mutagenesis - mutate a vector by deleting its promoter site (Jul/28/2010 )

i am working with puc18 vector. i want to remove its lacZ promoter and MCS site by primers in order to clone my own promoter over there. i have made mutated primers but with these primers i am constantly getting 1.3 and 1.2 kb band rather 2.6kb by using taq polymerase. once i got exact size band but of very very less quantity. could you suggest any useful way to sort out this problem??

I take it you are trying to remove the promoter by PCR? If so - it won't work well, you would be better off digesting the plasmid with something that cuts near the promoter site.