What you are seeing might be a result of the purification process or even how you ran the gel. Although you can run RNA on a 1% agarose gel, it sometimes isn't very accurate because the RNA can form secondary structures with itself and give a smeared appearance on the gel. To minimize this, you should only run the gel for about 15 minutes at about 90-100V. If you still get the smear, you might want to try running the gel with a different buffer with formaldehyde in it which keeps the RNA denatured. You can find directions on how to make the buffer here: [1], and directions on how to make formaldehyde loading dye here: [2].
[1]
http://www.ambion.com/techlib/append/supp/rna_gel.html
[2]
http://www.stratagene.com/manuals/200347.pdf pg. 15
For RNA prep, I wasn't using the same kit as you, but I had the same problem using two different kits. In RNA isolation, the problems are usually universal regardless of the kit used. If your gel isn't the problem, it gets more complicated because you could have introduced contamination anywhere during the protocol. Before trying the protocol again, wipe the ends of your pipettes with RNase Away. During the procedure, only use filter tips and epi's that are RNase free. When centrifuging, minimize centrifuging times to 15 secs. In the lab I worked in, I centrifuged for 15 secs at 13,000rpm for each step that required centrifuging. For the elution step, instead of using the elution buffer that came with the kits, I used 50uL-100uL pre-warmed TE buffer (pH 7.0) which was prepared with .1% DEPC ddH20 water. For elution, I centrifuged for a minute. After that I divided the sample into alliquots in RNase free epi's and stored the samples in the -80C. If you want to visualize on a gel, again use filter tips and RNase free epi's and do it as soon as you're finished. If you still get the smear after all that, one of the buffers in the kit might be contaminated. You might have to get new buffers if it didn't come with extra. Good luck. RNA experiments are a f pain.
