Expanding biosensing systems through synthetic functional deoxyribonucleic acids

DNA或脱氧核糖核酸是一种天然聚合物，由四种不同类型的核苷酸组成。DNA是我们广为人知的遗传物质--地球上所有活着的有机体都使用它来存储它们的遗传信息，这在很大程度上是因为DNA是一种高度稳定的聚合物，可以通过一种称为沃森-克里克碱基配对原理的可预测机制轻松复制。DNA的这两个突出特性也被许多科学家用来制造合成DNA分子来做有趣的事情。这项建议涉及两类合成DNA分子的研究，即DNA酶和DNA适配子。DNAzyme可以被视为DNA制造的“分子引擎”，能够加快化学反应，而DNA适配子是DNA构建的“分子侦探”，在从复杂的分子混合物中找到特定的分子目标方面非常出色，比如我们饮用水中的有毒金属或我们血液中的疾病指示物。它们统称为功能性DNA。大自然并不生产DNA适配子和DNA酶，但我们可以使用“体外选择”从DNA分子的人才库中找到它们。“体外选择”是一种基于实验室的技术，可以推动DNA池中单个DNA分子的竞争。我在麦克马斯特大学的团队擅长使用这种技术来寻找这样的DNA人才。我们对这些分子感兴趣的关键原因是最终使用它们来做有用的事情，比如用它们来开发治疗学或诊断学。然而，在我们能够将它们用于适当的应用之前，我们需要通过一个被称为“分子表征”的过程来了解它们的特征。这笔NSERC发现基金旨在发现新的DNA酶和DNA适配子，对它们进行良好的描述，并让它们做一些有用的事情。我们将追求四个具体目标。首先，我们希望找到一组新的DNAzyme，并将其作为分子工具来研究一种被称为“RNA修饰”的重要生物学过程。其次，我们想测试一种全新的想法，即制造更好的DNA适配子，使其具有更敏锐的检测能力，以便它们能够比现有的DNA适配子做更有效的检测工作。第三，我们希望开发一种使用颜色变化来报告DNA适配子的检测工作的方法，就像石蕊测试一样。最后，我们希望构建一系列环形DNA适配子或DNAzyme系统，并将它们锁定在一起，这样就可以同时做两件或两件以上的事情。总体而言，通过本提案中将要进行的工作，我们将产生关于DNA适配子和DNAzyme的新知识，开发新的或更好的DNA适配子和DNAzyme，并设计出将DNAzyme和DNA适配子用于环境、食品安全和医疗应用的新方法。除了做出重要的科学发现外，在这个项目中，我们将在未来五年与几名年轻学生合作，将他们培养成加拿大未来的高技能科学家。

DNA, or deoxyribonucleic acid, is a natural polymer made of four different types of building blocks called nucleotides. DNA is widely known to us as the genetic material - it is used by all of the living organisms on Earth to store their genetic information, largely because DNA is a highly stable polymer and it can be easily replicated through a predictable mechanism called the Watson-Crick base-pairing principle. These two outstanding properties of DNA have also been utilized by many scientists to make synthetic DNA molecules to do interesting things. This proposal concerns the study of two classes of synthetic DNA molecules known as DNAzymes and DNA aptamers. DNAzymes can be viewed as DNA-made "molecular engines” capable of speeding up chemical reactions, whereas DNA aptamers are DNA-constructed “molecular detectives” that are excellent in finding a specific molecular target from a complex molecular mixture, like a toxic metal in our drinking water or a disease indicator in our blood. Collectively they are referred to as functional DNAs. Mother Nature does not produce DNA aptamers and DNAzymes, but we can find them from a talent pool of DNA molecules using "in vitro selection", a laboratory-based technique that drives the competition of individual DNA molecules in the DNA pool. My group at McMaster University is skilled in using this technique to find such DNA talents. The key reason that we are interested in these molecules is to eventually use them to do useful things, such as using them to develop therapeutics or diagnostics. However, before we can use them for suitable applications, we need to know their traits through a process known as "molecular characterization". This NSERC Discovery grant aims to find new DNAzymes and DNA aptamers, characterize them well, and get them to do useful things. We will pursue four specific goals. First, we want to find a new group of DNAzymes and use them as molecular tools to study an important biological process known as "RNA modification". Second, we want to test a brand new idea for making better DNA aptamers with a much sharper detecting capability so that they can do more efficient detective work than existing DNA aptamers. Third, we want to develop an approach that uses color change to report the detective work by DNA aptamers, like a litmus test. Finally we want to construct a series of ring-shaped DNA aptamer or DNAzyme systems and lock them together so that can do two or more things at once. Overall, through the work to be performed in this proposal, we will generate new knowledge about DNA aptamers and DNAzymes, develop new or better DNA aptamers and DNAzymes, and devise new approaches that employ DNAzymes and DNA aptamers for environmental, food safety, and medical applications. Besides making important scientific discoveries, in this project we will work with several young students over the next five years and train them to become highly skilled scientists for the future of Canada.