Applied Science Projects

DNAzymes as therapeutics. Apoptosis (programmed cell death) is essential for both normal development and tissue homeostasis; abnormal regulation of apoptosis has been attributed to many human diseases, such as cancer, autoimmunity, and neurodegenerative disorders. Several anti-apoptotic members of the Bcl-2 protein family are known to dictate the apoptosis or survival of cancer cells; cancer cells can escape from chemo- or radiotherapy-induced apoptosis by overproducing these proteins. Therefore, these so-called apoptotic blocks are attractive candidates as therapeutic targets. RNA-cleaving DNAzymes (RNase DNAzymes) can perform sequence-specific cleavage of RNA, and therefore, they can be very useful enzymatic agents to degrade specific cellular RNA molecules in cells and have considerable therapeutic potential. We are working on creating and studying RNase DNAzymes that target the mRNAs of important anti-apoptotic proteins of the Bcl-2 family, with a long-term goal of developing RNase DNAzymes as anti-cancer therapeutics.


DNAzyme as protein biosensors. Currently the major classes of sensors for events in live cells are chemical dyes and fluorescence proteins. Both have significant limitations and there is a great need to develop both in-cell sensors and those that can be used in ‘mix and read’ assays. We are interested in developing novel protein sensors using signaling DNAzymes discussed above. Signaling DNAzyme sensors will perform three linked functions: ligand binding, catalysis and fluorescence generation; we believe they can be used as platform probes for engineering real-time fluorescent sensors for the detection of a specific protein of interest. For example, we are actively conducting a project aimed to create signaling DNAzymes for detecting some apoptotic factors in cancer cells and studying biological roles of proteins that regulate apoptosis, which is an important step in the understanding of molecular mechanism of cancer and can lead to the discovery of novel therapeutic targets for such a deadly disease. Certain apoptotic factors have also been implicated as biomarkers for diseases such as cancer; therefore, a convenient method to detect these protein molecules may eventually be developed into a diagnostic test.


Aptamers and DNAzymes as biosensors for food-borne pathogens. Testing for food-borne pathogens is essential to the public health. Highlighted by the recent Listeria outbreak at Maple Leaf Foods, there is a significant need to develop efficient, easy-to-use and cheap methods for food pathogen detection because existing methods are time consuming and labor-intensive processes, requiring highly skilled personnel and expensive reagents. We are developing biosensing aptamers and DNAzymes that are capable of performing speedy detection of food-borne pathogens such as Salmonella, Listeria and E. coli O157. For example, we are working on creating signaling DNAzyme based bacterial sensors. As discussed above, signaling DNAzymes are engineered to perform three linked functions: target recognition, enzymatic catalysis and fluorescence generation. The unmatched advantage of signaling DNAzyme technology is the development of a simple, ‘mix-and-read’ type of assay that is faster to perform and easier to use. The second advantage is the fact that signaling DNAzymes are a catalytic system and have a multiple turnover ability, resulting in faster reporting time. The third advantage is straightforward automation of such an assay for high-throughput sample analysis because manual DNA extraction or amplification is not required. In addition, the fact that the reagents are DNA provides for several practical benefits: signaling DNAzymes can be produced at a low cost, with high batch-to-batch consistency, and long shelf-life.


Bioactive papers.  It remains a significant challenge to develop simple, rapid, and inexpensive bioassays that can be applied for detection of biological agents in health, food and water. Currently, most of such analyses are performed in modern laboratories equipped with expensive instruments and staffed with highly qualified personnel. Although a few applications utilize simple test strips, generally speaking, most bioassays are not suited for use by average users. Thus, the development of easy-to-use biosensors is of tremendous interest in both research community and many industrial sectors. Such devices are deemed even more useful in the developing world where the access to sophisticated testing facilities is extremely limited. My lab is a member of a nationwide network called “Sentinel Bioactive Paper Network” and the goal of the network is to develop easy-to-use paper strips for medical diagnosis, food-borne pathogen detection, and environmental monitoring. We are actively developing paper strips that can detect toxic metals, organic pollutants, disease markers, or even whole cells (like food-borne pathogens or cancer cells). For example, we have recently successfully created a bioactive paper that can sensitively detect DNA.


DNA nanotechnology.  My lab is also interested in designing nanomaterials and nanomachines that contain DNAzymes or aptamers. Sensors made from nanomaterials (such as gold nanoparticles) modified with DNAzymes and DNA aptamers have the potential to achieve high sensitivity, low sample volume requirement, and capabilities for real time detection and high-throughput analysis-the major characteristics of an ideal biosensing technology. For example, we are very interested in developing DNA-modified gold nanoparticle (AuNP) as colorimetric biosensors. The ability to use AuNP as a colorimetric reporter relies on the fact that the dispersed AuNP solution is red whereas the aggregated AuNP solution is purple or blue. We have also established several forms of DNA-modified AuNP based assays that can be used to detect small molecules such as ATP and proteins such as enzymes. We have also found out that DNA-modified AuNPs can be printed on paper (like ink) and resultant bioactive papers can be used to perform the specific detection of a target of interest (including small molecules and proteins). These findings have given us the confidence that we can develop AuNP technologies that can be eventually commercialized for the detection of a variety of targets that are important to our health and lives.