This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplemental material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by He, Z.
Right arrow Articles by Zhou, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by He, Z.
Right arrow Articles by Zhou, J.
Agricola
Right arrow Articles by He, Z.
Right arrow Articles by Zhou, J.

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, July 2005, p. 3753-3760, Vol. 71, No. 7
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.7.3753-3760.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Empirical Establishment of Oligonucleotide Probe Design Criteria{dagger}

Zhili He,1 Liyou Wu,1 Xingyuan Li,2 Matthew W. Fields,3 and Jizhong Zhou1*

Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,1 Harbin Institute of Technology, Harbin, Heilongjiang, China 150001,2 Department of Microbiology, Miami University, Oxford, Ohio 450563

Received 16 September 2004/ Accepted 6 January 2005

Criteria for the design of gene-specific and group-specific oligonucleotide probes were established experimentally via an oligonucleotide array that contained perfect match (PM) and mismatch probes (50-mers and 70-mers) based upon four genes. The effects of probe-target identity, continuous stretch, mismatch position, and hybridization free energy on specificity were tested. Little hybridization was observed at a probe-target identity of ≤85% for both 50-mer and 70-mer probes. PM signal intensities (33 to 48%) were detected at a probe-target identity of 94% for 50-mer oligonucleotides and 43 to 55% for 70-mer probes at a probe-target identity of 96%. When the effects of sequence identity and continuous stretch were considered independently, a stretch probe (>15 bases) contributed an additional 9% of the PM signal intensity compared to a nonstretch probe (≤15 bases) at the same identity level. Cross-hybridization increased as the length of continuous stretch increased. A 35-base stretch for 50-mer probes or a 50-base stretch for 70-mer probes had approximately 55% of the PM signal. Little cross-hybridization was observed for probes with a minimal binding free energy greater than –30 kcal/mol for 50-mer probes or –40 kcal/mol for 70-mer probes. Based on the experimental results, a set of criteria are suggested for the design of gene-specific and group-specific oligonucleotide probes, and the experimentally established criteria should provide valuable information for new software and algorithms for microarray-based studies.

* Corresponding author. Mailing address: Environmental Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6038. Phone: (865) 576-7544. Fax: (865) 576-8646. E-mail: zhouj{at}ornl.gov.

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

Applied and Environmental Microbiology, July 2005, p. 3753-3760, Vol. 71, No. 7
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.7.3753-3760.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Barbosa-Morais, N. L., Dunning, M. J., Samarajiwa, S. A., Darot, J. F. J., Ritchie, M. E., Lynch, A. G., Tavare, S. (2009). A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Res 0: gkp942v1-gkp942 [Abstract] [Full Text]  
  • Weckx, S., Allemeersch, J., Van der Meulen, R., Vrancken, G., Huys, G., Vandamme, P., Van Hummelen, P., De Vuyst, L. (2009). Development and Validation of a Species-Independent Functional Gene Microarray That Targets Lactic Acid Bacteria. Appl. Environ. Microbiol. 75: 6488-6495 [Abstract] [Full Text]  
  • Berthrong, S. T., Schadt, C. W., Pineiro, G., Jackson, R. B. (2009). Afforestation Alters the Composition of Functional Genes in Soil and Biogeochemical Processes in South American Grasslands. Appl. Environ. Microbiol. 75: 6240-6248 [Abstract] [Full Text]  
  • Xu, Q., Schlabach, M. R., Hannon, G. J., Elledge, S. J. (2009). Design of 240,000 orthogonal 25mer DNA barcode probes. Proc. Natl. Acad. Sci. USA 106: 2289-2294 [Abstract] [Full Text]  
  • Rouillard, J.-M., Gulari, E. (2009). OligoArrayDb: pangenomic oligonucleotide microarray probe sets database. Nucleic Acids Res 37: D938-D941 [Abstract] [Full Text]  
  • Srivastava, G. P., Guo, J., Shi, H., Xu, D. (2008). PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands. Bioinformatics 24: 1837-1842 [Abstract] [Full Text]  
  • Wu, L., Kellogg, L., Devol, A. H., Tiedje, J. M., Zhou, J. (2008). Microarray-Based Characterization of Microbial Community Functional Structure and Heterogeneity in Marine Sediments from the Gulf of Mexico. Appl. Environ. Microbiol. 74: 4516-4529 [Abstract] [Full Text]  
  • 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]  
  • Wei, H., Kuan, P. F., Tian, S., Yang, C., Nie, J., Sengupta, S., Ruotti, V., Jonsdottir, G. A., Keles, S., Thomson, J. A., Stewart, R. (2008). A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets. Nucleic Acids Res 36: 2926-2938 [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]  
  • Koltai, H., Weingarten-Baror, C. (2008). Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction. Nucleic Acids Res 36: 2395-2405 [Abstract] [Full Text]  
  • Pozhitkov, A. E., Tautz, D., Noble, P. A. (2007). Oligonucleotide microarrays: widely applied poorly understood. Brief Funct Genomic Proteomic 0: elm014v1-8 [Abstract] [Full Text]  
  • Feng, S., Tillier, E. R.M. (2007). A fast and flexible approach to oligonucleotide probe design for genomes and gene families. Bioinformatics 23: 1195-1202 [Abstract] [Full Text]  
  • Brukner, I., El-Ramahi, R., Gorska-Flipot, I., Krajinovic, M., Labuda, D. (2007). An in vitro selection scheme for oligonucleotide probes to discriminate between closely related DNA sequences. Nucleic Acids Res 35: e66-e66 [Abstract] [Full Text]  
  • Clark, M. E., He, Q., He, Z., Huang, K. H., Alm, E. J., Wan, X.-F., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J.-Z., Fields, M. W. (2006). Temporal Transcriptomic Analysis as Desulfovibrio vulgaris Hildenborough Transitions into Stationary Phase during Electron Donor Depletion. Appl. Environ. Microbiol. 72: 5578-5588 [Abstract] [Full Text]  
  • He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. (2006). Energetic Consequences of Nitrite Stress in Desulfovibrio vulgaris Hildenborough, Inferred from Global Transcriptional Analysis.. Appl. Environ. Microbiol. 72: 4370-4381 [Abstract] [Full Text]  
  • Liebich, J., Schadt, C. W., Chong, S. C., He, Z., Rhee, S.-K., Zhou, J. (2006). Improvement of Oligonucleotide Probe Design Criteria for Functional Gene Microarrays in Environmental Applications. Appl. Environ. Microbiol. 72: 1688-1691 [Abstract] [Full Text]  
  • Li, X., He, Z., Zhou, J. (2005). Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res 33: 6114-6123 [Abstract] [Full Text]  
  • He, Z., Wu, L., Fields, M. W., Zhou, J. (2005). Use of Microarrays with Different Probe Sizes for Monitoring Gene Expression. Appl. Environ. Microbiol. 71: 5154-5162 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»