at lab, we run a typical DMS assay to footprint guanine sites in a 40 mer DNA single strands. however, we constantly meet two problems:
1). on denature PAGE gel, we see a slow moving band locating way above the original ss. Is there anyone knows what it is?
2). towards the end of gel, all lanes are moving together and eventually become one lane or one dark spot. Could you help us explain what it is going on?
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