Microfluidic DNA hybridization assays

Microfluidics and Nanofluidics

Volumn 11, Issue 4, 2011, Pages 367-383

  Weng, Xuan ^a   Jiang, Hai ^a   Li, Dongqing ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

Author keywords

Bead based; DNA hybridization assay; DNA microarray; Microfluidics; Point of care; Surface based

Indexed keywords

BEAD-BASED; DNA HYBRIDIZATION ASSAY; DNA MICROARRAY; POINT OF CARE; SURFACE-BASED;

ASSAYS; DNA;

MICROFLUIDICS;

EID: 84855961937     PISSN: 16134982     EISSN: 16134990     Source Type: Journal    
DOI: 10.1007/s10404-011-0858-6     Document Type: Review

References (95)

1. Ali MF, Kirby R, Goodey AP, Rodriguez MD, Ellington AD, Neikirk DP, McDevitt JT (2003) DNA hybridization and discrimination of single-nucleotide mismatches using chip-based microbead arrays. Anal Chem 75:4732-4739 (Pubitemid 37139772)
2. Benn JA, Hu J, Hogan BJ, Fry RC, Samson LD, Thorsen T (2006) Comparative modeling and analysis of microfluidic and conventional DNA microarrays. Anal Biochem 348:284-293 (Pubitemid 41832532)
3. Benoit V, Steel A, Torres M, Yu Y, Yang H, Cooper J (2001) Evaluation of three-dimensional microchannel glass biochips for multiplexed nucleic acid fluorescence hybridization assays. Anal Chem 73:2412-2420 (Pubitemid 32880638)
4. Berti F, Laschi S, Palchetti I, Rossier JS, Reymond F, Mascini M, Marrazza G (2009) Microfluidic-based electrochemical genosensor coupled to magnetic beads for hybridization detection. Talanta 77(3):971-978
5. Betanzos-Cabrera G, Harker BW, Doktycz MJ, Weber JL, Beattie KL (2008) A comparison of hybridization efficiency between flat glass and channel glass solid supports. Mol Biotechnol 38:71-80 (Pubitemid 351378098)
6. Blackburn CW (1993) Rapid and alternative methods for the detection of Salmonellas in foods. J Appl Bacteriol 75:199-214
7. Bottero MT, Dalmasso A, Soglia D, Rosati S, Decastelli L, Civera T (2004) Development of a multiplex PCR assay for the identification of pathogenic genes of Escherichia coli in milk and milk products. Mol Cell Probes 18:283-288 (Pubitemid 38951023)
8. Brennan D, Dillmore S, Moore E, Galvin P (2009) A rapid polymerisation process realizing 3D biocompatible structures in a microfluidic channel suitable for genetic analysis. Sens Actuators B Chem 142:383-388
9. Cano RJ, Torres MJ, Klem RE, Palomares JC, Casadesus J (1992) Detection of Salmonellas by DNA hybridization with a fluorescent alkaline phosphatase substrate. J Appl Bacteriol 72:393-399
10. Cao YC, Jin R, Mirkin CA (2002) Nanoparticles with raman spectroscopic fingerprints for DNA and RNA detection. Science 297:1536-1540 (Pubitemid 34970997)
11. Cao W, Su M, Zhang S (2010) Rapid and sensitive DNA target detection using enzyme amplified electrochemical detection based on microchip. Electrophoresis 31:659-665
12. Carlen ET, Weinberg MS, Dube CE, Zapata AM, Borenstein JT (2006) Micromachined silicon plates for sensing molecular interactions. Appl Phys Lett 89:173123
13. Cha M, Shin J, Kim J, Kim I, Choi J, Lee N, Kim B, Lee J (2008) Biomolecular detection with a thin membrane transducer. Lab Chip 8:932-937 (Pubitemid 351746710)
14. Chandler EL, Smith AL, Burden LM, Kasianowicz JJ, Burden DL (2004) Membrane surface dynamics of DNA-threaded nanopores revealed by simultaneous single-molecule optical and ensemble electrical recording. Langmuir 20:898-905
15. Chen L (2010) DNA hybridization on walls of electrokinetically controlled microfluidic channels. Dissertation, University of Toronto
16. Chen S, Yee A, Griffiths M, Larkin C, Yamashiro CT, Behari R, Paszko-Kolva C, Rahn K, Grandis SAD (1997) The evaluation of a fluorogenic polymerase chain reaction assay for the detection of Salmonella species in food commodities. Int J Food Microbiol 35:239-250
