AFM studies of DNA structures on mica in the presence of alkaline earth metal ions

As counterions of DNA on mica, Mg2+, Ca2+, Sr2+ and Ba2+ were used for clarifying whether DNA molecules equilibrate or are trapped on mica surface. End to end distance and contour lengths were determined from statistical analysis of AFM data. It was revealed that DNA molecules can equilibrate on mica when Mg2+, Ca2+ and Sr2+ are counterions. When Ba2+ is present, significantly crossovered DNA molecules indicate that it is most difficult for DNA to equilibrate on mica and the trapping degree is different under different preparation conditions. In the presence of ethanol, using AFM we have also observed the dependence of B–A conformational transition on counterion identities. The four alkaline earth metal ions cause the B–A transition in different degrees, in which Sr2+ induces the greatest structural transition.