Question

Difference between between eukaryotic and prokaryotic primer designs

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2.9 years ago

anasjamshed ▴ 140

Is there any difference between between eukaryotic and prokaryotic primer designing?

Is there any difference between conventional PCR and RT-PCR primer design?

Please help me

Primers Molecular-Biology • 1.9k views

ADD COMMENT • link updated 23 months ago by Ram 44k • written 2.9 years ago by anasjamshed ▴ 140

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Please search/ask on Biology StackExchange. This is more biology than bioinformatics IMO. Also, "plz help me" is not proper etiquette on professional/scientific forums.

ADD REPLY • link 2.9 years ago by Ram 44k

score 1 · Answer 1 · 2021-12-20

There is no fundamental difference in designing primers regardless of DNA source. However, there is a greater likelihood of potential problems with eukaryotic DNA during the PCR, and in particular when amplifying from genomic DNA. That's because of larger genomes (greater potential for mispriming), more repeats, etc. If one designs a 25-bp primer for a prokaryotic genome, it is a safe assumption even without checking that there aren't many sequences that are highly similar to it. It still doesn't hurt to check. For eukaryotic genomes, especially if amplifying repetitive sequences or regions near them, I would suggest checking the whole genome for other sites of full or partial priming.

With exception of people who are making announcements, people usually create these posts because they need help with something. I don't think you need to put extra calls for help in all your posts, or in any of them.