17. Chen X, Cui DF, Wang L, Wang M, Zhao Q (2002) Development and characterization of DNA hybridization reaction on PDMS microchip. Int J Nonlinear Sci Numer Simul 3:211-214
18. Chen L, Lee S, Lee M, Lim C, Choo J, Park JY, Lee S, Joo S, Lee K, Choi Y (2008) DNA hybridization detection in a microfluidic channel using two fluorescently labelled nucleic acid probes. Biosens Bioelectron 23:1878-1882
19. Chen B, Zhou X, Li C, Wang Q, Liu D, Lin B (2011) Rapid screening of phenylketonuria using a CD microfluidic device. J Chromatogr A 1218:1907-1912
20. Cheng I, Senapati S, Cheng X, Basuray S, Chang H, Chang H (2010) A rapid field-use assay for mismatch number and location of hybridized DNAs. Lab Chip 10:828-831
21. Choi J, Cha M, Lee J (2009) Thin membrane transducer detecting DNA hybridization on chip. In: IEEE sensors 2009 conference, October 25-28, 2009. IEEE, Christchurch, pp 815-818
22. Chung Y, Lin Y, Shiu M, Chang WT (2003) Microfluidic chip for fast nucleic acid hybridization. Lab Chip 3:228-233 (Pubitemid 41646528)
23. Chung Y, Lin Y, Chueh C, Ye C, Lai L, Zhao Q (2008) Microfluidic chip of fast DNA hybridization using denaturing and motion of nucleic acids. Electrophoresis 29:1859-1865 (Pubitemid 351663882)
24. Dhopeshwarkar R, Sun L, Crooks Richard M (2005) Electrokinetic concentration enrichment within a microfluidic device using a hydrogel microplug. Lab Chip 5:1148-1154 (Pubitemid 41453006)
25. Edelstein RL, Tamanaha CR, Sheehan PE, Miller MM, Baselt DR, Whitman LJ, Colton RJ (2000) The BARC biosensor applied to the detection of biological warfare agents. Biosens Bioelectron 14:805-813 (Pubitemid 30055361)
26. Erickson D, Liu X, Krull U, Li D (2004) Electrokinetically controlled DNA hybridization microfluidic chip enabling rapid target analysis. Anal Chem 76:7269-7277 (Pubitemid 39657997)
27. Esch MB, Locascio LE, Tarley MJ, Durst RA (2001) Detection of viable cryptosporidium parvum using DNA-modified liposomes in a microfluidic chip. Anal Chem 73:2952-2958 (Pubitemid 32868152)
28. Fan ZH, Mangru S, Granzow R, Heaney P, Ho W, Dong Q, Kumar R (1999) Dynamic DNA hybridization on a chip using paramagnetic beads. Anal Chem 71:4851-4859
29. Ferguson BS, Buchsbaum SF, Swensen JS, Hsieh K, Lou X, Soh HT (2009) Integrated microfluidic electrochemical DNA sensor. Anal Chem 81:6503-6508
30. Flowers RS, Klatt MJ, Mozola MA, Curiale MS, Gabis DA, Silliker JH (1987) DNA hybridization assay for detection of Salmonella in foods: collaborative study. J Assoc Off Anal Chem 70(3):521-529
31. Hatakeyama K, Tanaka T, Sawaguchi M, Iwadate A, Mizutani Y, Sasaki K, Tateishi N, Matsunaga T (2009) Microfluidic device using chemiluminescence and a DNA-arrayed thin film transistor photosensor for single nucleotide polymorphism genotyping of PCR amplicons from whole blood. Lab Chip 9:1052-1058
32. Heule M, Manz A (2004) Sequential DNA hybridisation assays by fast micromixing. Lab Chip 4:506-511 (Pubitemid 39468925)
33. Hill WE (1981) DNA Hybridization method for detecting enterotoxigenic Escherichia coli in human isolates and its possible application to food samples. J Food Saf 3:233-247
34. Huang SQ, Li CY, Lin BC, Qin JH (2010) Microvalve and micropump controlled shuttle flow microfluidic device for rapid DNA hybridization. Lab Chip 10:2925-2931
35. Javanmard M, Davis RW (2011) A microfluidic platform for electrical detection of DNA hybridization. Sens Actuators B 154:22-27
36. Jin SQ, Yin BC, Ye BC (2009) Multiplexed bead-based mesofluidic system for detection of food-borne pathogenic bacteria. Appl Environ Microbiol 75(21):6647-6654
