In three of the agarose gels that I have looked at by UV, I have seen these very small blurred bands at about 100 bp, despite sample type (RNA, PCR cDNA, or cleaned up PCR cDNA), and as mentioned even the cleanup kit is not eliminating this band. I have attached the photos of these agarose gels, the picture with 4 samples with many high concentrate bands is total RNA extracted from muscle, the picture with 4 samples with one high concentrate band is cDNA resulting from PCR using RT-PCR product and gene specific primers, and the picture with 1 sample is cleaned cDNA PCR product using a spin column. So basically these gel photos are in sequence of RNA extraction, RT-PCR with that RNA to get cDNA copy of mRNA using oligo DT primer, traditional PCR of RT-PCR product and gene specific primers to amplify my gene specifically, and finally a cleanup of the traditional PCR product to remove all the crap. All three gels are 1% agarose gels with ethidium bromide run at 110 V for about 45 minutes. The first two gels had 5 ul of sample + 1 ul of 6x load dye, however, the cleanup check gel had 2 ul of sample + .5 ul of 6x load dye.

So now that you have the details, my question is, what do you think these tiny blurry bands are, why isn't a cleanup kit getting rid of this band, and will this band interfere with ligation/transformation of my gene into a cloning vector? Are there any protocol changes I can do to eliminate these?