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Fingerprinting of single viral genomes

We demonstrate the use of technology developed for optical mapping to acquire DNA fingerprints from single genomes for the purpose of discrimination and identification of bacteria and viruses. Single genome fingerprinting (SGF) provides not only the size but also the order of the restriction fragmen...

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Published in:Analytical biochemistry 2005-02, Vol.337 (2), p.278-288
Main Authors: Ferris, Matthew M., Yoshida, Thomas M., Marrone, Babetta L., Keller, Richard A.
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description We demonstrate the use of technology developed for optical mapping to acquire DNA fingerprints from single genomes for the purpose of discrimination and identification of bacteria and viruses. Single genome fingerprinting (SGF) provides not only the size but also the order of the restriction fragments, which adds another dimension to the information that can be used for discrimination. Analysis of single organisms may eliminate the need to culture cells and thereby significantly reduce analysis time. In addition, samples containing mixtures of several organisms can be analyzed. For analysis, cells are embedded in an agarose matrix, lysed, and processed to yield intact DNA. The DNA is then deposited on a derivatized glass substrate. The elongated genome is digested with a restriction enzyme and stained with the intercalating dye YOYO-1. DNA is then quantitatively imaged with a fluorescence microscope and the fragments are sized to an accuracy ⩾90% by their fluorescence intensity and contour length. Single genome fingerprints were obtained from pure samples of adenovirus, from bacteriophages λ and T4 GT7, and from a mixture of the three viral genomes. SGF will enable the fingerprinting of uncultured and unamplified samples and allow rapid identification of microorganisms with applications in forensics, medicine, public health, and environmental microbiology.
doi_str_mv 10.1016/j.ab.2004.10.050
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subjects Adenovirus
Calibration
DNA
DNA Fingerprinting - methods
DNA, Viral - analysis
DNA, Viral - genetics
Fingerprint
Fluorescence
Fluorescence microscopy
Genome, Viral
Imaging
Particle Size
Single genome
Virus
title Fingerprinting of single viral genomes
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