Can anybody provide insight on why a sample of SYBR green mastermix, straight from the bottle, never amplified, never opened, would provide a band of ~900bp on an agarose gel? This was discovered while trying to troubleshoot contamination and all other sources have been eliminated.
Can SYBR green itself appear as a 900bp band?
Would have been helpful if you provide any image of your gel with the band you are referring to.
Hello,
SYBR green is a fluorescent dye that has high affinity for ds DNA. The mode of binding is by a combination of DNA intercalation and external binding.
SYBR green master mix will contain the SYBR dye, DNA polymerase, dNTPs, MgCl2 in an optimized buffer without the primers and template DNA.
So, if you are getting a 900 bp band on agarose gel it means that the SYBR green master mix vial is contaminated with ds DNA. You need to contact the manufacturer if you are sure that the contamination has not occurred at your end.
Best.
Are you re using running buffer for multiple agarose gels. My 2 thoughts are if the buffer is contaminated with dna from previous gels then this may enter your test gel and run as a band with smearing but the apparent size will be wrong.
Or possibly if you are adding loading dye with sucrose or glycerol and bugs are growing in the loading dye then you may be picking up bacterial dna...again probably a smeary band and at the wrong size
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