Collaborative Research: DNA Packing of Bacteriophages: Liquid Crystal Modeling through Analysis, Knot Theory and Numerical Simulation

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Bacteriophages are viruses that infect bacteria and whose genome is, in some cases, a double stranded DNA molecule. In order to develop strains of double stranded (ds) DNA bacteriophages that can be efficiently used in nanotechnology and for treatment of bacterial infections, a detailed mathematical and biophysical characterization of the packing and delivery of the viral genome is required. Paradoxically, very little is known about these processes due to the extreme density and pressure conditions that the DNA is subject to inside the virus. In the proposed research, the investigators will combine experimental work and the theory of liquid crystals to determine the properties and organization of the DNA molecule inside bacteriophages and of its release. The project will establish a firm theoretical framework for genome delivery in nano-technological applications. In particular, it will produce the first analytical model describing the liquid crystalline phase of DNA in confinement. Two postdoctoral fellows and at least two graduate students will be trained each year. Results and materials will be broadly disseminated, through open access as well as standard journals and conference presentations. Materials developed in this project will be presented at the UC Davis program for high school students COSMOS. Collaborations and contacts with device development laboratories will be established.The overarching hypothesis of the project is that the DNA molecule inside the viral capsid forms a hexagonal chromonic liquid crystal phase for which mathematical models are lacking. In the proposed project, the investigators will first build a mechanical model determined by an energy function that incorporates information from cryo-EM data, information from semiflexible polymers, results from Onsager theory of lyotropic liquid crystals and parameters from experiments on chromonic liquid crystals. Next, they will extend their mechanical model by including polyelectrolyte gel features, acknowledging the presence of water with many types of ions and their interaction with the negative charge of the DNA molecule. Third, the investigators will develop models of delivery of genomes with different biophysical properties. Furthermore, the investigators hypothesize that defects in the DNA liquid crystalline ordering are manifested as knots and DNA kinks. The proposed mathematical and computational models will be, both, guided and validated by multiple experimental techniques including cryo-EM, topological analysis, estimation of osmotic pressures and delivery of DNA sequences. The ultimate goal of this project is to construct and analyze a mathematical model of chromonic liquid crystals capable of making packing, pressure and delivery predictions.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.