Dynamics and Energetics of Viral DNA Packaging and Ejection

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This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).In this project the PI will study the physical principles of viral genome packaging using phi29 as a model system. The study will use previously developed technique based on optical tweezers for real time visualization of viral packaging processes. The project will examine the following effects on viral DNA packaging and ejection: (1) Screening of DNA by polyamine ions: Host cell polyamines including putrescine2+, spermidine3+, and spermine4+ are expected to substantially influence DNA packaging dynamics by affecting DNA mechanics and electrostatics, packing forces, and motor function. (2) Non-equilibrium dynamics: DNA packing forces will be investigated by studying the time-dependence of the internal forces resulting from changes in motor velocity induced by varying ATP concentration, and pauses in packaging induced with non-hydrolyzable ATP analogs at various capsid filling levels. Potential heterogeneity in packaging dynamics and force, as predicted in recent theoretical simulations, will also be investigated with ensembles of single molecule measurements. (3) Capsid shape: Different viruses have different capsid shapes that may affect DNA packaging dynamics. (4) DNA binding proteins: The PI will study the effect of protein "roadblocks" that interact with the DNA and create an additional load on the packaging motor. Topics of broad interest in physics and biology will be addressed, including polymer (DNA) conformation and dynamics, molecular motor function, ionic screening, protein-DNA interactions, and principles of viral assembly. Graduate and undergraduate students will be supervised by PIs with varying backgrounds and the students will perform research involving concepts and methods from the physical and biological sciences. Undergraduates will participate in this research and new undergraduate physics and biology course materials will be developed. Materials for K-12 science education will also be developed in collaboration with the R. H. Fleet Science Museum in San Diego.