CAREER: Experimental and Computational Studies of Biomolecular Topology

职业：生物分子拓扑的实验和计算研究

• 批准号: 2336744
• 负责人: Alexander Klotz
• 金额: $ 75.02万
• 依托单位: California State University-Long Beach Foundation
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2024
• 资助国家: 美国
• 起止时间: 2024-07-01 至 2029-06-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2336744&HistoricalAwards=false
• 关键词: CAREER; Experimental; Computational; Studies; Biomolecular

NON TECHNICAL SUMMARYEverything we make, we make out of atoms or molecules. We have a good understanding of how atoms and simple molecules behave, but it is harder to understand more complicated molecules. Some of the more complicated molecules are connected in ways that simpler molecules aren’t. Where simple molecules might connect like Lego bricks, more complicated molecules might connect like links on a chain. The challenge is that molecules are very small, too small to see with a microscope, and too fast to record with a camera. We overcome this challenge in two ways. One is by using bigger molecules. DNA is best known for containing our genetic code, but it’s also just an extremely large molecule that we can study in a microscope. We can do experiments with DNA to learn about how molecules behave, and apply those lessons to smaller molecules. For example, we measure how stretchy a single DNA molecule is, and use that information to understand how the molecules that make up rubber become stretchy. The other way is to use computer simulations, which can show us how molecules would behave if we could see them. The main molecules studied in this project are called kinetoplasts, which are like medieval chainmail armor made of thousands of connected loops of DNA. We study these with a microscope, and with computer simulations, to understand how much smaller chainmail-like molecules, which chemists are now learning to make, would behave. In the future, our understanding of chemical chainmail molecules could allow newer, fancier materials and nanomachines created atom by atom, if we first understand DNA chainmail. We will also teach a new generation of students to study molecules, by having them take microscopic videos of droplets full of molecules as they evaporate. Since nobody has observed those specific molecules evaporating in that way before, the students will learn what it’s like to discover something new, in addition to learning how to do the experiments. As part of the educational aspects of this grant, students at a minority-serving primarily-undergraduate institution will carry out original research as part of a course-based undergraduate research experience. The experience of a new discovery will build a sense of belonging in the scientific community and support their identities as scientists rather than just science students.TECHNICAL SUMMARYThe goal of this project is to understand the relationship between molecule topology and material properties of complex biopolymers through single-molecule experiments and coarse-grained simulations. Biopolymers serve as a mesoscopic system on the micron scale analogous to synthetic polymers on the nanometer scale. The experiments will largely focus on single-molecule fluorescence microscopy. Kinetoplasts, which are planar networks of topologically linked DNA, will be studied as a model system for synthetic polycatenanes and thermalized graphene. In particular, we are interested in how the topology of then network, which can be tuned by the action of enzymes, effects the elastic response to kinetoplasts in microfluidic shear flow. We will also develop assays to use genomic-length DNA as a tracer polymer in active fluids, which drive their own internal complex flows through the conversion of chemical energy. The fluctuations and conformations of the molecule will be used to determine how life-like systems approach and avoid maximum-entropy states, establishing rules that help us understand the physics of life. Additionally, we will explore the use of partial denaturation (a topological change in linear DNA) to improve nanopore genomic mapping technology. Simulations will use Langevin dynamics and gradient optimization to study the relationship between the topology of molecular chainmail and the large-scale structure of the sheets that they form, as well as to investigate the relationship between denaturation transitions and knotted molecular topologies. As part of the broader impacts of this grant, students at a minority-serving primarily-undergraduate institution will carry out original research as part of a course-based undergraduate research experience, initially studying nematic liquid crystals in Marangoni flow. The experience of a new discovery will build a sense of belonging in the scientific community and support their identities as scientists rather than just science students.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.

非技术摘要我们制造的一切都是由原子或分子制成的。我们对原子和简单分子的行为有很好的理解，但更难理解一些更复杂的分子以更简单的分子的方式连接。简单的分子可能像乐高积木一样连接，而更复杂的分子可能像链条上的链接一样连接，挑战在于分子非常小，太小而无法用显微镜看到，而且速度太快而无法用相机记录。我们分两步克服了这一挑战一种是使用更大的分子。DNA 因包含我们的遗传密码而闻名，但它也是一种非常大的分子，我们可以用 DNA 进行实验来了解分子的行为并加以应用。例如，我们测量单个 DNA 分子的弹性，并利用该信息来了解组成橡胶的分子如何变得有弹性。另一种方法是使用计算机模拟，它可以向我们展示分子如何变得有弹性。如果我们能看到他们，我们就会表现得很好。这个项目中研究的被称为动质体，它就像由数千个连接的 DNA 环组成的中世纪链甲盔甲，我们用显微镜和计算机模拟来研究它们，以了解化学家现在正在研究的类似链甲的分子有多少。未来，如果我们首先了解 DNA 链甲，我们对化学链甲分子的理解可以让更新、更奇特的材料和纳米机器产生原子。由于以前没有人观察到这些特定分子以这种方式蒸发，因此让他们拍摄充满分子的液滴蒸发的显微视频，除了学习如何做之外，学生还将了解发现新事物的感觉。作为这项资助的教育方面的一部分，少数族裔本科院校的学生将进行原创性研究，作为基于课程的本科研究体验的一部分，新发现的体验将建立一种归属感。科学界并支持他们科学家而不仅仅是理科生的身份。技术摘要该项目的目标是通过单分子实验和粗粒度模拟来了解复杂生物聚合物的分子拓扑和材料特性之间的关系。类似于纳米级的合成聚合物，实验将主要集中在单分子荧光显微镜上，它是拓扑连接的 DNA 的平面网络。作为合成聚链烯和热化石墨烯的模型系统，我们特别感兴趣的是可以通过酶的作用调节的网络拓扑如何影响微流体剪切流中动质体的弹性响应。使用基因组长度的 DNA 作为活性流体中的示踪聚合物，通过化学能的转换驱动其内部复合物流动，分子的波动和构象将用于确定类生命系统如何接近。并避免最大熵状态，建立帮助我们理解生命物理学​​的规则。此外，我们将探索使用部分变性（线性 DNA 的拓扑变化）来改进纳米孔基因组作图技术。优化研究分子链甲的拓扑结构和它们形成的片材的大规模结构之间的关系，以及研究变性转变和打结分子拓扑结构之间的关系作为该资助的更广泛影响的一部分，少数族裔本科院校的学生将进行原创性研究，作为基于课程的本科生研究经验的一部分，最初研究马兰戈尼流中的向列液晶，新发现的经验将建立对科学的归属感。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。