37. Jobs M, Fredriksson S, Brookes AJ, Landegren U (2002) Effect of oligonucleotide truncation on single-nucleotide distinction by solid-phase hybridization. Anal Chem 74:199-202 (Pubitemid 34044444)
38. Kang TJ, Lim D, Nam J, Kim YH (2010) Multifunctional nanocomposite membrane for chemomechanical transducer. Sens Actuators B 147:691-696
39. Kim JH, Marafie A, Jia X, Zoval JV, Madou MJ (2006a) Characterization of DNA hybridization kinetics in a microfluidic flow channel. Sens Actuators B 113:281-289 (Pubitemid 41831298)
40. Kim J, Heo J, Crooks RM (2006b) Hybridization of DNA to beadimmobilized probes confined within a microfluidic channel. Langmuir 22:10130-10134 (Pubitemid 46079295)
41. Kim S, Chen L, Lee S, Seong GH, Choo J, Lee EK, Oh C, Lee S (2007) Rapid DNA hybridization analysis using a PDMS microfluidic sensor and a molecular beacon. Anal Sci 23:401-405
42. Kwakye S, Baeumner A (2003) A microfluidic biosensor based on nucleic acid sequence recognition. Anal Bioanal Chem 376:1062-1068 (Pubitemid 40877923)
43. Lange SA, Benes V, Kern DP, Hörber JK, Bernard A (2004) Microcontact printing of DNA molecules. Anal Chem 76:1641-1647 (Pubitemid 38338408)
44. Lee HJ, Goodrich TT, Corn RM (2001) SPR imaging measurements of 1-D and 2-D DNA microarrays created from microfluidic channels on gold thin films. Anal Chem 73:5525-5531 (Pubitemid 33108564)
45. Lei IF, Roffey P, Blanchard C, Gu K (2008) Development of a multiplex PCR method for the detection of six common foodborne pathogens. J Food Drug Anal 16(4):37-43
46. Lewis CL, Choi C, Lin Y, Lee C, Yi H (2010) Fabrication of uniform DNA-conjugated hydrogel microparticles via rReplica molding for facile nucleic acid hybridization assays. Anal Chem 82:5851-5858
47. Li H, He Z (2009) Magnetic bead-based DNA hybridization assay with chemiluminescence and chemiluminescent imaging detection. Analyst 134:800-804
48. Li C, Dong X, Qin J, Lin B (2009) Rapid nanoliter DNA hybridization based on reciprocating flow on a compact disk microfluidic device. Anal Chim Acta 640:93-99
49. Lien KY, Lee GB (2010) Miniaturization of molecular biological techniques for gene assay. Analyst 135:1499-1518
50. Lingerfelt L, Karlinsey J, Landers J, Guiseppi-Elie A (2007) Impedimetric detection for DNA hybridization within microfluidic biochips. Methods Mol Biol 385:103-120
51. Liu DJ, Perdue RK, Sun L, Crooks RM (2004) Immobilization of DNA onto poly(dimethylsiloxane) surfaces and application to a microelectrochemical enzyme-amplified DNA hybridization assay. Langmuir 20:5905-5910
52. Maciorowski KG, Herrera P, Jones FT, Pillai SD, Ricke SC (2006) Cultural and immunological detection methods for Salmonella spp in animal feeds-a review. Vet Res Commun 30:127-137 (Pubitemid 43072284)
53. Mai JDH, Gaster RS, Wu A, Gu W, Mach K, Liao JC (2007) A microfluidic system for rapid bacterial pathogen detection. In: Proceedings of the 7th IEEE international conference on nanotechnology, August 2-5, 2007. IEEE, Hong Kong, pp 1330-1334
54. Malic L, Veres T, Tabrizian M (2009) Biochip functionalization using electrowetting-on-dielectric digital microfluidics for surface plasmon resonance imaging detection of DNA hybridization. Biosens Bioelectron 24:2218-2224
55. Misiakos K, Mayrogiannopoulou E, Petrou P, Kakabakos S (2009) Monolithic silicon optical microdevices for biomolecular sensing. In: IEEE sensors 2009 conference, October 25-28, 2009. IEEE, Christchurch, pp 17-20
56. Moseley SL, Huq I, Alim ARMA, So M, Samadpour-Motalebi M, Falkow S (1980) Detection of enterotoxigenic Escherichia coli by DNA colony hybridization. J Infect Dis 142:892-898 (Pubitemid 11153256)
