An integrated nanoliter DNA analysis device

Science

Volumn 282, Issue 5388, 1998, Pages 484-487

  Burns, Mark A ^a   Johnson, Brian N ^a   Brahmasandra, Sundaresh N ^a   Handique, Kalyan ^a   Webster, James R ^b   Krishnan, Madhavi ^a   Sammarco, Timothy S ^a   Man, Piu M ^b   Jones, Darren ^b   Heldsinger, Dylan ^a   Mastrangelo, Carlos H ^b   Burke, David T ^c  

^a UNIVERSITY OF MICHIGAN   (United States)

^b University of Michigan   (United States)

^c UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

DEVICE; DNA DETERMINATION; FLUORESCENCE; HEATING; PARTICLE SIZE; PRIORITY JOURNAL; REVIEW; SENSOR;

COSTS AND COST ANALYSIS; DNA; ELECTROPHORESIS, POLYACRYLAMIDE GEL; FLUORESCENCE; MINIATURIZATION; MOLECULAR BIOLOGY; SILICON; TEMPERATURE;

EID: 0032538386     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.282.5388.484     Document Type: Review

References (45)

1. M. A. Marra et al., Genome Res. 7, 1072 (1997); M. Rhodes et al., ibid., p. 81; C. Boysen, M. I. Simon, L. Hood, Biotechniques 23, 978 (1997); R. K. Wilson and E. R. Mardis, in Genome Analysis: A Laboratory Manual, B. Birren, E. D. Green, S. Klapholz, R. M. Myers, J. Roskams, Eds. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1997), vol. 1, p. 301.
2. M. A. Marra et al., Genome Res. 7, 1072 (1997); M. Rhodes et al., ibid., p. 81; C. Boysen, M. I. Simon, L. Hood, Biotechniques 23, 978 (1997); R. K. Wilson and E. R. Mardis, in Genome Analysis: A Laboratory Manual, B. Birren, E. D. Green, S. Klapholz, R. M. Myers, J. Roskams, Eds. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1997), vol. 1, p. 301.
3. M. A. Marra et al., Genome Res. 7, 1072 (1997); M. Rhodes et al., ibid., p. 81; C. Boysen, M. I. Simon, L. Hood, Biotechniques 23, 978 (1997); R. K. Wilson and E. R. Mardis, in Genome Analysis: A Laboratory Manual, B. Birren, E. D. Green, S. Klapholz, R. M. Myers, J. Roskams, Eds. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1997), vol. 1, p. 301.
4. M. A. Marra et al., Genome Res. 7, 1072 (1997); M. Rhodes et al., ibid., p. 81; C. Boysen, M. I. Simon, L. Hood, Biotechniques 23, 978 (1997); R. K. Wilson and E. R. Mardis, in Genome Analysis: A Laboratory Manual, B. Birren, E. D. Green, S. Klapholz, R. M. Myers, J. Roskams, Eds. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1997), vol. 1, p. 301.
5. R. A. Gibbs, Nature Genet. 11, 121 (1995); S. Ghosh et al., Genome Res. 7, 165 (1997).
6. R. A. Gibbs, Nature Genet. 11, 121 (1995); S. Ghosh et al., Genome Res. 7, 165 (1997).
7. For formation of the heaters, a 2-μm layer of p-xylylene was deposited as a moisture barrier and a reactive ion-hydrofluoric acid etch was used to form connections with the diodes. A 3.3-μm layer of Microposit 1400-37 photoresist was patterned to define the dual-meandering-line heaters (area 500 μm by 500 μm, line thickness 5 μm), and 50 nm of chromium was evaporated over the resist, followed by 400 nm of gold. Liftoff of the resist left the heaters on the surface. The heaters were then covered with a second, insulating layer of p-xylylene (2 μm thick).
