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

噬菌体是感染细菌的病毒，在某些情况下，其基因组是双链DNA分子。为了开发可有效用于纳米技术和治疗细菌感染的双链(DS)DNA噬菌体菌株，需要对病毒基因组的包装和传递进行详细的数学和生物物理表征。矛盾的是，由于DNA在病毒内部的极端密度和压力条件，人们对这些过程知之甚少。在这项拟议的研究中，研究人员将结合实验工作和液晶理论来确定噬菌体内DNA分子的性质和组织及其释放。该项目将为纳米技术应用中的基因组交付建立一个坚实的理论框架。特别是，它将产生第一个描述禁闭中DNA液晶相的分析模型。每年将培训两名博士后研究员和至少两名研究生。结果和材料将通过开放获取以及标准期刊和会议介绍广泛传播。在这个项目中开发的材料将在加州大学戴维斯分校面向高中生的COSMOS项目中展示。将与设备开发实验室建立合作和联系。该项目的总体假设是，病毒衣壳内的DNA分子形成一个六方色液晶相，缺乏数学模型。在拟议的项目中，研究人员将首先建立一个由能量函数确定的力学模型，该能量函数结合了来自冷冻-EM数据的信息、来自半柔性聚合物的信息、来自Onsager溶致液晶理论的结果以及来自显色液晶实验的参数。接下来，他们将通过包括聚电解质凝胶特征来扩展他们的力学模型，承认水与多种类型的离子的存在及其与DNA分子负电荷的相互作用。第三，研究人员将开发具有不同生物物理性质的基因组的输送模型。此外，研究人员假设，DNA液晶有序中的缺陷表现为打结和DNA扭结。所提出的数学和计算模型将由多种实验技术指导和验证，包括冷冻-EM、拓扑分析、渗透压估计和DNA序列传递。这个项目的最终目标是构建和分析一个能够做出包装、压力和输送预测的色调液晶的数学模型。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.