Category
Physical Science (i.e., Chemistry, Physics) and Mathematics
Faculty Mentor
Yulia Gerasimova
Faculty Mentor Primary Department
Department of Chemistry
Year of Presentation
2020
Project Abstract, Summary, or Creative Statement
Aptamers are nucleic acid “receptors” that selectively bind to small molecules. They can be isolated from a pool of randomized nucleic acid sequences to recognize a ligand. A DNA aptamer can be split to give high selectivity to a target gene, and when the split sequences come together, its ligand binding region can be formed. Significant fluorescent turn-on can be achieved when low-fluorescent dye ligands bind strongly to the aptamer. This has made the use of these aptamers a promising technique in bioanalysis and detection of small amounts of target biomolecules, including targets infected with pathogenic disease.
This study aimed to optimize fluorescent turn-on of the Dapoxyl aptamer, a DNA aptamer shown to increase fluorescence of Dapoxyl dye (Kato et al.).
Alternative dye screening designed to test the selectivity of the aptamer lead to the discovery that DAP binds to Auramine-O dye with higher affinity and produces higher turn-on with decreased background fluorescence.
Buffer analysis was performed to optimize buffer components for fluorescent turn-on. Mutation analysis was performed to investigate the role of each nucleotide region in the aptamer’s activity and discover the nucleotide regions that are essential for dye binding. Mutations were induced to single nucleotides or nucleotide regions, and the effect on fluorescent turn-on was measured.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Keywords
aptamer, dapoxyl aptamer, auramine-o, aptamer optimization, limit of detection, g-quadruplex, fluorescent turn-on, buffer optimization, mutation analysis
Included in
Biochemistry Commons, Chemistry Commons, Structural Biology Commons
Optimization of Dapoxyl Aptamer for Label-Free Bioanalysis