Enhancement of Cellular DNA Flexibility

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DESCRIPTION (provided by applicant): Our laboratory is interested in understanding the physical origin and biological management of DNA stiffness. It has long been appreciated that duplex DNA is among the stiffest of all natural polymers. Remarkably, the origin of DNA stiffness remains obscure after 50 years of study. A better understanding of the balance of forces within DNA would reveal what forces are overcome by DNA bending proteins such as histone octamers, and could allow control of DNA stiffness for nanomaterials and nanodevices. How living cells manage the stiff DNA polymer is also not understood in mechanistic detail. The bending and twisting flexibility of DNA within cells appears to be higher than in solution. Why? We have been studying sequence non-specific HMGB DNA bending proteins and other "architectural" proteins as models for understanding one mechanism by which DNA might be endowed with enhanced apparent flexibility in cells. Understanding and harnessing the properties of these proteins could have applications in artificial gene control by targeting the proteins to modulate the stability of DNA loops required for transcriptional regulation. During the previous funding period we made important progress toward understanding the origin and management of DNA stiffness. We now propose four aims to continue this fundamental research. Aim 1 will determine the relationship between DNA charge density, base stacking and DNA stiffness. Aim 2 will measure effects of HMGB protein binding on the flexibility and structure of DNA and chromatin in vitro. Aim 3 will improve our understanding of the basis for DNA looping enhancement by architectural proteins in E. coli. Finally, Aim 4 will measure the effects of HMGB proteins on DNA looping in yeast. PUBLIC HEALTH RELEVANCE: DNA molecules contain the information code for all living things. This information is contained in very long double-helix DNA molecules. These molecules are thread-like when considered at a distance, but are rod-like from the perspective of the proteins that must bind and read DNA. This proposal for renewed funding will allow our collaborative research group of molecular biologists, biochemists, and physicists to continue our productive projects to understand why DNA is stiff and rod-like locally, and how a special group of proteins called "architectural proteins" increase the flexibility of DNA by causing bends and kinks.