8. For the electrodes, 20 nm of titanium and 30 nm of platinum were deposited on top of the second p-xylylene layer, using the same liftoff procedure as for the heaters.
9. Channels were prepared on 500-μm-thick glass wafers (Dow Corning 7740) using standard aqueous-based etch procedures, as described (7). Al (1000 nm) was then evaporated and patterned using photoresist AZP4620 (Hoechst Celanese). The wafer was dipped in a solution of heptadecafluro-1,1,2,2-hydrodecyl dimethylchlorosilane to form hydrophobic regions on the surface, and the aluminum was then removed. Holes through the glass substrate at the ends of the fluid channels were drilled by applying 37 V to a metal point touching the glass surface in a 50 weight % sodium hydroxide solution. For assembly, the glass channel was placed on top of the silicon substrate, and optical adhesive (SK-9 Lens Bond; Sumers Laboratories, Fort Washington, PA) was applied to the edge of the channel and allowed to wick between the glass and silicon substrate. The adhesive did not enter the channel area and was cured under an ultraviolet lamp for 24 hours.
10. Raised polymer walls were fashioned around the buffer ports to prevent excess buffer from contacting the surface electronics. Monomer acrylamide electrophoresis gel material [10% acrylamide, 0.3% bis(acrylamide), 89 mM tris-HCl, 89 mM borate, 10 mM EDTA, 0.001% N,N,N′,N′-tetramethylethylenediamine (TEMED), and 0.01% ammonium persulfate] was allowed to wick into the two channels and polymerize for 30 min. In some cases, a hydrophobic patch at the crossed channels was used to aid in the formation of flat gel interfaces. The gel present in two of the four channels of the intersection serves to restrict the motion of the sample and to ensure that the DNA remains at the running gel interface.
11. M. A. Burns et al., Proc. Natl. Acad. Sci. U.S.A. 93, 5556 (1996).
12. G. T. Walker et al., Nucleic Acids Res. 20, 1691 (1992). The enzyme solution contained 100 mM sodium chloride, 70 mM potassium phosphate, 20 mM tris (pH 7.6), 10 mM magnesium acetate, 2 mM dithiothreitol, Bst polymerase (0.5 U/μl), and Bso B1 endonuclease (3.2 U/μl per 25 μl). The DNA solution contained 2.8 mM 2′-deoxycytosine 5′-O-(1-thiotriphosphate) (dCTP-α-S), 0.4 mM each deoxynucleoside 5′-triphosphate (dATP, dGTP, dTTP), 1 μM primers, 0.1 μM bumpers, and target DNA (0.04 ng/μl). The entire channel was rinsed with acetone, isopropyl alcohol, and bovine serum albumin (BSA) before each use. The target Mycobacterium tuberculosis DNA is 106 bp long and is the same as described in C. A. Spargo et al., Mol. Cell. Probes 10, 247 (1996). The amplified product was cloned into pGEM vector (pB959G) and sequenced for confirmation.
