Expanding biosensing systems through synthetic functional deoxyribonucleic acids

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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.