This question is related to design of a set of unique PCR primers.
Lets say I have 1000 oligonucleotide sequence which I synthesized chemically (e.g. using Agilent Sureprint or any other Array/Column based DNA synthesis) and stored. My objective is to fish out a given oligonucleotide, randomly from the oligo pool.
For this one obvious approach that I can follow is to attach 1000 unique PCR primers to each of these 1000 synthesized strand so that when I want to extract any given strand, using its corresponding PCR primer, I can extract and amplify.
My question is how to design such 1000 primers which can be used for PCR and they should be unique. What should be the minimum length for PCR primer design.
I don't have in-depth knowledge in mol-bio. So any suggestion would help.
DNA = A T G C => N = 4
you can use this calculator to compute the length required to make 1000 unique combination by fixing N = 4 and changing r (the lenght of your primer) : http://keisan.casio.com/exec/system/1223622559
You'll see that you need to use a length of 17 to get 1140 unique combinations.
Thanks Nicolas. The calculator is useful to say what should be the minimum length that we need to get unique set. But this wont be useful in my case since I need to design those.
One solution to my problem is: Instead of designing 1000 primers without any template, I can design PCR primer for 1000 unique genes from any organism.
Is there any site/tool available which lists primer sets for all known genes of an organism...kind of target enrichment using PCR??
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