13. G. T. Walker et al., Nucleic Acids Res. 20, 1691 (1992). The enzyme solution contained 100 mM sodium chloride, 70 mM potassium phosphate, 20 mM tris (pH 7.6), 10 mM magnesium acetate, 2 mM dithiothreitol, Bst polymerase (0.5 U/μl), and Bso B1 endonuclease (3.2 U/μl per 25 μl). The DNA solution contained 2.8 mM 2′-deoxycytosine 5′-O-(1-thiotriphosphate) (dCTP-α-S), 0.4 mM each deoxynucleoside 5′-triphosphate (dATP, dGTP, dTTP), 1 μM primers, 0.1 μM bumpers, and target DNA (0.04 ng/μl). The entire channel was rinsed with acetone, isopropyl alcohol, and bovine serum albumin (BSA) before each use. The target Mycobacterium tuberculosis DNA is 106 bp long and is the same as described in C. A. Spargo et al., Mol. Cell. Probes 10, 247 (1996). The amplified product was cloned into pGEM vector (pB959G) and sequenced for confirmation.
14. SDA does not work in the presence of intercalating dyes such as SYBR Green. For our integrated restriction digest runs, a separate dye injection step was not necessary; the dye was included in the DNA sample solution. Buffer was kept on the gel during reaction to prevent drying. The buffer was removed before the sample was loaded onto the gel.
15. Sample was removed after injection and replaced with buffer; runs were also performed without this step, but removing the sample led to more uniform and sharp peaks. Platinum electrodes placed in the buffer wells were used for both the injection and running of the sample.
16. A lock-in amplifier and data acquisition program were used to pulse a blue LED with accompanying low-pass filter at 288 Hz and to record the output of the microfabricated diode detector.
17. Diode detection limits for this system were obtained using dilute solutions of 4.0-kb plasmid DNA with intercalating dye. In a 50 μm by 500 μm channel over a 10 μm by 500 μm detector, DNA solutions at concentrations of 10 ng/μl were readily detected.
18. S. N. Brahmasandra, B. N. Johnson, J. R. Webster, data not shown.
19. D. J. Harrison, A. Manz, Z. Fan, H. Ludi, H. M. Widmer, Science 261, 895 (1993); J. M. Measros, G. Luo, J. Roeraade, A. G. Ewing, Anal. Chem. 65, 3313 (1993); C. S. Effenhouser, A. Paulus, A. Manz, H. M. Widmer, ibid. 66, 2949 (1994); S. C. Jacobson, L. B. Koutny, R. Hergenroder, A. W. Moore, J. M. Ramsey, ibid., p. 3472; A. T. Woolley and R. A. Mathies, Proc. Natl. Acad. Sci. U.S.A. 91, 11348 (1994); Anal. Chem. 67, 3676 (1995); R. M. McCormick, R. J. Nelson, M. G. Alonso-amigo, D. J. Benvegnu, H. H. Hooper, ibid. 69, 2626 (1997); C. S. Effenhauser, F. J. M. Bruin, A. Paulus, M. Ehart, ibid., p. 3451; P. C. Simpson et al., Proc. Natl. Acad. Sci. U.S.A. 95, 2256 (1998).
20. D. J. Harrison, A. Manz, Z. Fan, H. Ludi, H. M. Widmer, Science 261, 895 (1993); J. M. Measros, G. Luo, J. Roeraade, A. G. Ewing, Anal. Chem. 65, 3313 (1993); C. S. Effenhouser, A. Paulus, A. Manz, H. M. Widmer, ibid. 66, 2949 (1994); S. C. Jacobson, L. B. Koutny, R. Hergenroder, A. W. Moore, J. M. Ramsey, ibid., p. 3472; A. T. Woolley and R. A. Mathies, Proc. Natl. Acad. Sci. U.S.A. 91, 11348 (1994); Anal. Chem. 67, 3676 (1995); R. M. McCormick, R. J. Nelson, M. G. Alonso-amigo, D. J. Benvegnu, H. H. Hooper, ibid. 69, 2626 (1997); C. S. Effenhauser, F. J. M. Bruin, A. Paulus, M. Ehart, ibid., p. 3451; P. C. Simpson et al., Proc. Natl. Acad. Sci. U.S.A. 95, 2256 (1998).
