This Article
Right arrow Full Text
Right arrow Full Text (PDF)
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 Bavykin, S. G.
Right arrow Articles by Mirzabekov, A. D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bavykin, S. G.
Right arrow Articles by Mirzabekov, A. D.
Agricola
Right arrow Articles by Bavykin, S. G.
Right arrow Articles by Mirzabekov, A. D.

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, February 2001, p. 922-928, Vol. 67, No. 2
0099-2240/01/$04.00+0   DOI: 10.1128/AEM.67.2.922-928.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

Portable System for Microbial Sample Preparation and Oligonucleotide Microarray Analysis

Sergei G. Bavykin,1 James P. Akowski,1 Vladimir M. Zakhariev,2 Viktor E. Barsky,2 Alexander N. Perov,2 and Andrei D. Mirzabekov1,2,*

BioChip Technology Center, Argonne National Laboratory, Argonne, Illinois 60439,1 and Engelhardt Institute of Molecular Biology, Moscow 117984, Russia2

Received 5 June 2000/Accepted 7 November 2000

We have developed a three-component system for microbial identification that consists of (i) a universal syringe-operated silica minicolumn for successive DNA and RNA isolation, fractionation, fragmentation, fluorescent labeling, and removal of excess free label and short oligonucleotides; (ii) microarrays of immobilized oligonucleotide probes for 16S rRNA identification; and (iii) a portable battery-powered device for imaging the hybridization of fluorescently labeled RNA fragments with the arrays. The minicolumn combines a guanidine thiocyanate method of nucleic acid isolation with a newly developed hydroxyl radical-based technique for DNA and RNA labeling and fragmentation. DNA and RNA can also be fractionated through differential binding of double- and single-stranded forms of nucleic acids to the silica. The procedure involves sequential washing of the column with different solutions. No vacuum filtration steps, phenol extraction, or centrifugation is required. After hybridization, the overall fluorescence pattern is captured as a digital image or as a Polaroid photo. This three-component system was used to discriminate Escherichia coli, Bacillus subtilis, Bacillus thuringiensis, and human HL60 cells. The procedure is rapid: beginning with whole cells, it takes approximately 25 min to obtain labeled DNA and RNA samples and an additional 25 min to hybridize and acquire the microarray image using a stationary image analysis system or the portable imager.

* Corresponding author. Mailing address: BioChip Technology Center, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439. Phone: (630) 252-3161. Fax: (630) 252-9155. E-mail: amir{at}everest.bim.anl.gov.

Applied and Environmental Microbiology, February 2001, p. 922-928, Vol. 67, No. 2
0099-2240/01/$04.00+0   DOI: 10.1128/AEM.67.2.922-928.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.


This article has been cited by other articles:

