Fluorescence detection applied to nonelectrophoretic DNA diagnostics on oligonucleotide arrays

Jeffrey T. Ives, Yu Hui M Rogers, Valery L. Bogdanov, Eric Z. Huang, Michael Boyce-Jacino, Philip Goelet

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

DNA analysis based on template hybridization (or hybridization plus enzymatic processing) to an array of surface-bound oligonucleotides is well suited for high density, parallel, low cost and automatable processing. Direct fluorescence detection of labelled DNA provides the benefits of linearity, large dynamic range, multianalyte detection, processing simplicity and safe handling at reasonable cost. Molecular Tool has applied a proprietary enzymatic method of solid phase genotyping (Genetic Bit TM Analysis or GBA TM) to DNA processing in 96-well plates and glass microscope slides. Glass slides are an inexpensive, convenient format with relatively low fluorescence and the capability for microfabrication of miniature arrays of oligonucleotides. Detecting the fluor-labelled GBA TM dideoxynucleotides requires a detection limit of approximately 100 molecules/micrometer 2. Commercially available plate readers detect about 1000 molecules/micrometer 2, and an experimental setup with an Ar laser and thermoelectrically-cooled CCD can detect approximately 1 order of magnitude less signal. The current limit is due to glass fluorescence, and data is presented describing experimental modifications and analysis to improve the performance. Dideoxynucleotides labelled with fluorescein, eosin, tetramethylrhodamine, Lissamine and Texas Red are being characterized, and photobleaching, quenching and indirect detection with fluorogenic substrates have been investigated.

Original languageEnglish (US)
Title of host publicationProceedings of SPIE - The International Society for Optical Engineering
EditorsGerald E. Cohn, Steven A. Soper, C.H.W. Chen
Pages258-269
Number of pages12
Volume2680
StatePublished - 1996
Externally publishedYes
EventUltrasensitive Biochemical Diagnostics - San Jose, CA, USA
Duration: Jan 31 1996Feb 2 1996

Other

OtherUltrasensitive Biochemical Diagnostics
CitySan Jose, CA, USA
Period1/31/962/2/96

Fingerprint

oligonucleotides
Oligonucleotides
Fluorescence
Diagnostics
DNA
deoxyribonucleic acid
Dideoxynucleotides
fluorescence
Processing
chutes
Glass
micrometers
glass
Molecules
Safe handling
Photobleaching
Microfabrication
Detection Limit
Quenching
readers

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Condensed Matter Physics
  • Computer Science Applications
  • Electrical and Electronic Engineering
  • Applied Mathematics

Cite this

Ives, J. T., Rogers, Y. H. M., Bogdanov, V. L., Huang, E. Z., Boyce-Jacino, M., & Goelet, P. (1996). Fluorescence detection applied to nonelectrophoretic DNA diagnostics on oligonucleotide arrays. In G. E. Cohn, S. A. Soper, & C. H. W. Chen (Eds.), Proceedings of SPIE - The International Society for Optical Engineering (Vol. 2680, pp. 258-269)

Fluorescence detection applied to nonelectrophoretic DNA diagnostics on oligonucleotide arrays. / Ives, Jeffrey T.; Rogers, Yu Hui M; Bogdanov, Valery L.; Huang, Eric Z.; Boyce-Jacino, Michael; Goelet, Philip.

Proceedings of SPIE - The International Society for Optical Engineering. ed. / Gerald E. Cohn; Steven A. Soper; C.H.W. Chen. Vol. 2680 1996. p. 258-269.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Ives, JT, Rogers, YHM, Bogdanov, VL, Huang, EZ, Boyce-Jacino, M & Goelet, P 1996, Fluorescence detection applied to nonelectrophoretic DNA diagnostics on oligonucleotide arrays. in GE Cohn, SA Soper & CHW Chen (eds), Proceedings of SPIE - The International Society for Optical Engineering. vol. 2680, pp. 258-269, Ultrasensitive Biochemical Diagnostics, San Jose, CA, USA, 1/31/96.
Ives JT, Rogers YHM, Bogdanov VL, Huang EZ, Boyce-Jacino M, Goelet P. Fluorescence detection applied to nonelectrophoretic DNA diagnostics on oligonucleotide arrays. In Cohn GE, Soper SA, Chen CHW, editors, Proceedings of SPIE - The International Society for Optical Engineering. Vol. 2680. 1996. p. 258-269
Ives, Jeffrey T. ; Rogers, Yu Hui M ; Bogdanov, Valery L. ; Huang, Eric Z. ; Boyce-Jacino, Michael ; Goelet, Philip. / Fluorescence detection applied to nonelectrophoretic DNA diagnostics on oligonucleotide arrays. Proceedings of SPIE - The International Society for Optical Engineering. editor / Gerald E. Cohn ; Steven A. Soper ; C.H.W. Chen. Vol. 2680 1996. pp. 258-269
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