A band, smaller than the desired DNA fragment is present in the eluant. "

The smaller band may be a single-stranded form of the PCR product. The occurrence of it could be due to the elongation of the PCR product not being complete or the PCR product is denatured during the preparation. In this case, to re-anneal the single-stranded DNA, incubate the solution at 95ºC for 2 minutes and let it cool slowly to room temperature. The re-annealed PCR product can be used as usual in all downstream applications.