Opposite effect between intercalator and minor groove binding drug on the higher order structure of DNA as is visualized by fluorescence microscopy.

Fluorescence microscopy is applied to obtain the information on the change of the higher-order structure of giant DNA molecules in an aqueous solution. Using T4 DNA, it becomes clear that ethidium bromide, an intercalator, tends to extend the DNA, whereas minor groove binding drugs such as 4',6-diamidino-2-phenylindole and Hoechst 33258 tend to contract the DNA. These changes of higher-order structure have been quantitatively evaluated as the changes in persistent length together with the change of contour length. It is also confirmed that the persistent length obtained by use of fluorescence microscopy is reliable enough comparing with those reported for the shorter DNA by use of light scattering.