Chromatin Structural Dynamics Studied with DNA Origami Nanotechnology

了解基因组（由DNA组成）的物理特性对于确定如何控制基因表达、DNA复制和DNA修复等过程至关重要。许多生物体通过重复地将DNA包裹成称为核小体的小线轴来组织它们的基因组。随着基因的表达、复制或修复，核小体的组织被重新排列，该项目将开发一种新的方法来研究基因长度上的染色质结构动力学，从而使对基因如何开启和关闭的新的物理见解成为可能。跨学科培训将提供从分子生物学和生物化学到纳米技术和单分子生物物理学的广泛领域。研究人员将把这个项目整合到外展项目中，包括少数民族工程项目、工程女性和硕士到博士的桥梁项目，所有这些都有助于增加下一代STEM研究人员的多样性。染色质结构动力学控制着DNA复合体的可及性，这些复合体调节转录、修复DNA损伤和复制DNA。DNA调控复合体可接近的开放常染色质与不可接近的致密异染色质之间的转换对于基因组调控和加工至关重要。目前，缺乏在多个核小体上跨越10-100nm的特定DNA序列（即启动子区域）上探测基因调控过程中的关键事件的工具。为了解决这一挑战，主要研究人员将：(1)利用DNA折纸纳米技术开发纳米级铰链装置，定量测量染色质的中尺度构象动力学；(2)确定H1压实染色质的10-100nm结构动态。这些纳米铰链的构象变化将通过透射电子显微镜和单分子荧光检测。这些单分子方法的发展和应用将为染色质在不同功能状态之间转换时发生的结构事件提供新的工具和见解。该项目由生物科学理事会分子和细胞生物科学部遗传机制组和数学和物理科学理事会材料研究部联合资助。

Understanding the physical properties of the genome (which is composed of DNA) is essential to determining how processes such as gene expression, DNA replication, and DNA repair are controlled. A wide range of organisms organize their genome by repeatedly wrapping the DNA into small spools called nucleosomes. As a gene is expressed, replicated or repaired the organization of the nucleosomes is rearranged, and this project will develop a new approach to enable the study of chromatin structural dynamics over the length of a gene, thereby enabling new physical insights into how genes are turned on and off. Interdisciplinary training will be provided in a wide range of fields from molecular biology and biochemistry to nanotechnology and single molecule biophysics. The researchers will integrate this project into outreach programs including a Minority Engineering Program, Women in Engineering, and the Masters to PhD Bridge Program, all of which serve to increase the diversity of the next generation of STEM researchers. Chromatin structural dynamics control the accessibility of DNA to complexes that regulate transcription, repair DNA damage and replicate DNA. Conversion between open euchromatin that is accessible to DNA regulatory complexes and compact heterochromatin that is inaccessible is essential for genome regulation and processing. Currently, there is a lack of tools for probing critical events during gene regulation at specific DNA sequences (i.e. promoter regions) that span 10-100nm over multiple nucleosomes. To address this challenge, the principal investigators will: (1) develop nanoscale hinge devices using DNA origami nanotechnology to quantitatively measure mesoscale conformational dynamics of chromatin; and (2) determine the 10-100nm structural dynamics of H1 compacted chromatin. The conformational changes in these nano-hinges will be detected by transmission electron microscopy and single molecule fluorescence. The development and application of these single molecule methods will provide new tools and insight into the structural events that occur within chromatin as it converts between distinct functional states.This project is funded jointly by the Genetic Mechanisms Cluster in the Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences and the Division of Materials Research in the Directorate for Mathematical and Physical Sciences.