Nucleic acids are exquisitely adept at molecular recognition and self-assembly, enabling them to direct numerous key processes that make life possible. These capabilities have been fine-tuned by billions of years of evolution, and more recently, have been harnessed in the laboratory to enable the use of DNA and RNA for applications that are completely unrelated to their canonical biological roles. The common thread that is woven throughout our research program is the utilization of nucleic acid molecular recognition and self-assembly to generate functional architectures for biosensing and bioimaging. In the process of generating these functional nucleic acid systems, we place a high value on using our experimental results (both successes and failures) to gain a deeper understanding of the forces that drive small molecule-nucleic acid and nucleic acid-nucleic acid interactions. Our research program is comprised of the following distinct, yet synergistic, project areas:
Nucleic acid aptamers offer a promising alternative to antibodies for a wide range of biosensing applications. We have demonstrated the use of a split aptamer to transduce a small molecule signal into the output of a DNA ligation event. If present in solution, the target molecule directs assembly of the split aptamer, bringing DNA-appended reactive groups into close proximity and thus promoting a chemical ligation. We have demonstrated that this enables the sensitive and selective detection of drug molecules in an enzyme-linked format, which is the current gold standard in clinical diagnostics. We have also addressed an overarching challenge in this field – the dearth of split aptamer recognition elements – by developing a reliable method for the engineering of aptamers into split aptamers.
Moving beyond detection to characterization, we seek to address the challenging task of measuring small molecule enantiopurity, as this is a key factor in the synthesis of pharmaceutical intermediates and other high-value chemicals. Enantiopurity can be measured by chiral chromatographic methods, but this process is limited to a few thousand samples per day. Utilizing the principle of reciprocal chiral substrate selectivity, we have generated enantiomeric DNA biosensors capable of measuring small molecule enantiopurity with a direct fluorescence output, which provides significantly increased throughput. We envision application of this method to optimize stereoselectivity in reactions using either chemical or biological catalysts.
Fluorescent RNA labeling
The localization and dynamics of RNA play a key role in directing a wide variety ofcellular processes. Gaining a deeper understanding of mRNA localization patterns and the corresponding mechanisms of mRNA transport would provide a wealth of information regarding disease progression and potential therapeutic approaches. In collaboration with the Hollien Lab (Univ. of Utah Biology), we are developing a novel strategy for labeling and imaging of specific RNAs in living cells. Our method relies on the use of self-alkylating ribozymes, which can be fused to an RNA of interest and undergo covalent self-labeling with a fluorophore having an electrophilic reactive group. We envision using these ribozymes to track the localization of RNA in living cells and to identify the RNA-binding proteins that are responsible for RNA localization.
Modified peptide nucleic acids
Peptide nucleic acid (PNA) is a nucleic acid analog in which the phosphodiester backbone is replaced with a peptide-like aminoethylglycine unit. PNA shows great potential for use in vivo due to its higher affinity and selectivity for native nucleic acids as well as its increased resistance to degradation by nucleases and proteases. In order to expand the role of PNA in these applications, we have investigated the impact of backbone modification on binding with DNA and RNA. We are also exploring the ability of PNA funcitonalization to drive self-assembly into micellar architectures capable of acting as programmable materials.