I have designed a primer, the expected product length is 51, according to NCBI, is this product length accepted for real-time PCR?
There is nothing inherently bad with an amplicon of 51 bp. The issue arises when you do a melt curve analysis to ensure you amplified the one specific product of interest. Primer dimers in some cases can range up to 60-70 bp so a product length of 51 may be indistinguishable or difficult to interpret if you get any primer dimers. A more ideal product length is 100-150 bp. You can go up to 200 bp but there is no reason to go above that as Sybr Green melt curves do not easily distinguish between something at 150 bp and 250bp - they will melt at about the same temp. Of course melt temps are dependent on both size and GC content, but I would try for something a little larger in that 100-150 bp range.
There is nothing inherently bad with an amplicon of 51 bp. The issue arises when you do a melt curve analysis to ensure you amplified the one specific product of interest. Primer dimers in some cases can range up to 60-70 bp so a product length of 51 may be indistinguishable or difficult to interpret if you get any primer dimers. A more ideal product length is 100-150 bp. You can go up to 200 bp but there is no reason to go above that as Sybr Green melt curves do not easily distinguish between something at 150 bp and 250bp - they will melt at about the same temp. Of course melt temps are dependent on both size and GC content, but I would try for something a little larger in that 100-150 bp range.
To be on the safe side use a target amplicon of 75–200 bp. Although short PCR products in your case are typically amplified with higher efficiency than longer ones, the PCR product should be at least 75 bp long to easily distinguish it from any primer-dimers that could potentially form.
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