Hello,

I am a user of QuikChange II XL Site-Directed Mutagenesis Kit (Agilent) and I have performed SDM succesfully several times. I always introduce single nucleotide changes using a pair of mismatched complementary primers. According to the protocol, crucial part of SDM is to design primers with a melting temperature ≥ 78°C and of 25-45bp.

This time I have to deal with difficult template of very low GC content. Even when I pick very long primers (e.g. 55bp) for my DNA fragment, maximum Tm I can get for them is 73°C. I have checked Tm in several different tools available online and with regard to SDM reaction conditions. Primers reach Tm of 78°C with the length of about 100bp which is definately too long. I have also checked Tm in SnapGene that counts in a mismatch, it showed Tm of 64°C for 55bp primers.

Do you have any ideas how to optimize the SDM reaction so I could use primers with lower Tm (than it is said in the protocol)?

I was thinking of lowering annealing temperature but it might promote creating primer dimers (they are complementary and it happens in some level anyway) and I am afraid they would dissociate from the template during the extention step (68°C).

Thank you for any comments and ideas.

I would greatly appreciate your help!

Anna

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