Multiplexed fluorescence detection in microfabricated devices with both time-resolved and spectral-discrimination capabilities using near-infrared fluorescence

Analytical Biochemistry

Volumn 330, Issue 2, 2004, Pages 206-218

  Zhu, Li ^a   Stryjewski, Wieslaw J ^a   Soper, Steven A ^a  

^a LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

DNA sequencing; Microchip; Multiplexing; Near IR fluorescence; Time resolved

Indexed keywords

CAPILLARY ELECTROPHORESIS; COLOR; COLOR VISION; DNA SEQUENCES; GENE ENCODING; INFRARED DEVICES; MAXIMUM LIKELIHOOD ESTIMATION; MICROPROCESSOR CHIPS; MULTIPLEXING; OPTICAL FIBER FABRICATION; OPTICAL FIBERS; PARTICLE BEAMS; SEPARATION;

CAPILLARY GEL ELECTROPHORESIS; DNA SEQUENCING; ELECTROPHORETIC RESOLUTION; MAXIMUM LIKELIHOOD ESTIMATOR; MICROCHIP; NEAR-IR FLUORESCENCE; TIME-CORRELATED SINGLE PHOTON COUNTING; TIME-RESOLVED;

FLUORESCENCE;

ACRYLAMIDE DERIVATIVE; FLUORESCENT DYE;

ACCURACY; ANALYTICAL EQUIPMENT; ARTICLE; CALCULATION; CAPILLARY ELECTROPHORESIS; COLOR DISCRIMINATION; COMPUTER; DIODE LASER; DNA SEQUENCE; FLUORESCENCE ANALYSIS; FLUORESCENCE MICROSCOPE; FLUORESCENCE MICROSCOPY; GEL ELECTROPHORESIS; INFRARED RADIATION; NEAR INFRARED SPECTROSCOPY; PRIORITY JOURNAL;

EID: 2942566112     PISSN: 00032697     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ab.2004.03.047     Document Type: Article

References (52)

