I am using TBE-Urea gels in PAGE to analyze ssDNA. About half of the protocols (like Qiagen and Biorad) out there insist on pre-running the gel at constant wattage to pre-heat it. However, others (including suppliers like Thermo, invitrogen) do not say anything about pre-running.
Who should I trust and why ? Has anyone actually compared a normal gel to a pre-run gel (ideally for ssDNA) ? Is this dependant on wether you work with RNA or ssDNA ?
The theory would be that a preheated gel would ensure your ssDNA remains fully denatured and does not assume any secondary structure that might impact its mobility. Whether it matters or not is most likely going to depend upon the sequence of the DNA itself, so in most cases it probably doesn't matter, in some cases it might.
Preheated gel with denaturant can ensure your ssDNA in linear shape without secondary structure affecting the migration rate during gel electrophoresis. You might use software to predict if your interest sequence will have a secondary structure or not. Otherwise, you could try some in preheated gel with denaturant and some without preheated gel with no denaturant, and check you ssDNA integrity. There might be a smearing or not clear band when DNA/RNA takes secondary structure during gel electrophoresis.
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