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

这个项目关注的是新形式的DNA，这种DNA不仅是由天然DNA中发现的标准四个核苷酸构建而成，而且还有两个或四个额外的核苷酸，以形成一个“人工扩展的遗传信息系统”（AEGIS）。扩展DNA已经广泛应用于人类诊断和病原体的环境监测。这个项目将为我们对DNA的理解开辟新天地，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实现这一目标。由于AEGIS可以支持达尔文进化论，被许多人视为生命的本质，这个项目将推动对生命的更深层次的理解。此外，它将允许新功能材料的实验室进化，为生物技术中描述和设计不足的地方增加进化和适应。最后，该项目强调公众宣传工作和早期职业科学家的培训。该项目将完成细菌菌株的复制、进化和使用DNA的工程，这些DNA不是由4种不同的核苷酸构建的，而是由人工扩展的遗传信息系统（AEGIS）中的6或8种DNA构建的。这些菌株，“遗传进化的第二个例子”（SEGUE）将使用两个6个字母的遗传字母GACTKX和GACTZP中的一个（或两个）。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，关键点被整合在一起，以产生跨多个平台的有益结果：•通过在实验与研究历史和“科学的科学”的人之间建立直接联系，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SEGUE复制AEGIS DNA的聚合酶。这些技术本身在环境病原体监测、诊断和治疗开发以及为生物技术创造新材料方面都具有价值。•蛋白质工程构建代谢途径，在活细胞内生物合成AEGIS三磷酸，使AEGIS使用成本低廉。•研究AEGIS与活细胞之间的相互作用，特别是识别“第三方”基因和调控系统，这些基因和调控系统可以提高SEGUE中AEGIS的性能并降低成本。•更广泛的影响包括实验科学家在合成生物学的哲学和伦理特征方面的培训，iGEM项目，以及本科生和研究生的培训。整个科学的影响是巨大的，涉及到阴影生物圈的概念，火星和太阳系其他地方的生命，以及科学家和公众如何构想和理解一般的生命。克莱兰的《对宇宙生命理论的探索》和本纳的《生命、宇宙和科学方法》这两本书将为思考这些问题和其他问题提供一个框架。其他拓展材料将包括博客“原始独家”，从哲学和伦理的角度讨论科学和技术。教育材料将在全球范围内提供，包括在教室、博物馆和天文馆。该奖项反映了美国国家科学基金会的法定使命，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.