Book of Abstracts: Albany 2005
Ligand-Induced DNA Condensation: Choosing the Model
We study DNA condensation induced by binding of charged ligands such as natural polyamines. Experimentally, DNA condenses and aggregates at a critical ligand concentration. At much higher concentrations the aggregates resolubilize. Having performed the calculations in the frame of the two-state model without ligand-ligand interactions (Lando and Teif, 2002), we show that this simple model qualitatively predicts the reentrant aggregation-resolubilization behavior and its dependence on the ligand, Na+ and DNA concentrations reported in the literature. However the experimental ligand-binding curves are required for further tests.
Using 14C-labelled spermidine3+, we measure polyamine binding to condensed DNA in a wide range of spermidine3+ concentrations, from micromolar to molar. Our experiments show that the binding of polyamines to condensed DNA at the onset of condensation is highly cooperative. When DNA is converted to condensed state the polyamine binding saturates and the binding curve reaches a plateau. This gives a limiting stoichiometry of spermidine3+ binding to condensed DNA equal to 0.7 (NH4+ / PO3-). At higher spermidine3+ concentrations close to DNA resolubilization the degree of spermidine3+ binding increases. DNA resolubilizes due to further spermidine penetration between the double helices.
In order to account for the experimentally observed cooperativity in ligand binding to condensed DNA the ligand-ligand interactions should be introduced in the model. We show that both the contact and long-range interaction models may be used to describe the experimental data. A suitable contact cooperativity parameter is close to 2, which is much smaller than the typical values for protein binding to DNA. Possible physical mechanisms for the origin of ligand-binding cooperativity in DNA condensation will be discussed.
1Institute of Bioorganic Chemistry