Electronic Recognition of Gene Regulatory Proteins Bound to DNA

该项目的目的是使用固态纳米孔来识别和表征与基因组DNA结合的转录调控蛋白(转录因子或转录因子)。纳米孔已被广泛用于在单分子水平上表征DNA易位、DNA和RNA的解压以及DNA与酶的相互作用。这些方法将被扩展到绘制调控蛋白与DNA的相互作用图，并研究经典方法不容易解决的问题。在纳米孔转移实验中，将进行重点研究，以建立蛋白质的大小、形状、电荷和其他性质与离子阻断信号之间的关系。一个由生物物理学家(PI：Meller，纳米孔物理学)和生物医学工程师(co-PI：Weng，基因调节)组成的团队将在不同的条件下对蛋白质进行广泛的表征，如pH、离子强度和温度，以生成一个电子表格，将每个调节蛋白质(或调节蛋白质家族)与一组实验观察对象唯一地联系起来。这项研究将补充对同一蛋白质作为转录因子的能力的广泛的生物信息学分析。生物系统中的合作和竞争蛋白质结合的影响也将被讨论。这些研究与基因表达和调控直接相关，因此在基础科学以及基因治疗和药物发现方面具有广泛的意义。在教育方面，纳米孔物理及其在基因调控中的应用将作为高级主题在生物物理和生物信息学的课程中介绍，为生物物理、分子生物学和应用物理的学生提供机会探索其学科经典边界之外的最新研究成果。这项工作还将通过波士顿大学NSF资助的REU计划吸引暑期学生，并将通过为夏季住宿向上跳跃计划(每年85名来自接近贫困水平的家庭的学生)开发基于项目的动手活动，让市中心的高中生参与这项跨学科的尖端研究。这项计划将大大加强科学教育，并为第一次上大学的高中生提供机会。

The aim of this project is to use solid-state nanopores to recognize and characterize transcriptional regulatory proteins (transcription factors or TFs) bound to genomic DNA. Nanopores have been extensively used to characterize DNA translocation, DNA and RNA unzipping, and DNA-enzyme interactions, at the single molecule level. These methods will be extended to map the interactions of regulatory proteins with DNA, and to study questions that are not easily addressable by classical methods. Focused research will be conducted to establish the relationships between the proteins' size, shape, charge and other properties and the ion blockade signal in the nanopore translocation experiments. A team of a biophysicist (PI: Meller, nanopore physics) and a biomedical engineer (co-PI: Weng, gene regulation) will conduct extensive characterizations of proteins under different conditions such as pH, ionic strength and temperature to generate an electronic table, which uniquely relates each regulatory protein (or regulatory protein family) with a set of experimental observables. This study will be complemented with a broad bioinformatics analysis of the same protein in its capacity as a transcription factor. The effects of cooperative and competitive protein binding in biological systems will be also addressed. These studies are directly related to gene expression and regulation, and therefore have broad implications in basic sciences as well as in gene therapy and drug discovery. On the educational side, nanopore physics and its applications to gene regulation will be introduced in lectures in Biological Physics and Bioinformatics as advanced topics, providing opportunities for students in biophysics, molecular biology, and applied physics to explore state of the art research outsides the classical boundaries of their disciplines. The work will also engage summer students through the Boston University NSF funded REU program and will engage inner-city high school students in this interdisciplinary cutting-edge research, by developing project-based, hands-on activities for the summertime residential Upward Bound program (85 students per year from near poverty-level households). This program will significantly enhance the science education and opportunities for first time college-bound high school students.