21. D. J. Harrison, A. Manz, Z. Fan, H. Ludi, H. M. Widmer, Science 261, 895 (1993); J. M. Measros, G. Luo, J. Roeraade, A. G. Ewing, Anal. Chem. 65, 3313 (1993); C. S. Effenhouser, A. Paulus, A. Manz, H. M. Widmer, ibid. 66, 2949 (1994); S. C. Jacobson, L. B. Koutny, R. Hergenroder, A. W. Moore, J. M. Ramsey, ibid., p. 3472; A. T. Woolley and R. A. Mathies, Proc. Natl. Acad. Sci. U.S.A. 91, 11348 (1994); Anal. Chem. 67, 3676 (1995); R. M. McCormick, R. J. Nelson, M. G. Alonso-amigo, D. J. Benvegnu, H. H. Hooper, ibid. 69, 2626 (1997); C. S. Effenhauser, F. J. M. Bruin, A. Paulus, M. Ehart, ibid., p. 3451; P. C. Simpson et al., Proc. Natl. Acad. Sci. U.S.A. 95, 2256 (1998).
22. D. J. Harrison, A. Manz, Z. Fan, H. Ludi, H. M. Widmer, Science 261, 895 (1993); J. M. Measros, G. Luo, J. Roeraade, A. G. Ewing, Anal. Chem. 65, 3313 (1993); C. S. Effenhouser, A. Paulus, A. Manz, H. M. Widmer, ibid. 66, 2949 (1994); S. C. Jacobson, L. B. Koutny, R. Hergenroder, A. W. Moore, J. M. Ramsey, ibid., p. 3472; A. T. Woolley and R. A. Mathies, Proc. Natl. Acad. Sci. U.S.A. 91, 11348 (1994); Anal. Chem. 67, 3676 (1995); R. M. McCormick, R. J. Nelson, M. G. Alonso-amigo, D. J. Benvegnu, H. H. Hooper, ibid. 69, 2626 (1997); C. S. Effenhauser, F. J. M. Bruin, A. Paulus, M. Ehart, ibid., p. 3451; P. C. Simpson et al., Proc. Natl. Acad. Sci. U.S.A. 95, 2256 (1998).
23. D. J. Harrison, A. Manz, Z. Fan, H. Ludi, H. M. Widmer, Science 261, 895 (1993); J. M. Measros, G. Luo, J. Roeraade, A. G. Ewing, Anal. Chem. 65, 3313 (1993); C. S. Effenhouser, A. Paulus, A. Manz, H. M. Widmer, ibid. 66, 2949 (1994); S. C. Jacobson, L. B. Koutny, R. Hergenroder, A. W. Moore, J. M. Ramsey, ibid., p. 3472; A. T. Woolley and R. A. Mathies, Proc. Natl. Acad. Sci. U.S.A. 91, 11348 (1994); Anal. Chem. 67, 3676 (1995); R. M. McCormick, R. J. Nelson, M. G. Alonso-amigo, D. J. Benvegnu, H. H. Hooper, ibid. 69, 2626 (1997); C. S. Effenhauser, F. J. M. Bruin, A. Paulus, M. Ehart, ibid., p. 3451; P. C. Simpson et al., Proc. Natl. Acad. Sci. U.S.A. 95, 2256 (1998).
24. D. J. Harrison, A. Manz, Z. Fan, H. Ludi, H. M. Widmer, Science 261, 895 (1993); J. M. Measros, G. Luo, J. Roeraade, A. G. Ewing, Anal. Chem. 65, 3313 (1993); C. S. Effenhouser, A. Paulus, A. Manz, H. M. Widmer, ibid. 66, 2949 (1994); S. C. Jacobson, L. B. Koutny, R. Hergenroder, A. W. Moore, J. M. Ramsey, ibid., p. 3472; A. T. Woolley and R. A. Mathies, Proc. Natl. Acad. Sci. U.S.A. 91, 11348 (1994); Anal. Chem. 67, 3676 (1995); R. M. McCormick, R. J. Nelson, M. G. Alonso-amigo, D. J. Benvegnu, H. H. Hooper, ibid. 69, 2626 (1997); C. S. Effenhauser, F. J. M. Bruin, A. Paulus, M. Ehart, ibid., p. 3451; P. C. Simpson et al., Proc. Natl. Acad. Sci. U.S.A. 95, 2256 (1998).
