In this study, polyethylenimine (PEI) binding to DNA was examined by isothermal titration calorimetry. Two types of binding modes were found to describe the interactions between these polyelectrolytes in buffers and in water. One type of binding involves PEI binding to the DNA groove because the enthalpy change of this binding mode is positive, and PEI is deprotonated to bind to DNA. Another likely binding mode involves external binding of PEI to the DNA phosphate backbone, accompanied with DNA condensation. The enthalpy change is negative and PEI is protonated when it binds to DNA in this mode. The intrinsic enthalpy change of first binding mode is 1.1 kJ/mol and -0.88 kJ/mol for the second binding mode. This result implies that the PEI is rearranged from the groove to the phosphate backbone of DNA when DNA is condensed. The mechanism of DNA condensation caused by PEI is discussed in this study.

No abstract

In a continuation of our series of studies on drug-DNA interaction, [1][2][3] we have examined topographic images of such interacting molecules, using an atomic force microscope. Atomic force microscopy (AFM) is an emerging technique for direct observation of biological macromolecules and their assemblies. [4][5][6][7][8][9] One of the advantages of AFM, over other high-resolution microscopies (electron microscopy, for example), is that sample preparation is relatively simple. It does not involve negative staining or shadow casting with a metal coating. In addition, the sample does not need to be kept in vacuum. Through this technique, we have succeeded in viewing the tertiary structure of plasmid pBR322 DNA, kept in a proper solution, in single molecule resolution. How and to what extent is such an image of the tertiary structure altered by the binding of various drugs? This question has been the subject of our recent investigation.Quite recently, Pope et al. 10) published their AFM studies of changes in the pBR322 DNA tertiary structure induced by the binding of ethidium bromide. The results of their observation are different in some respects from what we have observed of the same drug-DNA system. It would be significant, therefore, to publish our results on the ethidiumpBR322 DNA interaction here, before publishing our results on other drug-DNA interaction.One of the main differences between the Pope et al. investigation and ours is in the sample morphology. In the Pope et al. experiments, the plasmid DNA solution was spotted on mica, and the mica was rinsed with H 2 O, and blown dry with compressed N 2 . In our experiments, the DNA solution was placed in a liquid cell, which was placed on mica, and the DNA sample, adsorbed on mica, was kept in the solution during the measurement without drying. It is another advantage of AFM that the imaging is permitted in buffer solution without drying the sample. This is certainly advantageous, not only because biological samples can be kept intact, but also because the results of imaging can be correlated with other experimental results in solution. On the interaction of ethidium bromide and pBR322 DNA in solution, various pieces of information were established by our previous study.1) One molecule of ethidium bromide, when it is intercalated into a double-helical DNA, is known to unwind the DNA duplex so that the base pair to base pair angle (viewed along the helix axis) is reduced. Therefore, a relaxed closed circular pBR322 DNA molecule is predicted to change into a positively supercoiled form on an ethidium bromide binding. We can also predict an approximate number of supercoils (which is nearly equal to writhing number t) in the plasmid molecules kept at a given concentration in an aqueous solution which contains a given amount of ethidium bromide. How do the individual molecules look in such a solution?The results of our observation regarding this question will be given below. ExperimentalMaterials The sample of plasmid pBR322 DNA was purchased from Takara Shuzo Co...

No abstract