I'm planing to insert random mutations in a protein (100 aa) to check its binding affinity to another short polypeptide.
my planing is to insert this random mutations using EP-PCR.
I checked the available kits and I found Gene Morph II, Its about 1200 UDS for 30 rxns, Is it worth this money or I can get same results if I used EP-PCR protocol by play with salt and dNTBs concentrations?
I would suggest that you design synthetic DNA oligos with restriction sites at the ends of the oligos to match the sites in your cloning vector, and introduce mixed nucleotides at positions of your interest during synthesis. The rate of mutations (or incorporation of a different nucleotide at that position may be modulated by mixing in different ratios of the four nucleotides). I think this would be cheaper than what you proposed to do using the kits, and you would have more control over what mutations you want to introduce.
I also would suggest to use higher dNTP's concentration (four time excess over the recommended concentration in standard PCR works best for me).
Additionally use Taq polymerase as it does not proofread the errors. Finally, supplement the standard reaction buffer with 0.1-0.5mM manganese as this will enhance error prone DNA synthesis. Be careful with increasing amount of dNTP's and adding manganese as excess of the both can decrease efficiency of your PCR. Finally, you can also buy some damaged dNTP's (8oxoGTP, dUTP) from Jena biosciences and "contaminate" your PCR reaction to introduce more errors.
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