Chaotropic agents used in silica-based DNA purification can induce DNA denaturation and these single-stranded forms of DNA will have faster mobility in a gel. If present, we recommend using salt and heat to renature your sample. Adding NaCl to 10mM and heating the sample to 95°C for one minute followed by a slow cooling to room temperature should promote re-annealing of the denatured strands. Alternatively, if the sample will be used in an enzymatic reaction, the purified DNA can be added to the reaction with the enzyme omitted, heated to 95°C for one minute, and cooled to the reaction temperature followed by adding the enzyme.