Is their any maximum limit for an insert size in terms of nucleotides for mutagenesis? My insert size is 14nt and plasmid size 4.2kb so will their be a problem?
I dont know which method are you using for mutagenesis, but changing or inserting 14 nucleotides is not a problem. I have done this both by Kunkel mutagenesis and by quickchange mutagenesis. It should also be possible with overlapping PCR.