I designed genus-specific primers for LAMP (Loop Mediated Isothermal Amplification) using Primer Explorer V5.
I want to amplify a gene region from different species of a specific genus avoiding other closely related genera amplification
Does anyone know any tool/software (other than NCBI BLAST) to check my LAMP primers before ordering and to be sure that will amplify only my target genus?
I used Primer Explorer V5 software many years ago. Before one designs primers, one needs to align sequences of different genera and be sure which part of the sequence has the most variability to design primers from... Once the best part of the sequence is known to design primers, another trouble may pop out. Primer Explorer V5 software may not exactly pick primers from the best sequence part. The software has to care about delta G values so that loops are formed and the LAMP reaction works. If the sequence is poor GC, it is more problematic... And LAMP primers are not expensive, you may try many sets of primers. Best of luck!
Mustafa Munawar Thank you for your answer. Do you know other software to design LAMP primers?
Marwa Mourou There are other software too. For instance https://lamp.neb.com/#!/
One may also design LAMP primers manually from a sequence of choice but in such a scenario, the sequence part with the lowest delta G (Gibbs free energy) should be dedicated to loop formation. I guess the primer parts (F1c & B1c part of primers) are responsible to make loops... Please double-check things, I read about LAMP several years ago.
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