In my new lab, we assess RNA quality using formaldehyde. I have four different RNA concentrations: 405, 232.3, 1216.7, and 3772. To standardize the concentrations, I normalized them and then diluted them with RNAse free water for the first four wells. However, for the second set of wells, I didn't dilute the RNA but used different ratios: 3:3 for the first two gels, 2:3 for the third gel, and 1.3:3 for the last one. The first four wells were run at 60v, 3.00A for 1 hour, while the last four wells were run at 60v, 3.00A for 30 minutes. the outcome of the gel picture looks poor.
Without a size marker properly loaded along with each batch of RNAs, it is impossible to compare the sizes of your (smudgy) bands.
If you have access to it, use an Agilent Bioanalyzer or TapeStation to determine the quality of your RNAs.
Hope you already found a solution to your problem... Still...
Try to use autoclaved water for gel preparation and dilutions it will reduce the smearing and use precooled buffer for running the gel.
Please reply if that helped in any way
You can sometimes get sharper bands by briefly heating your samples then cooling them. Try 65 degrees for 10 minutes, ice 1 min, spin down and run on your gel.
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