I have two kind of oligo DNA (90 nt). One of them is linear. And another is circular. Can I distinguished the linear from the circular by electrophoresis? For example, by native PAGE.
Yes you can distinguish the two forms of Oligo DNA. You can try 1.5% Agarose gel or evn 2% Agarose gel. Generally we use PAGE for 20-60 bp containing oligos. Load 100 bp DNA in first lane, sample A in second lane and sample B ( different form of same DNA) in the third lane. Allow the electrophoretic run for around 20-25 minutes at 100 V constant voltage. Visualise the agarose gel under UV light. You will find two band in either second or third lane. That sample lane will correspond to the circular form of DNA. One representing the open circular form and the others reprsenting the covalently closed circular DNA. The lane having single band will correspond to linear DNA. Hope this helps.