  • Pozhitkov, A., Chernov, B., Yershov, G., Noble, P. A. (2005). Evaluation of Gel-Pad Oligonucleotide Microarray Technology by Using Artificial Neural Networks. Appl. Environ. Microbiol. 71: 8663-8676 [Abstract] [Full Text]  
  • Peytavi, R., Raymond, F. R., Gagne, D., Picard, F. J., Jia, G., Zoval, J., Madou, M., Boissinot, K., Boissinot, M., Bissonnette, L., Ouellette, M., Bergeron, M. G. (2005). Microfluidic Device for Rapid (<15 min) Automated Microarray Hybridization. Clin. Chem. 51: 1836-1844 [Abstract] [Full Text]  
  • Smoot, L.M., Smoot, J.C., Smidt, H., Noble, P.A., Konneke, M., McMurry, Z.A., Stahl, D.A. (2005). DNA Microarrays as Salivary Diagnostic Tools for Characterizing the Oral Cavity's Microbial Community. ADR 18: 6-11 [Full Text]  
  • Pemov, A., Modi, H., Chandler, D. P., Bavykin, S. (2005). DNA analysis with multiplex microarray-enhanced PCR. Nucleic Acids Res 33: e11-e11 [Abstract] [Full Text]  
  • Chandler, D. P., Jarrell, A. E. (2004). Automated Purification and Suspension Array Detection of 16S rRNA from Soil and Sediment Extracts by Using Tunable Surface Microparticles. Appl. Environ. Microbiol. 70: 2621-2631 [Abstract] [Full Text]  
  • Nasedkina, T. V., Zharinov, V. S., Isaeva, E. A., Mityaeva, O. N., Yurasov, R. N., Surzhikov, S. A., Turigin, A. Y., Rubina, A. Y., Karachunskii, A. I., Gartenhaus, R. B., Mirzabekov, A. D. (2003). Clinical Screening of Gene Rearrangements in Childhood Leukemia by Using a Multiplex Polymerase Chain Reaction-Microarray Approach. Clin. Cancer Res. 9: 5620-5629 [Abstract] [Full Text]  
  • Adamczyk, J., Hesselsoe, M., Iversen, N., Horn, M., Lehner, A., Nielsen, P. H., Schloter, M., Roslev, P., Wagner, M. (2003). The Isotope Array, a New Tool That Employs Substrate-Mediated Labeling of rRNA for Determination of Microbial Community Structure and Function. Appl. Environ. Microbiol. 69: 6875-6887 [Abstract] [Full Text]  
  • Sebat, J. L., Colwell, F. S., Crawford, R. L. (2003). Metagenomic Profiling: Microarray Analysis of an Environmental Genomic Library. Appl. Environ. Microbiol. 69: 4927-4934 [Abstract] [Full Text]  
  • Urakawa, H., El Fantroussi, S., Smidt, H., Smoot, J. C., Tribou, E. H., Kelly, J. J., Noble, P. A., Stahl, D. A. (2003). Optimization of Single-Base-Pair Mismatch Discrimination in Oligonucleotide Microarrays. Appl. Environ. Microbiol. 69: 2848-2856 [Abstract] [Full Text]  
  • Chandler, D. P., Newton, G. J., Small, J. A., Daly, D. S. (2003). Sequence versus Structure for the Direct Detection of 16S rRNA on Planar Oligonucleotide Microarrays. Appl. Environ. Microbiol. 69: 2950-2958 [Abstract] [Full Text]  
  • El Fantroussi, S., Urakawa, H., Bernhard, A. E., Kelly, J. J., Noble, P. A., Smidt, H., Yershov, G. M., Stahl, D. A. (2003). Direct Profiling of Environmental Microbial Populations by Thermal Dissociation Analysis of Native rRNAs Hybridized to Oligonucleotide Microarrays. Appl. Environ. Microbiol. 69: 2377-2382 [Abstract] [Full Text]  
  • Reyes-Lopez, M. A., Mendez-Tenorio, A., Maldonado-Rodriguez, R., Doktycz, M. J., Fleming, J. T., Beattie, K. L. (2003). Fingerprinting of prokaryotic 16S rRNA genes using oligodeoxyribonucleotide microarrays and virtual hybridization. Nucleic Acids Res 31: 779-789 [Abstract] [Full Text]  
  • Koizumi, Y., Kelly, J. J., Nakagawa, T., Urakawa, H., El-Fantroussi, S., Al-Muzaini, S., Fukui, M., Urushigawa, Y., Stahl, D. A. (2002). Parallel Characterization of Anaerobic Toluene- and Ethylbenzene-Degrading Microbial Consortia by PCR-Denaturing Gradient Gel Electrophoresis, RNA-DNA Membrane Hybridization, and DNA Microarray Technology. Appl. Environ. Microbiol. 68: 3215-3225 [Abstract] [Full Text]  
  • Lapa, S., Mikheev, M., Shchelkunov, S., Mikhailovich, V., Sobolev, A., Blinov, V., Babkin, I., Guskov, A., Sokunova, E., Zasedatelev, A., Sandakhchiev, L., Mirzabekov, A. (2002). Species-Level Identification of Orthopoxviruses with an Oligonucleotide Microchip. J. Clin. Microbiol. 40: 753-757 [Abstract] [Full Text]  
  • Urakawa, H., Noble, P. A., El Fantroussi, S., Kelly, J. J., Stahl, D. A. (2002). Single-Base-Pair Discrimination of Terminal Mismatches by Using Oligonucleotide Microarrays and Neural Network Analyses. Appl. Environ. Microbiol. 68: 235-244 [Abstract] [Full Text]  
  • Small, J., Call, D. R., Brockman, F. J., Straub, T. M., Chandler, D. P. (2001). Direct Detection of 16S rRNA in Soil Extracts by Using Oligonucleotide Microarrays. Appl. Environ. Microbiol. 67: 4708-4716 [Abstract] [Full Text]  
  • Mikhailovich, V., Lapa, S., Gryadunov, D., Sobolev, A., Strizhkov, B., Chernyh, N., Skotnikova, O., Irtuganova, O., Moroz, A., Litvinov, V., Vladimirskii, M., Perelman, M., Chernousova, L., Erokhin, V., Zasedatelev, A., Mirzabekov, A. (2001). Identification of Rifampin-Resistant Mycobacterium tuberculosis Strains by Hybridization, PCR, and Ligase Detection Reaction on Oligonucleotide Microchips. J. Clin. Microbiol. 39: 2531-2540 [Abstract] [Full Text]  
  • Zhang, Y., Price, B. D., Tetradis, S., Chakrabarti, S., Maulik, G., Makrigiorgos, G. M. (2001). Reproducible and inexpensive probe preparation for oligonucleotide arrays. Nucleic Acids Res 29: e66-e66 [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»