Two-dimensional condensation of DNA

Specimen preparation scheme for the observation of 2-D condensation of DNA on cationic lipids in solution

The preparation of supported cationic lipid bilayers has allowed us to directly visualize the pitch of membrane-bound DNA in solution with the atomic force microscope. The binding of DNA to the cationic lipid bilayer has a lower limit of about 5 kcal/mol per helical turn. The pitch of DNA is detected directly.

DNA molecules adsorbed onto supported cationic lipid membranes are highly condensed. The 2-D condensation requires the presence of free DNA molecules in the solution for a period about 12 hours, in which the ratio of adsorbed DNA to the free DNA is about 5% or less. Once condensed, the adsorbed DNA molecules remain on the membrane after removing free DNA molecules in the solution. The adsorption-condensation of both the linear and the circular forms of DNA onto the cationic membrane is independent of the length of DNA. The fluidity of the membrane is essential to induce the close-packing of the adsorbed DNA.

A specimen of condensed plasmid DNA (~6.6 kbp) on DPDAP. In some segments, we observe sharp turns of DNA segments. Since the sharp turn needs very high bending energy, their condensation on the 2-D DPDAP membrane indicates the attraction must be even stronger.

This is an example of DNA fragments on DPDAP. These DNA fragments vary in size from 8 bp to 587 bp. We have also observed the close-packing of DNA for Lamda DNA molecules. Thus, the 2-D condensation of DNA on cationic lipids is independent of the size of DNA and disregard whether the DNA is linear circular of relaxed or supercoiled form.

At the present status of the technology, direct observation of the pitch of DNA is realized. Here is an example. This opens new avenues for studies of the structure of DNA and DNA-protein complexes at the molecular level.