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Applied and Environmental Microbiology, February 2006, p. 1688-1691, Vol. 72, No. 2
0099-2240/06/$08.00+0     doi:10.1128/AEM.72.2.1688-1691.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

SHORT REPORT

Improvement of Oligonucleotide Probe Design Criteria for Functional Gene Microarrays in Environmental Applications{dagger}

Jost Liebich,1,2 Christopher W. Schadt,1 Song C. Chong,1 Zhili He,1 Sung-Keun Rhee,1,3 and Jizhong Zhou1*

Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,1 Agrosphere Institute (ICG IV), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany,2 Department of Microbiology, Chungbuk National University, Cheungju 361-763, Korea3

Received 9 June 2005/ Accepted 18 November 2005

To optimize oligonucleotide probe design criteria, PCR products with different similarities to probes were hybridized to a functional gene microarray designed to detect homologous genes from different organisms. In contrast to more restrictive probe designs based on a single criterion, simultaneous consideration of the percent similarity (≤90%), the length of identical sequence stretches (≤20 bases), and the binding free energy (≥–35 kcal mol–1) was found to be predictive of probe specificity.

* Corresponding author. Present address: Institute for Environmental Genomics, University of Oklahoma, Stephenson Research & Technology Center, 101 David L. Boren Blvd., Norman, OK 73019. Phone: (405) 325-6073. Fax: (405) 325-3442. E-mail: jzhou{at}ou.edu.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, February 2006, p. 1688-1691, Vol. 72, No. 2
0099-2240/06/$08.00+0     doi:10.1128/AEM.72.2.1688-1691.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

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  • He, Z., Zhou, J. (2008). Empirical Evaluation of a New Method for Calculating Signal-to-Noise Ratio for Microarray Data Analysis. Appl. Environ. Microbiol. 74: 2957-2966 [Abstract] [Full Text]  
  • Miller, S. M., Tourlousse, D. M., Stedtfeld, R. D., Baushke, S. W., Herzog, A. B., Wick, L. M., Rouillard, J. M., Gulari, E., Tiedje, J. M., Hashsham, S. A. (2008). In Situ-Synthesized Virulence and Marker Gene Biochip for Detection of Bacterial Pathogens in Water. Appl. Environ. Microbiol. 74: 2200-2209 [Abstract] [Full Text]  
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