DNA & PROTEIN DNA COMPLEXES

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Martin Guthold joined the project December 1, 1997 to work with external biologists using the nanoManipulator in their investigations. He will also be continuing his investigations of DNA. We have initiated an investigation of DNA and protein-DNA complexes using the nanoManipulator and complementary biochemical studies. High-resolution images of DNA in air can now be obtained routinely. In initial pushing experiments of DNA adsorbed on mica in air, we were able to rupture DNA in a controlled matter. After proper calibration of the lateral force constant of the cantilever we will determine the rupture force of DNA. Experiments to determine the frictional force, the friction coefficient and the activation energy to move DNA on the surface are currently pursued. We have determined the binding energy of a 25 bp DNA fragment for adsorption onto mica for one set of conditions. The free energy of adsorption for this fragment was determined to be about 4.2 kT, the entropic energy loss was calculated to be about 1 kT, and the enthalpy of binding was, therefore, about 3.2 kT. Binding experiments will be done for different buffer and substrate conditions and for DNA fragments of different length. We are developing a theoretical framework to describe the adsorption of DNA to a substrate. Using a simple model, we have derived formulas for the length dependence of the free energy, enthalpy and entropy of adsorption. A complete model including the aforementioned parameters plus frictional parameters and the activation energy for motion on the surface will be developed in the future.