I did 1% agarose gel to separate 2kbp ssDNA and dsDNA. According to some papers, they described ssDNA should run faster than dsDNA, however, I ran the mixed sample after purifying the mixture with a PCR purification kit, and the low mobility signal line disappeared. Does anyone have some experience with this?
Figure description: #1: purified 2kbp ds DNA; #2: 2kbp ssDNA & ds DNA mixture; #3: purified 2kbp ssDNA & dsDNA mixture.
In agarose and acrylamide gels I always found that ssDNA ran slower ( looked larger) than dsDNA possibly due to conformation and surface charge effects
Hi Paul Rutland, thanks for your helpful answer. However, 2kbp ssDNA also could run faster than dsDNA in agarose gel, which described in this paper Article In vitro synthesis of gene-length single-stranded DNA
. So have you run 2kbp length ssDNA and dsDNA before in agarose gel before?
Thank you for that paper Lijian Zhan which makes it clear that larger fragments of ssDNA run faster than the dsDNA. All of my work was done using mainly PAGE gels and fragments smaller than 400bp to detect changes using SSCP technique. Possibly longer fragments have more homologous regions making them look and behave more like dsDNA
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