Non-specific band after gel purification of PCR products

[omnivore]

I'm trying to purify my PCR products (obtained by using barcoded fusion primes) by gel purification to increase the quality of amplicon pyrosequencing.

My problem is that non-specific band of about 1200 bp is not removed by gel purification process (please see the attached pdf file. My product size is about 600 bp and I usually cut out gel slices between 550 and 650 bp).

Do you know how it can occur? And, If I run these samples without further purification, how badly does the non-specific band affect the overall sequencing results?

Thanks in advance.

[PatrickJ]

You might try a nested PCR reaction on the gel-purified product

[cali4nia]

any progress omnivore? I got the same problem now. ty. the sequencing worked fine tho.

[GA-J]

It will not affect your seq, or limited affect. It may be a dimer of your product.