Cracking the Color Code of DNA-stabilized Metal Nanoclusters with Rapid Optical Array Characterization and Machine Learning

利用快速光学阵列表征和机器学习破解 DNA 稳定金属纳米团簇的颜色代码

• 批准号: 1309410
• 负责人: Elisabeth Gwinn
• 金额: $ 30万
• 依托单位: University of California-Santa Barbara
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-09-15 至 2018-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1309410&HistoricalAwards=false
• 关键词: Cracking; Color; Code; DNA; stabilized

Technical Abstract Elisabeth Gwinn of the University of California, Santa Barbara is supported by an award from the Computational and Data Driven Materials Research program for research to combine computational machine learning tools with strategic data obtained from fast, array format optical characterization, with the goal of discovering and developing a versatile new class of photonic nanomaterial. Specifically, the work will investigate fluorescent, DNA-stabilized, few-atom metal nanoclusters, or DNA-mNCs. DNA-mNCs based on silver clusters are already beginning to be used in innovative imaging, molecular logic, and selective sensor applications. The recent discovery of copper-based DNA-mNCs suggests that the formation of fluorescent clusters in DNA hosts may generalize to other coinage metals.The PI's prior work revealed the special sensitivity of silver cluster fluorescence to the sequence and secondary structure of the host DNA. Studies of small sets of various DNA strands have found DNA-AgNCs with fluorescence colors spanning 500 - 900 nm. Together with the compact sizes of DNA-mNCs, which are compatible with the finest resolutions accessed by DNA nanotechnology, this wide color space may open new arenas beyond current solution applications, in nanoscale photonic arrays for information processing and signaling of biochemical and physical events. However, there is essentially no current understanding of how the properties of DNA-mNCs relate to the sequence of the host DNA. Even for the relatively well-studied DNA-AgNCs, there are no identified sequence motifs that govern fluorescence color, brightness or stability. This is despite the fundamental importance of these properties to all applications, and to the underlying materials science. But, only ~100 strands have been examined as potential hosts for chemically stable DNA-AgNCs. This is a miniscule sampling of the space of possible sequences. This research aims to crack the code for the sequence characteristics that govern the properties of DNA-mNCs, by applying machine learning tools to much larger, strategically selected data sets. The data will be acquired by robotic synthesis and rapid array optical characterization of Ag-based DNA-mNCs. Strand selection will leverage the knowledge of DNA-AgNCs developed in the PI's prior work. To elucidate the role of the specific metal from which the cluster is formed, experiments on other coinage metals, including copper, will also be made.The undergraduate and graduate students who participate in the work will be trained in advanced techniques encompassing materials science, computer science and nanotechnology. High school students will be exposed to aspects of the work through UCSB's School for Scientific Thought (SST).Non-Technical AbstractThis work focuses on tiny clusters composed of just a few atoms of metal, that are made stable in water by wrapping the clusters up in short strands of DNA. It has been known for many years that "bare" clusters made of a few metal atoms have very interesting optical properties. In particular, they can be fluorescent, meaning that the clusters emit photons after they are placed in an excited state. These DNA-encapsulated, few-atom metal nanoclusters may have many potential uses, such as fluorescent sensing of toxic ions and of targeted DNA and RNA strands. The most fascinating and potentially useful feature of these materials is the fact that different DNA sequences can produce clusters of different color. Cracking the code for the DNA sequence characteristics that govern this color is the focus of this work. The primary focus will be on silver clusters, building on previous work, but to elucidate the role of the specific metal from which the cluster is formed, experiments on other metals, including copper, will also be carried out. The undergraduate and graduate students who participate in the work will be trained in advanced techniques encompassing materials science, computer science and nanotechnology. High school students will be exposed to aspects of the work through UCSB's School for Scientific Thought (SST).

技术摘要加州大学圣巴巴拉分校的Elisabeth Gwinn获得了计算和数据驱动材料研究项目的一项奖励，该项目的研究将联合收割机计算机器学习工具与从快速阵列格式光学表征中获得的战略数据相结合，目标是发现和开发一种多功能的新型光子纳米材料。 具体来说，这项工作将研究荧光，DNA稳定，少原子金属纳米团簇，或DNA-mNC。基于银簇的DNA-mNC已经开始用于创新成像、分子逻辑和选择性传感器应用。最近铜基DNA-mNCs的发现表明，在DNA宿主中形成荧光团簇的现象可能推广到其他铜金属。PI的前期工作揭示了银团簇荧光对宿主DNA的序列和二级结构的特殊敏感性。对各种DNA链的小集合的研究已经发现具有跨越500 - 900 nm的荧光颜色的DNA-AgNC。与紧凑尺寸的DNA-mNC（与DNA纳米技术获得的最佳分辨率兼容）一起，这种宽的颜色空间可能会在当前解决方案应用之外开辟新的领域，在纳米级光子阵列中用于生物化学和物理事件的信息处理和信号传递。然而，目前基本上没有理解DNA-mNC的性质如何与宿主DNA的序列相关。 即使对于相对充分研究的DNA-AgNC，也没有确定的序列基序来控制荧光颜色、亮度或稳定性。尽管这些性质对所有应用和基础材料科学具有根本的重要性。但是，只有约100条链被检查为化学稳定的DNA-AgNC的潜在宿主。这是对可能序列空间的极小采样。这项研究的目的是通过将机器学习工具应用于更大的、战略性选择的数据集，来破解控制DNA-mNC特性的序列特征的代码。将通过机器人合成和基于Ag的DNA-mNC的快速阵列光学表征来获取数据。链选择将利用PI先前工作中开发的DNA-AgNC知识。 为了阐明形成团簇的特定金属的作用，还将对包括铜在内的其他钴金属进行实验。参与工作的本科生和研究生将接受包括材料科学、计算机科学和纳米技术在内的先进技术培训。高中生将通过UCSB的科学思想学院（SST）接触到这项工作的各个方面。非技术摘要这项工作的重点是由几个金属原子组成的微小簇，通过将簇包裹在短链DNA中，使其在水中稳定。 多年来，人们已经知道由几个金属原子组成的“裸”团簇具有非常有趣的光学性质。 特别是，它们可以是荧光的，这意味着簇在处于激发态后会发射光子。这些DNA封装的少原子金属纳米团簇可能具有许多潜在用途，例如有毒离子和靶向DNA和RNA链的荧光传感。 这些材料最吸引人和潜在有用的特性是，不同的DNA序列可以产生不同颜色的簇。 破解控制这种颜色的DNA序列特征的密码是这项工作的重点。 主要重点将放在银团簇上，以以前的工作为基础，但为了阐明形成团簇的特定金属的作用，还将对包括铜在内的其他金属进行实验。参与这项工作的本科生和研究生将接受包括材料科学、计算机科学和纳米技术在内的先进技术的培训。高中生将通过UCSB的科学思想学院（SST）接触到这项工作的各个方面。