Prior to purification, amplified libraries can be visualized using gel electrophoresis, however the low concentration of the amplified materials requires a 5% TBE polyacrylamide gel optimized for sensitivity. We find that adding 0.6x SYBR Green I to libraries provides excellent signal-to-noise without the need for post-staining. We routinely load 15 ng of 100 bp NEB ladder with 0.6x SYBR Green I as a DNA marker. Although, in principle any instrument containing a blue-light source or imaging systems equipped with a laser that emits at 488 nm can be used to visualize DNA stained with SYBR Green I dye, we use the Typhoon TRIO Variable Mode Imager from Amersham Biosciences for improved sensitivity. Images are best obtained by digitizing at 100 microns pixel size resolution with a 520 nm band-pass emission filter to screen out reflected and scattered excitation light and background fluorescence, see Figure 2a for an example.
