Mathematical modeling of the voltage driven translocation of polyelectrolytes thr

描述（由申请人提供）：纳米尺度孔隙最近在生物技术中出现了许多应用，部分原因是它们在生物学环境中的功能。这项提议涉及一种探索性方法，通过电场驱动DNA和其他具有生物学意义的线性聚电解质通过单个纳米孔来测序。类似的场介导的纳米孔转移被认为是真核细胞正常分子水平机制的一部分。自1996年Kasianowicz、Brandin、brandon和Deamer发表里程碑式的论文以来，已经积累了相当数量的实验数据。[j].科学通报，2004,(1):1 - 3。演示通过观察电流信号来检测单个分子通过纳米孔的可能性。最近的原子水平分子动力学模拟增强了我们对这些易位背后的详细机制的理解。然而，简单的分析模型很少能得出诸如转运速度和缩放指数之类的明确公式。本建议旨在解决我们知识上的这一差距。有人提出，易位过程可以理解为带电物体在离子流体中通过有限空间的电泳问题。利用这样的描述，加上一个漂移扩散模型来描述布朗涨落，寻求可以直接与实验数据进行比较的定量预测。初步结果表明，这种方法是成功的。所提议的活动的预期广泛影响是：(A)正在开发的理论模型将为开发基于纳米孔思想的可行的超快速DNA测序技术的实验工作提供急需的指导。以目前方法的一小部分成本进行DNA测序的能力对人类健康具有众所周知的巨大而广泛的影响。(B)理论模型将导致对活细胞在分子水平上的功能的一个至关重要的部分的有价值的见解。这种理解具有各种已知的和迄今未知的实际意义：例如，它可能导致改进基因治疗中向细胞核注射DNA的方法，它可能导致开发基于破坏病原体细胞周期中蛋白质易位步骤的原理的新药，反过来，通过设计化学物质来纠正易位过程失败而引起的疾病。公共卫生相关性：拟议的活动旨在进一步了解线性聚电解质通过纳米孔的电压介导转移的生物物理过程。这一过程是提出的超快速DNA测序方法的基础，该方法已经进行了大约十年的深入研究，也是真核细胞正常功能的基本步骤。除了超快速DNA测序技术，其巨大的潜在影响已经被广泛讨论，提高对易位过程的理解可能会导致基因治疗技术的改进，以及旨在促进或破坏（在病原体的情况下）细胞易位过程的药物设计。

DESCRIPTION (provided by applicant): A number of applications of nanometer scale pores have emerged recently in biotechnology inspired partly by their function in the biological context. This proposal relates to an exploratory method for sequencing DNA and other linear polyelectrolytes of biological significance by driving them through a single nanopore using an electric field. Analogous field mediated transfer across nanopores is believed to be part of the normal molecular level machinery of eukaryotic cells. A fair amount of experimental data has accumulated since the landmark 1996 paper by Kasianowicz, Brandin, Branton and Deamer [Proc. Natl. Acad. Sci. 93, 13770 - 13773 (1996)]. demonstrating the possibility of detecting the passage of individual molecules through a nanopore by observing the current signal. Recent atomic level molecular dynamic simulations have enhanced our understanding of the detailed mechanism behind these translocations. Simple analytical models that result in explicit formulas for such things as translocation speeds and scaling exponents are however rare. This proposal seeks to address this gap in our knowledge. It is proposed that the translocation process may be understood as a problem of electrophoresis of charged objects through confined spaces in an ionic fluid. Using such a description, coupled with a drift diffusion model to describe the Brownian fluctuations, quantitative predictions are sought that can be directly compared to experimental data. Preliminary results indicating the success of such an approach are presented. The expected broad impact of the proposed activity are: (A) The theoretical models being developed would provide much needed guidance in the experimental efforts to develop a viable ultra rapid DNA sequencing technology based on the nanopore idea. The ability to sequence DNA at a fraction of the cost of current methods has vast and broad implications for human health that are well known. (B) The theoretical models would lead to valuable insight on a vital and essential part of the molecular level functioning of a living cell. Such understanding has a variety of known and as yet unknown practical implications: it could, for example, lead to improved methods of injecting DNA into the cell nucleus in gene therapy, it could result in the development of new drugs based on the principle of disrupting the protein translocation step in the cell cycle of pathogens and conversely cure diseases caused by the failure of the translocation process by designing chemicals to rectify the defect. PUBLIC HEALTH RELEVANCE: The proposed activity is aimed at furthering fundamental understanding of the biophysical process of voltage mediated transfer of linear polyelectrolytes across nanopores. This process is the basis for a proposed ultra-fast DNA sequencing method that has been the subject of intensive research for about a decade and is also a basic step in the normal functioning of a eukaryotic cell. Besides the ultra-fast DNA sequencing technology, the enormous potential impact of which has been widely discussed, improved understanding of the translocation process could lead to improvements in techniques of gene therapy as well as the designing of drugs meant to promote or disrupt (in case of pathogens) the translocation process in cells.