How do you estimate PCR product size ? - How do you estimate PCR product size ? (May/31/2010 )

Hello everyone

I am in a bit of a dilemma.

I am isolating soil genomic DNA and am using fungal specific primers to isolate certain families of fungi that I plan to clone and sequence. The soil genomic DNA mix that I extract is a mixture of all sorts of DNA and using fungal specific primers I hope to locate various fungi specific to those primers. In other words, there is not fixed product size that I am working with. The way these primers have been designed is through multiple sequence alignments of these fungi. These primers have been used before in other papers.

My reverse primer is (5' to 3') is say X and my forward primers for 4 classes of fungal specific primers are (5' to 3') A,B,C,D.

For each soil genomic DNA samples, I set-up 4 PCR reactions, A and X, B and X, C and X, D and X.

I had some very basic questions:

- When I BLAST my forward primer, I obtain results for various fungal species specific to those primers. They give me lengths and the starting point for that primer.

- When I BLAST the reverse primer, do I reverse complement it or reverse it or just keep it the way it is to obtain results ? This is a very basic question but I am confused !

After that, do I, for example, pick one of the BLAST matches common to BOTH the primers, search for my primer matches in THAT particular sequence and THEN estimate product size ? Even so, that's just one estimate. how do I get ballpark figures for all sorts of species for that particular family specific primer ?

Thanks a lot !

Blast will work for the either the forward sequence or the reverse complement. The start and end numbers of the matching sequence will indicate which direction you are going. Presumably your two primers will only match one gene exactly for any given species. Just figure out what gene you are working with and it should be easy to figure out how big of a piece you are amplifying.

Hi,

You can also use Primer-BLAST, which is quite easy. Put your template sequence, then add the sequences of your for and rev primers (5'->3', as you ordered them) and it will give you a nice figure where the primers will match, and the size of your PCR product.

I don't see any easier way to visualize your PCR product. It can also give you off-targets while selecting an organism (or several), which can also be quite useful.

Hope it'll help!

Hello Noumy and Doxorubicin



Thank you all very much for your suggestions !

I got what I wanted !!