In agarose gel electrophoresis smaller nucleic acids usually create a smear, especially in low percentage gels like 0.8%. I would regard it as normal.

If your goal is to resolve the small nucleic acids however, you could try increasing the agarose percentage of your gel (up to 3%) or use an Urea-PAGE, which is very well suited for resolving smaller nucleic acids (see picture and pdf attached).

Circular DNA fragments can have different conformations and therefore run at different heights. You have to linearize them first in order to observe their true size within gel electrophoresis. (For explanation just google coiled plasmid electrophoresis)

Hope i could help,

David

try running the gel slower. The ladders are getting diffuse at smaller sizes which usually means the gel is hot and thermal diffusion is spreading the bands. This may be why lanes 2 and 3 are blurred but the smear in track 4 looks real. If you want good results at both ends of the gel take the gel out at 1/3 of the running time and get a good picture of the small bands but the large one will hardly have left the wells. Then out the gel back in the electrophoresis tank and run it further for a good picture of the larger bands. Only the smaller bands will be blurred because small molecules diffuse further at high temperatures as they move around more.

Both tips are very helpful.

Thank you very much Paul Rutland and David Scherf !