SYBR Green II

General information

• nucleic acid dye, better for RNA
• membrane permeant
• excited by 488 laser (maximally at 497 nm with secondary excitation peak at 254nm)
• SYBR Green II stained RNA fluoresces green (maximum emission at 521 nm)
• tends to be used as a gel stain more often but also cited in flow cytometry
• Staining agarose/formaldehyde gels with SYBR Green II does not interfere with the transfer of RNA to membranes or subsequent hybridization in Northern blot analysis as long as 0.1% -0.3% SDS is included in prehybridization and hybridization buffers to remove the dye.
• SYBR Green II is not selective for RNA staining but does exhibit a higher quantum yield when bound to RNA (~0.54) than to double-stranded DNA (~0.36).
• The fluorescence quantum yield of the RNA/SYBR Green II complex is over seven times greater than that of the RNA/ethidium bromide complex (~0.07).

Detection limits

• The detection limit is 500 pg of RNA per band in non-denaturing gels with 300 nm transillumination.
• Can detect down to 100 pg with 254 nm epi-illumination).
• On denaturing agarose/formaldehyde gels and polyacrylamide/urea gels, the sensitivity of SYBR Green II RNA gel stain is reduced, though still superior to that of ethidium bromide. Without any washing or destaining steps, SYBR Green II can detect as little as 1 ng RNA per band in agarose/formaldehyde gel or polyacrylamide/urea gel using 254 nm epi-illumination, and about 4 ng RNA per band using 300 nm trans illumination.

Reference

• Sigma-Aldrich technical bulletin (source of much of the information above)
• Product Information from Molecular Probes