SYBR Green I

General information

• nucleic acid dye, better for DNA
• membrane permeant
• excited by 488 laser (maximally excited at 497nm but has a second excitation peak near 254 nm.
• fluorescence emission of SBYR Green I-stained DNA is green (maximum at 521 nm)
• tends to be used as a gel stain more often
• The fluorescence quantum yield of the DNA/SYBR Green I complex (~0.8) is over five times greater than that of the DNA/ethidium bromide complex (~0.15).
• Gels can be precast with SYBR Green I; however, the greatest sensitivity is achieved with post-staining.
• The presence of SYBR Green I bound to DNA does not inhibit the activity of many common restriction endonucleases, including Hind III and EcoR I.1,2 SYBR Green I does not need to be removed for in-gel digestion and ligation techniques.
• Commonly used for Real-time PCR.

Detection limits in gels

• Detection limit is ~60 pg per band with 300 nm transillumination (down to 20 pg with 254 nm epi-Illumination). This sensitivity is 25 times greater than can be achieved with ethidium bromide using standard 300 nm transillumination.
• SYBR Green I can also be used to detect single-stranded DNA and RNA in denaturing agarose/formaldehyde and polyacrylamide/urea gels without any prewashing steps, although the sensitivity is lower (approximately 100 to 300 pg per band using 254 nm epi-illumination).
• SYBR Green I is also a very sensitive stain for oligonucleotides, allowing for detection of as little as 1-2 ng of a synthetic 24-mer on a 5% polyacrylamide gel, which is 50-100 times greater sensitivity than obtained with ethidium bromide.
• Staining agarose gels with SYBR Green I does not interfere with the transfer of nucleic acids to membranes or subsequent hybridization in Southern or Northern blot analysis as long as 0.1% -0.3% SDS is included in prehybridization and hybridization buffers to remove the dye.

References

Sigma-Aldrich technical bulletin (most of the information here is from this source)