I am performing a blunt end assembly and in preparation have cut a plasmid backbone and insert with overhang restriction enzymes, treated them with Klenow to blunt the ends and treated the backobone with CIP to remove the 5' phosphate. However When I heated the fragments to 65C (to prevent hybridization) and ran ana analysis on agarose gel, a smaller band appeared to dominate the backbone lane and I'm worried it is effecting my ligation efficiency. Does anyone have any advice on how to reverse this or whether it even matters for assembly?