What is the difference in sensitivity when using an intercalating dye (e.g. SYBR Green) vs a 5’ nuclease assay probe (e.g. PrimeTime® qPCR Assays) to detect PCR product?

Intercalation dyes such as SYBR® Green will bind to any double-stranded DNA in the sample. They will detect the amplicon of interest but also additional non-specific products and primer dimers. Thus, use of intercalation dyes can result in a false positive signal and loss of sensitivity when examining products with low copy numbers. Along with the primer set, PrimeTime® qPCR Assays include a probe that is specific to the target product. Therefore, signal will only result when the actual product of interest is amplified and will not result from non-specific products or primer dimers. This allows for a great degree of increased specificity in the assay.

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