I ran gel electrophoresis of DNA samples, got glowy wells, and smeared DNA bands. Though the primary reason is contamination, I want to know the specific reasons and solutions.
You did not specify if these were supposed to be Plasmid DNA preps or genomic. The answer is a bit different for the two.
If this was supposed to be plasmid prep then it seems you have heavy contamination by genomic DNA. This probably comes from being too vigorous when mixing during the different steps in the plasmid lysis protocol. Once you had the lysis solution you need to be gentle and mix only by gentle inversion. If you vortex or shake hard you will release the genomic DNA.
If this is supposed to be genomic DNA then either you sheared the DNA through excessive pipetting or too vigorous mixing. Or it may be that you have a small amount of nuclease contamination. This may especially be common if the strain is EndA+
If your sample is genomic DNA, then you would expect to see a smear.
You should go talk with your supervisor/mentor - they need to tell you more about what you should expect for your experiment.
Good luck!
Thank you Katie A S Burnette and Michael J. Benedik for your guidance.
It should not affect PCR amplification as long as a reasonable portion of the DNA has an average size larger than the band you are trying to amplify.
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