I run this denaturing PAGE in a 20% polyacrylamide gel (8M urea), using 1x TBE as running buffer. All samples (5 ul), including ladder, were treated with 5 ul formamide at 95ºC for 5 min and then placed into ice for 3 min prior loading. The buffer in which samples were diluted was 1xTBE (same as running one).
The electrophoresis was run at 120 V during 1,5 h at RT.
The resulting bands appear together with big "arms", except from the ladder. The arms are also present even when low concentrations of DNA are used, so it is not a problem of high concentrated sample.
Most of the samples are commercial oligos purified by RP-HPLC, so it is not a problem of contamination.
Does anyone know what could be the reason of the appearance of these arms?
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