25. D. J. Harrison, A. Manz, Z. Fan, H. Ludi, H. M. Widmer, Science 261, 895 (1993); J. M. Measros, G. Luo, J. Roeraade, A. G. Ewing, Anal. Chem. 65, 3313 (1993); C. S. Effenhouser, A. Paulus, A. Manz, H. M. Widmer, ibid. 66, 2949 (1994); S. C. Jacobson, L. B. Koutny, R. Hergenroder, A. W. Moore, J. M. Ramsey, ibid., p. 3472; A. T. Woolley and R. A. Mathies, Proc. Natl. Acad. Sci. U.S.A. 91, 11348 (1994); Anal. Chem. 67, 3676 (1995); R. M. McCormick, R. J. Nelson, M. G. Alonso-amigo, D. J. Benvegnu, H. H. Hooper, ibid. 69, 2626 (1997); C. S. Effenhauser, F. J. M. Bruin, A. Paulus, M. Ehart, ibid., p. 3451; P. C. Simpson et al., Proc. Natl. Acad. Sci. U.S.A. 95, 2256 (1998).
26. D. J. Harrison, A. Manz, Z. Fan, H. Ludi, H. M. Widmer, Science 261, 895 (1993); J. M. Measros, G. Luo, J. Roeraade, A. G. Ewing, Anal. Chem. 65, 3313 (1993); C. S. Effenhouser, A. Paulus, A. Manz, H. M. Widmer, ibid. 66, 2949 (1994); S. C. Jacobson, L. B. Koutny, R. Hergenroder, A. W. Moore, J. M. Ramsey, ibid., p. 3472; A. T. Woolley and R. A. Mathies, Proc. Natl. Acad. Sci. U.S.A. 91, 11348 (1994); Anal. Chem. 67, 3676 (1995); R. M. McCormick, R. J. Nelson, M. G. Alonso-amigo, D. J. Benvegnu, H. H. Hooper, ibid. 69, 2626 (1997); C. S. Effenhauser, F. J. M. Bruin, A. Paulus, M. Ehart, ibid., p. 3451; P. C. Simpson et al., Proc. Natl. Acad. Sci. U.S.A. 95, 2256 (1998).
27. D. J. Harrison, A. Manz, Z. Fan, H. Ludi, H. M. Widmer, Science 261, 895 (1993); J. M. Measros, G. Luo, J. Roeraade, A. G. Ewing, Anal. Chem. 65, 3313 (1993); C. S. Effenhouser, A. Paulus, A. Manz, H. M. Widmer, ibid. 66, 2949 (1994); S. C. Jacobson, L. B. Koutny, R. Hergenroder, A. W. Moore, J. M. Ramsey, ibid., p. 3472; A. T. Woolley and R. A. Mathies, Proc. Natl. Acad. Sci. U.S.A. 91, 11348 (1994); Anal. Chem. 67, 3676 (1995); R. M. McCormick, R. J. Nelson, M. G. Alonso-amigo, D. J. Benvegnu, H. H. Hooper, ibid. 69, 2626 (1997); C. S. Effenhauser, F. J. M. Bruin, A. Paulus, M. Ehart, ibid., p. 3451; P. C. Simpson et al., Proc. Natl. Acad. Sci. U.S.A. 95, 2256 (1998).
28. S. N. Brahmasandra, B. N. Johnson, J. R. Webster, data not shown.
29. K. Handique, B. P. Gogoi, D. T. Burke, C. H. Mastrangelo, M. A. Burns, SPIE Proc. 3224, 185 (1997).
30. B. N. Johnson, D. Jones, V. Namasivayam, M. A. Burns, data not shown.
31. When the reaction chamber is at 52°C, a thermocouple at the top surface of the glass (500 μm above) measures ∼48°C. Therefore, the vertical temperature difference in the 50-μm-high channel is on the order of 0.5°C. A finite-difference solution of the heat-transfer equations for the system, using a constant-temperature boundary condition at the heater and a natural convection heat-transfer coefficient at the top, gives a similar result (T. S. Sammarco and M. A. Burns, data not shown).
32. Nanoliter reactions may be affected by evaporation and surface adsorption. Evaporation was reduced in our design by having only a few small openings from the device to the outside. Surface adsorption was reduced by pretreatment of the microfluidic channels with a dilute protein solution (BSA); other researchers have solved the adsorption problem in different ways [for example, M. A. Shoffner, J. Cheng, G. E. Hvichia, L. J. Kricka, P. Wilding, Nucleic Acids Res. 24, 375 (1996)].
33. D. T. Burke, M. A. Burns, C. H. Mastrangelo, Genome Res. 7, 189 (1997).
