I have designed MicroRNA forward specific primer which I have used along with universal reverse primer in my QPCR reaction. Is there any web based tool which I can get the amplicon size in a predictive perspective? I run the products on gel and seems they are about or less than 100bp using a molecular marker. But how I know exactly my product length prior to gel running? Any answers are appreciated.
Because your specific Fw prmer covers pretty much most of the microRNA, the size of your product will primarily depend on the position where your universal reverse primer anneals within the stem-loop structure you used in RT. I am not aware of any web-sites that can visualise this for you, but if you simply paste the Fw, Rev and stem-loop structure sequences in a Word doc you will be able to quickly find and highlight your primers and see the amplicon size. Under 100 bp sounds about right, as long as the band is not primer-dimer (check the negative control for bands). All best..
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