57. Mulvaney SP, Cole CL, Kniller MD, Malito M, Tamanaha CR, Rife JC, Stanton MW, Whitman LJ (2007) Rapid, femtomolar bioassays in complex matrices combining microfluidics and magnetoelectronics. Biosens Bioelectron 23(2):191-200 (Pubitemid 47391559)
58. Noerholm M, Bruus H, Jakobsen MH, Tellemanb P, Ramsing NB (2004) Polymer microfluidic chip for online monitoring of microarray hybridizations. Lab Chip 4:28-37 (Pubitemid 38405224)
59. Olsen KG, Ross DJ, TarlovMJ (2002) Immobilization of DNA hydrogel plugs in microfluidic channels. Anal Chem 74:1436-1441 (Pubitemid 34233337)
60. Park S, Taton TA, Mirkin CA (2002) Array-based electrical detection of DNA with nanoparticle probes. Science 22:1503-1506 (Pubitemid 34174000)
61. Peytavi R, Raymond FR, Gagné D, Picard FJ, Jia G, Zoval J,Madou M, Boissinot K, Boissinot M, Bissonnette L, Ouellette M, Bergeron MG (2005) Microfluidic device for rapid (15 min) automated microarray hybridization. Clin Chem 51(10):1836-1844 (Pubitemid 41368174)
62. Ramsay G (1998) DNA chips: state-of-the art. Nat Biotechnol 16:40-44 (Pubitemid 28035946)
63. Russom A (2005) Microfluidic bead-based methods for DNA analysis. Dissertation, Royal Institute of Technology, Stockholm, Sweden
64. Sabourin D, Petersen J, Snakenborg D, Brivio M, Gudnadson H, Wolff A, Dufva M (2010) Microfluidic DNA microarrays in PMMA chips: streamlined fabrication via simultaneous DNA immobilization and bonding activation by brief UV exposure. Biomed Microdevices 12:673-681
65. Satyanarayana S, McCormick DT, Majumdar A (2006) Parylene micro membrane capacitive sensor array for chemical and biological sensing. Sens Actuators B 115:494-502
66. Sawada K, Oda C, Takao H, Ishida M (2007) Smart microfluidic electrochemical DNA sensors with signal processing circuits. Jpn J App Phys 46(5A):3135-3313
67. Schaechter M, Lederberg J (2004) The desk encyclopedia of microbiology. Academic Press, San Diego, CA, USA
68. Schüler T, Asmus T, Fritzsche W, Möller R (2009a) Screen printing as cost-efficient fabrication method for DNA-chips with electrical readout for detection of viral DNA. Biosens Bioelectron 24(7):2077-2084
69. Schüler T, Kretschmer R, Jessing S, Urban M, Fritzsche W, Möller R, Popp J (2009b) A disposable and cost efficient microfluidic device for the rapid chip-based electrical detection of DNA. Biosens Bioelectron 25:15-21
70. Senapati S, Mahon AR, Gordon J, Nowak C, Sengupta S, Powell THQ, Feder J, Lodge DM, Chang H (2009) Rapid on-chip genetic detection microfluidic platform for real world applications. Biomicrofluidics 3:022407
71. Seong GH, Zhan W, Crooks RM (2002) Fabrication of microchambers defined by photopolymerized hydrogels and weirs within microfluidic systems: application to DNA hybridization. Anal Chem 74:3372-3377 (Pubitemid 34764942)
72. Shamansky LM, Davis CB, Stuart JK, Kuhr WG (2001) Immobilization and detection of DNA on microfluidic chips. Talanta 55:909-918 (Pubitemid 33095478)
73. Sonntag F, Schmieder S, Danz N, Mertig M, Schilling N, Klotzbach U, Beyer E (2009) Novel lab-on-a-chip system for label-free detection of DNA hybridization and protein-protein interaction by surface plasmon resonance (SPR). In: Rodíguez-Vázquez, Ángel B (eds) Bioengineered and bioinspired systems IV, vol 7365. Proc SPIE, pp 73650Q-73650Q-9
74. Sun Y, Kwok YC (2006) Polymeric microfluidic system for DNA analysis. Anal Chim Acta 556(1):80-96 (Pubitemid 43042579)
75. Sung W, Chen H, Makamba H, Chen S (2009) Functionalized 3Dhydrogel plugs covalently patterned inside hydrophilic poly (dimethylsiloxane) microchannels for flow-through immunoassays. Anal Chem 81:7967-7973
76. Swaminathan B, Feng P (1994) Rapid detection of food-borne pathogenic bacteria. Annu Rev Microbiol 48:401-426 (Pubitemid 24334103)