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35. M. V. Olson, Science 270, 394 (1995); L. Rowen, G. Mahairas, L. Hood, ibid. 278, 605 (1997); P. Green, Genome Res. 7, 410 (1997).
36. M. V. Olson, Science 270, 394 (1995); L. Rowen, G. Mahairas, L. Hood, ibid. 278, 605 (1997); P. Green, Genome Res. 7, 410 (1997).
37. A. T. Woolley et al., Anal. Chem. 68, 4081 (1996); A. G. Hadd, D. E. Raymond, J. W. Halliwell, S. C. Jacobson, J. M. Ramsey, ibid. 69, 3407 (1997); A. T. Woolley, K. Lao, A. N. Glazer, R. A. Mathies, Ibid. 70, 684 (1998).
38. A. T. Woolley et al., Anal. Chem. 68, 4081 (1996); A. G. Hadd, D. E. Raymond, J. W. Halliwell, S. C. Jacobson, J. M. Ramsey, ibid. 69, 3407 (1997); A. T. Woolley, K. Lao, A. N. Glazer, R. A. Mathies, Ibid. 70, 684 (1998).
39. A. T. Woolley et al., Anal. Chem. 68, 4081 (1996); A. G. Hadd, D. E. Raymond, J. W. Halliwell, S. C. Jacobson, J. M. Ramsey, ibid. 69, 3407 (1997); A. T. Woolley, K. Lao, A. N. Glazer, R. A. Mathies, Ibid. 70, 684 (1998).
40. M. S. Chee et al., Science 274, 610 (1996), D. G. Wang et al., ibid. 280, 1077 (1998); R. G. Sosnowski, E. Tu, W. F. Butler, J. P. O'Connell, M. J. Heller, Proc. Natl. Acad. Sci. U.S.A. 94, 1119 (1997); H. F. Arlinghaus, M. N. Kwoka, K. B. Jacobson, Anal. Chem. 69, 3747 (1997).
41. M. S. Chee et al., Science 274, 610 (1996), D. G. Wang et al., ibid. 280, 1077 (1998); R. G. Sosnowski, E. Tu, W. F. Butler, J. P. O'Connell, M. J. Heller, Proc. Natl. Acad. Sci. U.S.A. 94, 1119 (1997); H. F. Arlinghaus, M. N. Kwoka, K. B. Jacobson, Anal. Chem. 69, 3747 (1997).
42. M. S. Chee et al., Science 274, 610 (1996), D. G. Wang et al., ibid. 280, 1077 (1998); R. G. Sosnowski, E. Tu, W. F. Butler, J. P. O'Connell, M. J. Heller, Proc. Natl. Acad. Sci. U.S.A. 94, 1119 (1997); H. F. Arlinghaus, M. N. Kwoka, K. B. Jacobson, Anal. Chem. 69, 3747 (1997).
43. M. S. Chee et al., Science 274, 610 (1996), D. G. Wang et al., ibid. 280, 1077 (1998); R. G. Sosnowski, E. Tu, W. F. Butler, J. P. O'Connell, M. J. Heller, Proc. Natl. Acad. Sci. U.S.A. 94, 1119 (1997); H. F. Arlinghaus, M. N. Kwoka, K. B. Jacobson, Anal. Chem. 69, 3747 (1997).
44. As an example of the cost of these devices, a slightly more compact version of the current design would yield about 30 devices per wafer. The costs for 25 silicon and glass substrates are about $600 and $200, respectively. The lithography ($500), ion implants and oxidation ($100), high-pass optical filter ($800), passivation layer ($200), and depositions ($500), along with laboratory fees ($1700) to process 25 wafers, would therefore be $3800, yielding a total device cost of just over $6 per device. An optimized design combined with a larger batch run could easily bring the cost down by at least an order of magnitude.
45. Supported by the National Center for Human Genome Research, NIH (R01-HG01044, R01-HG01406). We thank Becton Dickinson for its support during M.A.B.'s sabbatical and L. Lawton for her help in performing SDA. Computer files for generating the fabrication masks and for the computer instrumentation controls are available on request.