1. Chang K.Y., Force R.K. Time-resolved laser-induced fluorescence study on dyes used in DNA sequencing. Appl. Spectrosc. 47:2000;24-29
2. Lakowicz J.R. Radiative decay engineering: biophysical and biomedical applications. Anal. Biochem. 298:2001;1-24
3. Lieberwirth U., Arden-Jacob J., Drexhage K.H., Herten D.P., Muller R., Neumann M., Schulz A., Siebert S., Sagner G., Klingel S., Sauer M., Wolfrum J. Multiplex dye DNA sequencing in capillary gel electrophoresis by diode laser-based time-resolved fluorescence detection. Anal. Chem. 70:1998;4771-4779
4. Neumann M., Herten D.P., Dietrich A., Wolfrum J., Sauer M. Capillary array scanner for time-resolved detection and identification of fluorescently labelled DNA fragments. J. Chromatogr. A. 871:2000;299-310
5. Sauer M., Arden-Jacob J., Drexhage K.H., Gobel F., Lieberwirth U., Muhlegger K., Muller R., Wolfrum J., Zander C. Time-resolved identification of individual mononucleotide molecules in aqueous solution with pulsed semiconductor lasers. Bioimaging. 6:1998;14-24
6. Sauer M., Angerer B., Han K.T., Zander C. Detection and identification of single dye labeled mononucleotide molecules released from an optical fiber in a microcapillary: first steps towards a new single molecule DNA sequencing technique. Phys. Chem. Chem. Phys. 1:1999;2471-2477
7. Sauer M., Angerer B., Ankenbauer W., Foldes-Papp Z., Gobel F., Han K.T., Rigler R., Schulz A., Wolfrum J., Zander C. Single molecule DNA sequencing in submicrometer channels: state of the art and future prospects. J. Biotechnol. 86:2001;181-201
8. Seeger S., Bachteler G., Drexhage K.H., Ardenjacob J., Deltau G., Galla K., Han K.T., Muller R., Kollner M., Rumphorst A., Sauer M., Schulz A., Wolfrum J. Biodiagnostics and polymer identification with multiplex dyes. J. Ber. Buns.-Ges.-Phys. Chem. Chem. Phys. 97:1993;1542-1548
9. Waddell E., Wang Y., Stryjewski W., McWhorter S., Henry A.C., Evans D., McCarley R.L., Soper S.A. High-resolution near-infrared imaging of dna microarrays with time-resolved acquisition of fluorescence lifetimes. Anal. Chem. 72:2000;5907-5917
10. Waddell E., Lassiter S., Owens C.V., Soper S.A. Time-resolved near-IR fluorescence detection in capillary electrophoresis. J. Liq. Chromatogr. Relat. Technol. 23:2000;1139-1158
11. Zhang Y.L., Soper S.A., Middendorf L.R., Wurm J.A., Erdmann R., Wahl M. Simple near-infrared time-correlated single photon counting instrument with a pulsed diode laser and avalanche photodiode for time-resolved measurements in scanning application. Appl. Spectrosc. 53:1999;497-504
12. Lassiter S.J., Stryjewski W., Legendre B.J., Erdmann R., Wahl M., Wurm J., Peterson R., Middendorf L., Soper S.A. Time-resolved fluorescence imaging of slab gels for lifetime base-calling in DNA sequencing applications. Anal. Chem. 72:2000;5373-5382
13. Soper S.A., Flanagan J.H., Legendre B.L., Williams D.C., Hammer R.P. Near-infrared, laser-induced fluorescence detection for DNA sequencing applications. IEEE J. Sel. Top. Quantum Electron. 2:1996;1129-1139
14. Soper S.A., Legendre B.L., Williams D.C. Online fluorescence lifetime determinations in capillary electrophoresis. Anal. Chem. 67:1995;4358-4365
15. Lassiter S.J., Stryjewski W., Owens C.V., Flanagan J.H., Hammer R.P., Khan S., Soper S.A. Optimization of sequencing conditions using near-infrared lifetime identification methods in capillary gel electrophoresis. Electrophoresis. 23:2002;1480-1489
16. Lassiter S.J., Stryjewski W.J., Wang Y., Soper S.A. Shedding light on DNA analysis multiplexed detection and identification using fluorescence lifetime methods. Spectroscopy. 17:2002;14-+
17. Flanagan J.H., Owens C.V., Romero S.E., Waddell E., Kahn S.H., Hammer R.P., Soper S.A. Near-Infrared heavy-atom-modified fluorescent dyes for base-calling in DNA-sequencing applications using temporal discrimination. Anal. Chem. 70:1998;2676-2684
18. Zhu L., Stryjewski W.J., Lassiter S.J., Soper S.A. Fluorescence multiplexing with time-resolved and spectral discrimination using a near-IR detector. Anal. Chem. 75:2003;2280-2291
19. Nunnally B.K., He H., Li L.C., Tucker S.A., McGown L.B. Characterization of visible dyes for four-decay fluorescence detection in DNA sequencing. Anal. Chem. 69:1997;2392-2397
20. He H., Nunnally B.K., Li L.C., McGown L.B. On-the-fly fluorescence lifetime detection of dye-labeled DNA primers for multiplex analysis. Anal. Chem. 70:1998;3413-3418
21. He H., McGown L.B. DNA sequencing by capillary electrophoresis with four-decay fluorescence detection. Anal. Chem. 72:2000;5865-5873
22. Li L.J., McGown L.B. Comparison of sieving matrices for on-the-fly fluorescence lifetime detection of dye-labeled DNA fragments. Fresenius J. Anal. Chem. 369:2001;267-272
23. Li L.C., McGown L.B. Improving signal to background ratio for on-the-fly fluorescence lifetime detection in capillary electrophoresis. Electrophoresis. 21:2000;1300-1304
24. Li L.J., McGown L.B. Effects of gel material on fluorescence lifetime detection of dyes and dye-labeled DNA primers in capillary electrophoresis. J. Chromatogr. A. 841:1999;95-103
25. Li L.C., He H., Nunnally B.K., McGown L.B. On-the-fly fluorescence lifetime detection of labeled DNA primers. J. Chromatogr. B. 695:1997;85-92
