Collaborative Research: Synthetic and Systems Biology Approaches to Semi-synthetic Cells with Expanded DNA Alphabets

该项目的重点是新形式的DNA，不仅是从天然DNA中发现的标准四个核苷酸，而是与两个或四个额外的核苷酸，以形成一个“牺牲扩展的遗传信息系统”（AEGIS）。扩增的DNA已经广泛用于人类诊断和病原体的环境监测。 该项目将在发展我们对DNA的理解方面开辟新天地，并为商业，国防和健康开发新技术。它将通过研究AEGIS DNA及其组分与活微生物细胞的相互作用来做到这一点。由于AEGIS可以支持被许多人视为生命本质的达尔文进化论，因此该项目将推动对生命的更深入理解。此外，它将允许新功能材料的实验室进化，在生物技术中描述和设计不足的地方增加进化和适应。最后，该项目强调公共宣传努力和对早期职业科学家的培训。该项目将完成复制，进化和使用DNA的细菌菌株的工程，这些DNA不是由4种不同的核苷酸构建的，而是由6或8种DNA构建的，在一个扩展的遗传信息系统（AEGIS）中。这些菌株，“正在进化的遗传学的第二个例子”（SEGUE）将使用两个6字母遗传字母表中的一个（或两个），GACTKX和GACTZP。一个由化学家、分子生物学家、哲学家和生物工程师组成的多学科团队将利用全面的初步数据。在这里，关键点被整合，以产生跨多个平台有益的结果：·通过实验和那些研究科学的历史和“科学”的人之间的直接接触，在培训，推广和风险分析方面产生更广泛的影响。致力于开发在体外和体内复制AEGIS DNA的聚合酶SEGUE。它们本身将在环境病原体监测、诊断和治疗开发以及生物技术新材料的创造方面具有价值。通过蛋白质工程构建代谢途径，在活细胞内生物合成AEGIS三磷酸盐，从而使AEGIS能够廉价使用。研究AEGIS和活细胞之间的相互作用，特别是识别“第三方”基因和调节系统，以提高SEGUE中AEGIS的性能并降低其成本。·更广泛的影响包括对实验科学家进行合成生物学的哲学和伦理特征的培训，iGEM项目以及对本科生和研究生的培训。整个科学的影响是巨大的，涉及阴影生物圈的概念，火星和太阳系其他地方的生命，以及科学家和公众如何构思和理解一般生命。两本更新的书将为思考这些和其他问题提供一个框架，克莱兰的《对生命的普遍理论的探索》和本纳的《生命、宇宙和科学方法》。“其他宣传材料将包括博客：“原始独家新闻”，从哲学和伦理角度讨论科学和技术。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

This project focuses on novel forms of DNA that are not built only from the standard four nucleotides found in natural DNA, but with two or four additional nucleotides, to form an "Artificially Expanded Genetic Information System" (AEGIS). Expanded DNA has already seen widespread use in human diagnostics and environmental surveillance for pathogens. This project will break new ground in developing our understanding of DNA, and develop new technology for business, defense, and health. It will do so by studying the interaction of AEGIS DNA and its components with living microbial cells. As AEGIS can support Darwinian evolution, seen by many as the essence of life, this project will drive a deeper understanding of life. Further, it will allow laboratory evolution of new functional materials, adding evolution and adaptation to points in biotechnology where description and design are inadequate. Finally, this project emphasizes public outreach efforts and the training of early career scientists. This project will complete engineering of bacterial strains that replicate, evolve, and use DNA built not from 4 different nucleotides, but from 6 or 8, DNA in an Artificially Expanded Genetic Information System (AEGIS). These strains, "Second Examples of Genetics Undergoing Evolution" (SEGUE) will use one (or both) of two 6-letter genetic alphabets, GACTKX and GACTZP. A multidisciplinary team of chemists, molecular biologists, philosophers, and bioengineers will exploit comprehensive preliminary data. Here, critical points are integrated to yield results beneficial across multiple platforms:• Broader Impacts in training, outreach, and risk analysis by having direct contact between experiments and those who study the history of and "science of" science.• Work to develop polymerases that replicate AEGIS DNA in vitro and in vivo SEGUE. These will themselves have value in environmental pathogen surveillance, diagnostics, and therapeutic development, as well as the creation of new materials for biotechnology.• Protein engineering to build a metabolic pathway to biosynthesize, inside of living cells, AEGIS triphosphates, allowing AEGIS to be used inexpensively.• Study of interactions between AEGIS and living cells, specifically to identify "third party" genes and regulatory systems that improve the performance and lower the cost of AEGIS in SEGUE.• Broader impacts include the training of experimental scientists in philosophical and ethical features of synthetic biology, iGEM projects, and training for undergraduate and graduate students. The implications throughout science are enormous, and touch on concepts of shadow biospheres, life on Mars and elsewhere in the Solar System, and how life in general is conceived and understood by scientists and the general public alike. Two updated books will provide a framework for thinking about these and other issues, Cleland's "The Quest for a Universal Theory of Life" and Benner's "Life, the Universe, and the Scientific Method." Other outreach materials will include the blog: "Primordial Scoop", which discusses science and technology from philosophical and ethical perspectives. Educational materials will be internationally available, including in classrooms, museums, and planetariums.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.