Statistical mechanics of DNA-protein interactions and chromosome organization

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TECHNICAL SUMMARYThis award supports theoretical research in the general area of statistical-mechanical theories of biopolymers and complexes composed of biopolymers. The focus of the research will be on DNA-protein interactions and studies of physical mechanisms underlying the organization of large DNA molecules into folded and functional chromosomes. The PI will use equilibrium and non-equilibrium statistical mechanics to describe single-molecule biological physics experiments carried out in vitro, and to develop models for chromosome dynamics in vivo. The research will be aimed at three thrusts:1. Developing theoretical models for the structure of double-stranded DNA under tensile and twisting stress as studied in single-molecule micromanipulation experiments, where there is a rather complex competition between formation of writhed "supercoiled" states, and structural reconstructions of the double helix into alternative conformations, denatured "L"- and "P"-DNA states. The same general methods will be used to develop theories of "braided" double helix DNAs, which are key substrates being used for studying DNA topoisomerases. 2. Studying the self-organization of proteins along DNA, as occurs in vivo in chromosomes, and in vitro in single-molecule experiments on protein-DNA interactions. A major objective will be development of a theory for recently observed "protein exchange" dynamics, whereby off-rates are controlled by solution-phase protein concentration. The PI will also build on his recent work on models of nucleosome dynamics, including effects of post-translational modification of nucleosomes, and competition of nucleosomes with transcription factors. The PI will examine the role played by boundary conditions on chromosomal domains, and in single-DNA experiments on DNA conformational fluctuations that may affect enzyme rates through modulation of DNA conformational fluctuations. 3. Developing models to establish higher-order chromosome structure, especially by the action of Structural Maintenance of Chromosome protein complexes, and studying how the folding of DNA by those complexes can generate the topological simplification of chromosomes, their spontaneous disentanglement, that is observed to occur during cell division.The award also supports graduate student training. Their training, in highly interdisciplinary research at the boundaries of theoretical condensed matter and materials research and molecular biology, will be of interest to biologists, physicists, materials scientists, chemists and engineers. In addition, high school and undergraduate research experiences will be provided as part of the educational activities of the project. NONTECHNICAL SUMMARYThis award supports theoretical research and education focused on the understanding of the fundamental mechanisms that underlie the organization of the very large DNA molecules that carry all genetic information in living cells. The large "chromosome" DNAs found in micron-sized bacterial cells are millions of base pairs - millimeters - in length, while those found in human cells are hundreds of millions of base pairs - centimeters - in length. The problem of organizing these unwieldy molecules is magnified by the requirement that they be replicated and separated from one another with near-perfect fidelity - for a cell to successfully divide. Broken or erroneously segregated chromosomes can lead to death of a cell, or worse, erratic cell behavior that can lead to organism-endangering diseases such as cancer. This award is focused on understanding how DNA molecules can be organized in the cell, by the action of a variety of protein molecules that interact with the double helix so as to fold it up, and to pass it through itself to disentangle it. "Single-molecule" technologies have made possible precise, quantitative experiments to study interactions of biological molecules. These types of experiments turn out to be most naturally studied from the point of view of statistical mechanics which deals with the random motion and collective behaviors of atoms and molecules. This project will also focus on how the double helix alone behaves when placed under mechanical stress, as can be precisely controlled in such experiments. Finally, this project includes work on transferring the models developed to describe single-molecule studies of protein-DNA interactions in the "test tube" to describe biomolecule behavior in living cells. One of the overarching objectives of the project will be to try to understand how the small protein molecules along a DNA are able to effect separation of large and potentially entangled DNA molecules from one another.This award supports the education of graduate students working closely with the PI. The work done by this group will be the main research training of the graduate students which leads to their Ph.D. theses; they will be educated to take methods from theoretical condensed matter physics and to apply them to problems of biological materials and biology. In addition, younger students will be involved in the research project, exposing them to research frontiers at an early stage in their scientific training.