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Designing NKK degenerate PCR primers

Designing NKK degenerate PCR primers - Molecular Cloning Forum

Designing NKK degenerate PCR primers - DNA cloning forum. Discuss the cloning of plasmids, vectors, DNA, RNA, cDNA, proteins, and other molecules for expression, sub-cloning, and other methods. Also discuss digestion, ligation, transformation, plasmid preparation, cDNA library screening, and competent cells here.


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Old 07-18-2012, 12:55 PM
Pipette Filler
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Question Designing NKK degenerate PCR primers



Hello,

I've never designed or worked with NKK degenrate priemrs before, so I'm a bit lost. (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
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Old 07-19-2012, 06:25 AM
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Default 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?
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Old 07-24-2012, 06:47 AM
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Default 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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