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DNA Gel Staining Cost Comparisons

DNA staining with either Ethidium bromide or Syto 60

Figure 1. Comparison of DNA in Agarose Gels Stained With Syto60 and Ethidium Bromide and Imaged with the Odyssey Classic, the Odyssey Fc and a UV Transilluminator to Acquire a Polaroid Film Image. A 1.2% agarose gel was imaged using the Odyssey Imaging System (panel A), Odyssey Fc Imaging System (panel B) or a UV transilluminator and the image captured using Polaroid 667 film (Panel C). Lane 1) 1µg 1Kb ladder Lane 2) 0.5 µg 1Kb ladder Lane 3) 0.25 µg 1Kb ladder Lane 4) 0.5 µg pUC 19 Lane 5) 0.5 µg pUC19/HindIII / XmnI Lane 6) 1 µg 50bp ladder Lane 7) 0.5 µg 50bp ladder Lane 8) 0.25 µg 50bp ladder. The gel was electrophoresed for 8 V/cm in 1X TAE buffer for 1 hr. The Odyssey intensity setting for the 700 nm channel was 8 and focus offset was 0.5 with the gel face down. The Odyssey Fc acquisition was 2 minutes, gel face up.

Syto® dyes are cell-permeant cyanine dyes that bind to nucleic acids. Nucleic acids stained with the Syto 60 stain can be detected and quantified on the Odyssey® CLx, Odyssey Sa, and Odyssey Fc Imaging Systems using the 700nm channel. LI-COR's application note, Syto® 60 Staining of Nucleic Acids in Gels (2010), presents 3 methods for using the Syto 60 stain. The choice of method depends on the end result the user desires. The purpose of method I is to obtain an archivable, digital image of a DNA agarose gel using an Odyssey Imaging System. Method II is used if digital image with an Odyssey Imaging Systems is required prior to visualizing DNA bands on a UV transilluminator for excision of target bands. Method III is a post-staining method that can be used if the time to obtain the DNA image is not restricted as this method requires at least 45 minutes post electrophoresis staining and also uses more concentrated stain.

Cost Comparisons

Dilution Staining Method
Syto 60 stain 1:1000 Method I or II $0.006 (1µI/well, 8 wells)
Syto 60 stain 1:20000 Method I $0.0003 (1µI/well, 8 wells)
Syto 60 stain 1:2500 Method III $7.44 (25 ml)
EtBr 1:500 Method II $0.00007 (1µI/well, 8 wells)
EtBr 1:2000 Method III $0.05 (25 ml)

1. Syto 60 Staining of Nucleic Acids on Gels LI-COR Biosciences (2010)



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