77. Taton TA, Mirkin CA, Letsinger RL (2000) Scanometric DNA array detection with nanoparticle probes. Science 8:1757-1760
78. Tavares AJ, Petryayeva E, Algar WR, Chen L, Krull UJ (2010) Toward a hybridization assay using fluorescence resonance energy transfer and quantum dots immobilized in microfluidic channels. Proc SPIE 7750:775003
79. Thomas G, El-Giar EM, Locascio LE, Tarlov MJ (2006) Methods in molecular biology. In: Minteer SD (ed) Microfluidic techniques: reviews and protocols, vol 321. Humana Press Inc, Totowa, NJ, pp 1-247
80. Wang L, Li PCH (2011) Microfluidic DNA microarray analysis: a review. Anal Chim Acta 687:12-27
81. Wang Y, Vaidya B, Farquar HD, Stryjewski W, Hammer RP, McCarley RL, Soper SA (2003) Microarrays assembled in microfluidic chips fabricated from poly (methyl methacrylate) for the detection of low-abundant DNA mutations. Anal Chem 75:1130-1140 (Pubitemid 36402642)
82. Wang J, Chen Z, Mauk M, Hong K, Li M, Yang S, Bau HH (2005) Self-actuated, thermo-responsive hydrogel valves for Lab on a Chip. Biomed Microdevices 7(4):313-322
83. Wang CH, Lien KY, Wu JJ, Lee GB (2011a) A magnetic bead-based assay for the rapid detection of methicillin-resistant Staphylococcus aureus by using a microfluidic system with integrated loopmediated isothermal amplification. Lab Chip 11:1521-1531
84. Wang X, Chen X, Ma X, Kong X, Xu Z, Wang J (2011b) Fast DNA hybridization on a microfluidic mixing device based on pneumatic driving. Talanta 84:565-571
85. Wen J, Yanga X, Wang K, Tana W, Zhou L, Zuo X, Zhang H, Chen Y (2007) One-dimensional microfluidic beads array for multiple mRNAs expression detection. Biosens Bioelectron 22(11):2759-2762 (Pubitemid 46505257)
86. Wirth D, Pratt DM (1982) Rapid identification of Leishmania species by specific hybridization of kinetoplast DNA in cutaneous lesions. Proc Natl Acad Sci USA 79:6999-7003 (Pubitemid 13170918)
87. Yamashita K, Yamaguchi Y, Miyazaki M, Nakamura H, Shimizu H, Maeda H (2004) Sequence-selective DNA detection using multiple laminar streams: a novel microfluidic analysis method. Lab Chip 4:1-3 (Pubitemid 38405218)
88. Yang X, Zhao X, Zuo X, Wang K, Wen J, Zhang H (2009) Nucleic acids detection using cationic fluorescent polymer based on onedimensional microfluidic beads array. Talanta 77:1027-1031
89. Yuen PK, Li GS, Bao YJ, Muller UR (2003) Microfluidic devices for fluidic circulation and mixing improve hybridization signal intensity on DNA arrays. Lab Chip 3:46-50 (Pubitemid 41646515)
90. Zangmeister RA, Tarlov MJ (2003) UV graft polymerization of polyacrylamide hydrogel plugs in microfluidic channels. Langmuir 19:6901-6904
91. Zangmeister RA, Tarlov MJ (2004) DNA displacement assay integrated into microfluidic channels. Anal Chem 76:3655-3659 (Pubitemid 38868826)
92. Zangmeister RA, Tarlov MJ (2009) Selective DNA screening in microfluidic channels by electrophoresis through hydrogel matrices. The National Institute of Standards and Technology (NIST) Web. http://www.nt.ntnu.no/users/skoge/prost/ proceedings/aiche2004/pdffiles/papers/137c.pdf. Accessed 18 August 2009
93. Zaytseva NV, Goral VN, Montagna RA, Baeumner AJ (2005) Development of a microfluidic biosensor module for pathogen detection. Lab Chip 5:805-811 (Pubitemid 41117306)
94. Zhang H, Yang X, Wang K, Tan W, Li H, Zuo X, Wen J (2008) Onchip oligonucleotide ligation assay using one-dimensional microfluidic beads array for the detection of low-abundant DNA point mutations. Biosens Bioelectron 23:945-951 (Pubitemid 351181278)
95. Zhang Y, Yu H, Dong X, Qin J, Lin B (2009) Immobilization of DNA hydrogel plugs in glass microfluidic channels and its applications. Chem J Chin Universities 30(6):1128-1130