cell lysis, mixing/pumping and DNA amplification. J. Micromech. Microeng., 15, 1215-1223, 2005.
107. R.H. Liu, J. Yang, R. Lenigk, J. Bonanno, and P. Grodzinski. Self-contained, fully integrated biochip for sample preparation, polymerase chain reaction amplification, and DNA microarray detection. Anal. Chem., 76, 1824-1831, 2004.