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Nucleic Acids Research, Vol 24, Issue 23 4759-4767, Copyright © 1996 by Oxford University Press

ARTICLES

Real-time imaging of the reorientation mechanisms of YOYO-labelled DNA molecules during 90 degrees and 120 degrees pulsed field gel electrophoresis

S Gurrieri, SB Smith, KS Wells, ID Johnson and C Bustamante
Dipartimento di Scienze Chimiche, Universita di Cantania, Italy. sgurrieri@dipchi.unict.it

Pulsed field gel electrophoresis (PFGE) techniques have been developed to overcome the limitations of conventional electrophoresis and to increase the separation to DNA chromosomes of few megabase pairs in size. Despite of the large success of these techniques, the various separation protocols employed for PFGE experiments have been determined empirically. However, a deep understanding of the molecular mechanisms of motion responsible for DNA separation becomes necessary for the rational optimization of these techniques. This paper shows the first clear observations of individual molecules of DNA during the reorientation process in 90 degrees PFGE and 120 degrees PFGE. Real- time visualization of the DNA dynamics during PFGE was possible with the use of an epi-illumination fluorescence microscope specifically equipped to run these experiments and by staining the DNA with YOYO-1 (1,1'-(4,4,7,7-tetramethyl-4,7-diazaundecamethylene)-bis-4-[3-meth yl - 2,3-dihydro-(benzo-1,3-oxazole)-2-methyl-idene]-quinolinium tetraiodide). This dye forms a very stable, highly fluorescent complex with double-stranded DNA and dramatically improves the quality of the DNA images. The results of computer simulations used to reproduce the molecular mechanisms of motion as well as the DNA separation features are also discussed.
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 Proc. Natl. Acad. Sci. USAHome page
S. Gurrieri, S. B. Smith, and C. Bustamante
Trapping of megabase-sized DNA molecules during agarose gel electrophoresis
PNAS, January 19, 1999; 96(2): 453 - 458.
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