Hybridization and Selective Release of DNA Microarrays

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DNA microarrays contain sequence specific probes arrayed in distinct spots numbering from 10,000 to over 1,000,000, depending on the platform. This tremendous degree of multiplexing gives microarrays great potential for environmental background sampling, broad-spectrum clinical monitoring, and continuous biological threat detection. In practice, their use in these applications is not common due to limited information content, long processing times, and high cost. The work focused on characterizing the phenomena of microarray hybridization and selective release that will allow these limitations to be addressed. This will revolutionize the ways that microarrays can be used for LLNL's Global Security missions. The goals ... continued below

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PDF-file: 7 pages; size: 4.5 Mbytes

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Beer, N R; Baker, B; Piggott, T; Maberry, S; Hara, C M; DeOtte, J et al. November 29, 2011.

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DNA microarrays contain sequence specific probes arrayed in distinct spots numbering from 10,000 to over 1,000,000, depending on the platform. This tremendous degree of multiplexing gives microarrays great potential for environmental background sampling, broad-spectrum clinical monitoring, and continuous biological threat detection. In practice, their use in these applications is not common due to limited information content, long processing times, and high cost. The work focused on characterizing the phenomena of microarray hybridization and selective release that will allow these limitations to be addressed. This will revolutionize the ways that microarrays can be used for LLNL's Global Security missions. The goals of this project were two-fold: automated faster hybridizations and selective release of hybridized features. The first study area involves hybridization kinetics and mass-transfer effects. the standard hybridization protocol uses an overnight incubation to achieve the best possible signal for any sample type, as well as for convenience in manual processing. There is potential to significantly shorten this time based on better understanding and control of the rate-limiting processes and knowledge of the progress of the hybridization. In the hybridization work, a custom microarray flow cell was used to manipulate the chemical and thermal environment of the array and autonomously image the changes over time during hybridization. The second study area is selective release. Microarrays easily generate hybridization patterns and signatures, but there is still an unmet need for methodologies enabling rapid and selective analysis of these patterns and signatures. Detailed analysis of individual spots by subsequent sequencing could potentially yield significant information for rapidly mutating and emerging (or deliberately engineered) pathogens. In the selective release work, optical energy deposition with coherent light quickly provides the thermal energy to single spots to release hybridized DNA. This work leverages LLNL expertise in optics, microfluids, and bioinformatics.

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PDF-file: 7 pages; size: 4.5 Mbytes

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  • Report No.: LLNL-TR-519311
  • Grant Number: W-7405-ENG-48
  • DOI: 10.2172/1033734 | External Link
  • Office of Scientific & Technical Information Report Number: 1033734
  • Archival Resource Key: ark:/67531/metadc837272

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Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

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  • November 29, 2011

Added to The UNT Digital Library

  • May 19, 2016, 3:16 p.m.

Description Last Updated

  • Dec. 8, 2016, 8:13 p.m.

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Beer, N R; Baker, B; Piggott, T; Maberry, S; Hara, C M; DeOtte, J et al. Hybridization and Selective Release of DNA Microarrays, report, November 29, 2011; Livermore, California. (digital.library.unt.edu/ark:/67531/metadc837272/: accessed December 13, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.