The goal of this research is to understand how polyamines and proteins cause the condensation of DNA and affect its helical structure, and how condensation and helical perturbations are related. It is induced by multivalent cations. This hypothesis will be investigated in several ways: . Size distributions of condensed DNA particles will be used to develop and test a statistical thermodynamic theory for a successive association model of condensation, including various attractive and repulsive intermolecular force terms. . The theory will be tested against existing data, and additional experiments will be performed using DNA of various lengths and circularity/linearity, with trivalent condensing agents of different chemical type and concentration. This should allow determination of the dependence of theoretical parameters, especially the solute-solvent interaction energy, on solution conditions, and enable testing of the distorted secondary structure hypothesis. . Electron microscopy and light scattering measurements of kinetics will be used to develop quantitatively consistent equilibrium and kinetic models of condensation. Kinetics may also explain the relative proportions of toroids and rods found with different DNAs or under different condensing conditions. . Direct evidence will be sought that condensation and aggregation are accompanied by secondary structure transitions in the DNA duplex. Preliminary data from calorimetry and Raman spectroscopy will be extended and augmented by FT-IR and chemical probes, using DNAs of suitable composition, sequence, and topology. . The most direct way to demonstrate helix distortions attendant on ligand binding is by scanning tunneling microscopy (STM). Technical development of STM, especially ways to maintain physiological salt and hydration, will be pursued in order to look reliably at double helix distortions. . STM will also be used to look at complexes between DNA and proteins that involve structural adjustments of the partners, including leucine zipper protein, anti-Z-DNA antibodies, and the single-stranded DNA binding protein encoded by the virE gene of Agrobacterium tumefaciens. The condensation and helical distortion of DNA are pertinent to a number of health-related issues, including assembly of viruses, regulation of gene expression, and susceptibility to radiation damage.
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