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Applied and Environmental Microbiology, September 2003, p. 5673-5678, Vol. 69, No. 9
0099-2240/03/$08.00+0     DOI: 10.1128/AEM.69.9.5673-5678.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Use of DNA and Peptide Nucleic Acid Molecular Beacons for Detection and Quantification of rRNA in Solution and in Whole Cells

Chuanwu Xi,1,2 Michal Balberg,2 Stephen A. Boppart,2,3 and Lutgarde Raskin1,2*

Department of Civil and Environmental Engineering,1 Department of Electrical and Computer Engineering and Bioengineering Program,3 Beckman Institute for Advanced Sciences and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 618012

Received 17 March 2003/ Accepted 16 June 2003

DNA and peptide nucleic acid (PNA) molecular beacons were successfully used to detect rRNA in solution. In addition, PNA molecular beacon hybridizations were found to be useful for the quantification of rRNA: hybridization signals increased in a linear fashion with the 16S rRNA concentrations used in this experiment (between 0.39 and 25 nM) in the presence of 50 nM PNA MB. DNA and PNA molecular beacons were successfully used to detect whole cells in fluorescence in situ hybridization (FISH) experiments without a wash step. The FISH results with the PNA molecular beacons were superior to those with the DNA molecular beacons: the hybridization kinetics were much faster, the signal-to-noise ratio was much higher, and the specificity was much better for the PNA molecular beacons. Finally, it was demonstrated that the combination of the use of PNA molecular beacons in FISH and flow cytometry makes it possible to rapidly collect quantitative FISH data. Thus, PNA molecular beacons might provide a solution for limitations of traditional FISH methods, such as variable target site accessibility, poor sensitivity for target cells with low rRNA content, background fluorescence, and applications of FISH in microfluidic devices.

* Corresponding author. Mailing address: Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave., Urbana, IL 61801. Phone: (217) 333-6964. Fax: (217) 333-6968. E-mail: lraskin{at}uiuc.edu.

Applied and Environmental Microbiology, September 2003, p. 5673-5678, Vol. 69, No. 9
0099-2240/03/$08.00+0     DOI: 10.1128/AEM.69.9.5673-5678.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.



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