26. Li L.C., McGown L.B. On-the-fly frequency-domain fluorescence lifetime detection in capillary electrophoresis. Anal. Chem. 68:1996;2737-2743
27. McIntosh S.L., Nunnally B.K., Nesbit A.R., Deligeorgiev T.G., Gadjev N.I., McGown L.B. Fluorescence lifetime for on-the-fly multiplex detection of DNA restriction fragments in capillary electrophoresis. Anal. Chem. 72:2000;5444-5449
28. Soper S.A., Legendre B.L. Error analysis of simple algorithms for determining fluorescence lifetimes in ultradilute dye solutions. Appl. Spectrosc. 48:1994;400-405
29. Schmalzing D., Adourian A., Koutny; L., Ziaugra L., Matsudaira P., Ehrlich D. DNA sequencing on microfabricated electrophoretic devices. Anal. Chem. 70:1998;2303-2310
30. Schmalzing D., Tsao N., Koutny L., Chisholm D., Srivastaba A., Adourian A., Linton L., McEwan P., Matsudaira P., Ehrlich D. Toward real-world sequencing by microdevice electrophoresis. Genome Res. 9:1999;853-858
31. Koutny L., Schmalzing D., Salas-Solano O., El-Difrawy S., Adourian A., Buonocore S., Abbey K., McEwan P., Matsudaira P., Ehrlich D. Eight hundred-base sequencing in a microfabricated electrophoretic device. Anal. Chem. 72:2000;3388-3391
32. Liu S., Shi Y., Ja W.W., Mathies R.A. Optimization of high-speed DNA sequencing on microfabricated capillary electrophoresis channels. Anal. Chem. 71:1999;566-573
33. Backhouse C., Caamano M., Oaks F., Nordman E., Carrillo A., Johnson B., Bay S. DNA sequencing in a monolithic microchannel device. Electrophoresis. 21:2000;150-156
34. Paegel B.M., Emrich C.A., Wedemayer G.J., Scherer J.R., Mathies R.A. High throughput DNA sequencing with a microfabricated 96-lane capillary array electrophoresis bioprocessor. Proc. Natl. Acad. Sci. USA. 99:2002;574-579
35. Liu S., Ren H., Gao Q., Roach D.J., Loder R.T. Jr., Armstrong T.M., Mao Q., Blaga I., Barker D.L., Jovanovich S.B. Automated parallel DNA sequencing on multiple channel microchips. Proc. Natl. Acad. Sci. USA. 97:2000;5369-5374
36. Hall P., Selinger B. Better estimates of multiexponential decay parameters. Z. Phys. Chem. Neue Folge. 141:1984;77-89
37. Hall P., Selinger B. Better estimates of exponential decay parameters. J. Phys. Chem. 85:1981;2941-2946
38. Wu S., Dovichi N.J. High-sensitivity fluorescence detector for fluorescein isothiocyanate derivatives of amino acids separated by capillary zone electrophoresis. J. Chromatogr. 480:1989;141
39. Elkin C.J., Richardson P.M., Fourcade H.M., Hammon N.M., Pollard M.J., Predki P.F., Glavina T., Hawkins T.L. High-throughput plasmid purification for capillary sequencing. Genome Res. 11:2001;1269-1274
40. Deangelis M.M., Wang D.G., Hawkins T.L. Solid-phase reversible immobilization for the isolation of PCR products. Nucleic Acids Res. 23:1995;4742-4743
41. Hawkins T.L., McKernan K.J., Jacotot L.B., MacKenzie B., Richardson P.M., Lander E.S. DNA sequencing: a magnetic attraction to high-throughput genomics. Science. 276:1997;1887-1889
42. Hawkins T.L., Oconnormorin T., Roy A., Santillan C. DNA purification and isolation using a solid-phase. Nucleic Acids Res. 22:1994;4543-4544
43. Elkin C.;, Kapur N., Smith T., Humphries D., Pollard M.J., Hammon N.M., Hawkins T. Magnetic bead purification of labeled DNA fragments for high-throughput capillary electrophoresis sequencing. BioTechniques. 32:2002;1296-1302
44. Ruiz-Martinez M.C., Salas-Solano O., Carrilho E., Kotler L., Karger B.L. A sample purification method for rugged and high-performance DNA sequencing by capillary electrophoresis using replaceable polymer solutions. A. Development of the cleanup protocol. Anal. Chem. 70:1998;1516-1527
45. Salas-Solano O., Ruiz-Martinez M.C., Carrilho E., Kotler L., Karger B.L. A sample purification method for rugged and high-performance DNA sequencing by capillary electrophoresis using replaceable polymer solutions. B. Quantitative determination of the role of sample matrix components on sequencing analysis. Anal. Chem. 70:1998;1528-1535
46. Salas-Solano O., Carrilho E., Kotler L., Miller A.W., Goetzinger W., Sosic Z., Karger B.L. Routine DNA sequencing of 1000 bases in less than one hour by capillary electrophoresis with replaceable linear polyacrylamide solutions. Anal. Chem. 70:1998;3996-4003
47. Oleschuk R.D., Shultz-Lockyear L.L., Ning Y.B., Harrison D.J. Trapping of bead-based reagents within microfluidic systems: on-chip solid-phase extraction and electrochromatography. Anal. Chem. 72:2000;585-590
48. Yu C., Davey M.H., Svec F., Frechet J.M.J. Monolithic porous polymer for on-chip solid-phase extraction and preconcentration prepared by photoinitiated in situ polymerization within a microfluidic device. Anal. Chem. 73:2001;5088-5096
49. Olsen K.G., Ross D.J., Tarlov M.J. Immobilization of DNA hydrogel plugs in microfluidic channels. Anal. Chem. 74:2002;1436-1441
50. Ross D., Locascio L.E. Microfluidic temperature gradient focusing. Anal. Chem. 74:2002;2556-2564
51. Tian H.J., Huhmer A.F.R., Landers J.P. Evaluation of silica resins for direct and efficient extraction of DNA from complex biological matrices in a miniaturized format. Anal. Biochem. 283:2000;175-191
52. Paegel B.M., Yeung S.H., Mathies R.A. Microchip bioprocessor for integrated nanovolume sample purification and DNA sequencing. Anal. Chem. 74:2002;5092-5098