After electrophoretic separation of nucleic acid samples, you are ready to stain your DNA gels, image, and analyze. With LI-COR, you have imaging options.
Use the D-DiGit® Gel Scanner to image and extract DNA bands without concern for UV damage to your DNA samples or the hazards related to UV light and ethidium bromide. You can scan nucleic acid gels (large or small; image area: 17.8 cm x 12.7 cm), excise bands, document your work and analyze your data with this compact, easy-to- use gel scanner. After capture, images can be imported into Image Studio™ Lite Software for convenient analysis, annotation and storage.
See the complete list of safe stains compatible with the D-DiGit Scanner.
Use the 700nm channel of Odyssey® CLx Imager (image area: 25 cm x 25 cm), Odyssey Sa Imager, or Odyssey Fc Imager (Figure 1) to image DNA gels stained with SYTO® 60 fluorescent nucleic acid stain.
For more information, read the detailed protocol entitled Imaging Nucleic Acids Gels on the Odyssey Fc Imager. You can also refer to SYTO 60 Staining of Nucleic Acids in Gels for protocols on how to use near-infrared fluorescent dyes to stain nucleic acids and image on Odyssey Imaging Systems.
Sensitivity is high and background fluorescence is low when using SYTO 60 red fluorescent nucleic acid stain to visualize DNA gels on the LI-COR Odyssey Infrared Imagers. The detection sensitivity and lower limit of detection for SYTO 60 with any of the Odyssey Imagers are better than those of ethidium bromide detected with either a Polaroid camera or a CCD imaging system.
If you need to image ethidium bromide, SYBR Safe DNA stains, or other DNA stains in your nucleic acid gels in the 600nm region, use the Odyssey Fc Imaging System.
Table 1. SYTO 60: Limit of Detection (LOD) with Odyssey Imaging
DNA Fragment (bp) | LOD (pg) | LOD (fmol) |
---|---|---|
100 | 375 | 5.7 |
500 | 95 | 0.29 |
1500 | 44 | 0.044 |
Table 2. Ethidium Bromide: Limit of Detection (LOD) with Polaroid Imaging
DNA Fragment (bp) | LOD (pg) | LOD (fmol) |
---|---|---|
100 | 3000 | 45 |
500 | 1500 | 4.5 |
1500 | 700 | 0.7 |
Table 3. Ethidium Bromide: Limit of Detection (LOD) with CCD Imaging
DNA Fragment (bp) | LOD (pg) | LOD (fmol) |
---|---|---|
100 | 750 | 11.4 |
500 | 375 | 1.14 |
1500 | 175 | 0.18 |
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 Classic, Odyssey Sa, and Odyssey Fc Imaging Systems using the 700nm channel.
This 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 result the user desires.
Stain | Dilution | Staining Method | Cost |
---|---|---|---|
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) |