Functional DNA Amplicons

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The long-term objectives of my research program are to further develop additional tools in the repertoire of methods for biomolecule immobilization. Primarily, we aim to investigate the nature of DNA and RNA superstructures formed from rolling circle amplification of functional nucleic acids (FNAs), including DNA and RNA aptamers and DNA enzymes, to expand the use of such assemblies as a platform for biomolecule immobilization, and to apply these assemblies to a range of bioanalytical devices where we will exploit their potential for various biosensing, catalysis and affinity separation applications. For the new funding period, we will pursue the following four short term aims that build upon the momentum of our ongoing DG funded program.Aim 1 Fabrication of FNA Amplicons: The key goal of this project is to expand the repertoire of FNA amplicon NFs, and evaluate the properties of FNAs within NFs. This work is foundational for the proposal, and will provide important insights into the versatility of 3D amplicon superstructures, and how to control the behavior of these novel structures.Aim 2 Protein-Amplicon Conjugates: This project will aim to extend the amplicon platform beyond functional DNA species by binding DNA-oligomer-modified proteins to amplicons via hybridization or aptamer-protein interactions, and using these species for the applications noted above (columns, paper sensors). This will open up a completely new area of study in our group, and is likely to produce a number of breakthroughs in bioanalysis using immobilized proteins.Aim 3 DNA Amplicon Affinity Columns: This work will address a fundamental problem in the use of sol-gel based bioaffinity columns the restriction to small molecule analytes. The proposed study will build on our recent report on amplicon-doped columns and will expand the types of functional nucleic acids used to form amplicon columns and the overall applications of these columns. Aim 4 Paper-based Sensors Utilizing Amplicons: Immobilization of biomolecules onto heterogeneous surfaces, such as the cellulose network of paper, remains a challenge. We will investigate the use of FNA amplicons as a platform for producing multiplexed paper sensors, and will investigate the properties of printed amplicons and how they behave on paper surfaces. Signficance and Impact: The proposed research program will develop a new method for immobilization of biological agents (DNA aptamers, DNAzymes and proteins) that is compatible with fabrication of affinity columns, biosensors or other bioactive surfaces. The outcome will be a highly versatile, generic biointerface platform, which is highly tunable and can be adapted to multiple applications. The new discoveries from our DG funded program will create new technologies and add new tools to the arsenal of scientists and engineers involved in development of bioactive materials.