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labrat_2012 07-18-2012 12:55 PM

Designing NKK degenerate PCR primers
 
Hello,

I've never designed or worked with NKK degenrate priemrs before, so I'm a bit lost.:withstupid: (Admittedly, I'm not the most experienced person when it comes to primer design or cloning, so please forgive any stupid questions).

I want to design an NKK degenerate primer for creating a mutagenesis library for evolving an enzyme. However, I cannot really figure out how to desgin them. The software available ususally focuses on designing these primers using sequence alignments or using them for sequencing purposes.

Does anyone have experience with this designing type of PCR/ primers?

Thanks,
Labrat

labrat_2012 07-19-2012 06:25 AM

Re: Designing NKK degenerate PCR primers
 
As an afterthought: could you hust design a ''normal'' primer and insert the NKK-bases instead of the ones for the amino acid?

labrat_2012 07-24-2012 06:47 AM

Re: Designing NKK degenerate PCR primers
 
Ok, no one has answered so far.....

So, I'll just answer the question myself:

If you guys ever want to make priemrs that contain NKK (or any other degenerate codons) use the OligoIDT Analyzer


But be aware of the degenerate codons and their complementary bases when designing the primers

Best,
the labrat


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