Studies of DNA replication and single-molecule dynamics

DNA复制和单分子动力学研究

• 批准号: 105732-2010
• 负责人: Bechhoefer, John
• 金额: $ 4.37万
• 依托单位: Simon Fraser University
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2015
• 资助国家: 加拿大
• 起止时间: 2015-01-01 至 2016-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=569109
• 关键词: Studies; DNA; replication; single; molecule

In this application, I propose three interrelated projects in biophysics and statistical physics. The primary focus is on issues related to DNA replication, with both modeling and experimental aspects. The modeling aspects exploit the recent advances in experimental techniques that are giving large sets of data about the "replication state" (depicting, at a given region of the genome, which parts have and which have not been replicated at a given time). With large datasets and with the tools we have previously developed to understand replication, our group is uniquely positioned to answer many questions about how replication proceeds, under both normal and abnormal conditions. In particular, we shall begin to compare the replication "programs" of different organisms, to look at how replication changes during development, and to look at how replication is altered in mutants and in cancer cells. We are also extending our modeling formalism to be able to analyze different kinds of problems that arise during replication (such as nicks in a strand of DNA or double-strand breaks). In conjunction with biologist collaborators, we will also begin development of apparatus to study replication at the single-cell level, in contrast to the population studies done to date. Having single-cell data solves, first of all, the technical problem of interpreting data from cells whose cell cycles are not well-synchronized. Even more important, it will allow us to assess whether the kinds of variability seen in nominally identical cells for gene transcription is also present for replication. Finally, we are building and shall use a "feedback trap" to study nanoparticles and molecular interactions. Such a trap will contribute to a better understanding of such fundamental questions in statistical mechanics as "Maxwell's demon" as well as questions for DNA-protein interactions under more "natural" conditions.

在这个应用程序中，我提出了生物物理学和统计物理学中三个相互关联的项目。主要关注与DNA复制相关的问题，包括建模和实验方面。建模方面利用了实验技术的最新进展，这些技术提供了大量关于“复制状态”的数据（描述在给定的基因组区域，哪些部分在给定的时间被复制，哪些部分没有被复制）。有了大型数据集和我们之前开发的工具来理解复制，我们的团队处于独特的位置，可以回答许多关于正常和异常条件下复制如何进行的问题。特别是，我们将开始比较不同生物体的复制“程序”，看看在发育过程中复制是如何变化的，看看在突变体和癌细胞中复制是如何改变的。我们还扩展了我们的建模形式，以便能够分析复制过程中出现的不同类型的问题（例如DNA链上的刻痕或双链断裂）。