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.

我们做出的非技术摘要，我们是由原子或分子组成的。我们对原子和简单分子的行为有很好的了解，但是很难理解更复杂的分子。一些更复杂的分子以简单分子没有的方式连接。在简单的分子可能像乐高积木一样连接的地方，更复杂的分子可能会像链上的链接一样连接。面临的挑战是分子很小，太小，无法用显微镜看到，并且太快了，无法用相机记录。我们通过两种方式克服了这一挑战。一种是使用更大的分子。 DNA以包含我们的遗传密码而闻名，但它也只是一个非常大的分子，我们可以在显微镜中研究。我们可以使用DNA进行实验，以了解分子的行为方式，并将这些课程应用于较小的分子。例如，我们测量单个DNA分子的弹力，并使用该信息来了解组成橡胶的分子如何变得弹力。另一种方法是使用计算机模拟，这可以向我们展示分子如果可以看到它们的行为。该项目中研究的主要分子称为动力学成形术，就像中世纪的链式装甲由数千个连接的DNA环制成。我们使用显微镜和计算机模拟研究它们，以了解化学家现在正在学习制造的较小的类似链式的分子。将来，如果我们首先了解DNA链序，我们对化学链式分子的理解可能会允许原子创建的较新，更奇特的材料和纳米机器。我们还将教新一代学生学习分子，让他们在蒸发时拍摄充满分子的液滴的微观视频。由于以前没有人观察到那些以这种方式蒸发的特定分子，因此除了学习如何进行实验外，学生还将学习发现新事物的感觉。作为这笔赠款的教育方面的一部分，作为基于课程的本科研究经验的一部分，少数派的初级高级学院的学生将进行原始研究。新发现的经验将在科学界建立一种归属感，并支持他们作为科学家的身份，而不仅仅是科学专业的学生。该项目的目的是通过单粒分子实验和粗粒子模拟来了解分子拓扑与复杂生物聚合物的材料特性之间的关系。生物聚合物在微米尺度上充当纳米尺度上类似于合成聚合物的介观系统。实验将主要集中在单分子荧光显微镜上。动力学成形剂是拓扑连接的DNA的平面网络，将被研究为合成聚会烯烯和热层石墨烯的模型系统。特别是，我们对当时可以通过酶的作用来调整的网络的拓扑感兴趣，这会影响微流体剪切流中动力体的弹性反应。我们还将开发主张，将基因组长度DNA用作活性流体中的示踪聚合物，这些DNA可以通过化学能的转化来驱动自己的内部复合物流动。分子的波动和构象将用于确定类似生活的系统方法如何接近和避免最大的内部状态，建立有助于我们理解生命物理学​​的规则。此外，我们将探讨使用部分变性（线性DNA的拓扑变化）来改善纳米孔基因组映射技术。模拟将使用langevin动力学和梯度优化来研究分子链序拓扑与它们形成的薄片的大规模结构之间的关系，并研究变性跃迁与打结的分子拓扑之间的关系。作为这笔赠款的更广泛影响的一部分，作为基于课程的本科研究经验的一部分，少数派的初级研究生机构的学生将进行原始研究，最初研究Marangoni流量中的nematic液晶。新发现的经验将建立在科学界的归属感，并支持其作为科学家的身份，而不仅仅是科学专业的学生。该奖项反映了NSF的法定任务，并通过使用基金会的知识分子和更广泛影响的评估审查标准来评估，被认为是宝贵的支持。