UC Riverside

ABSTRACT OF THE THESIS

Exploration of Nanomaterial-Assisted CE-SELEX in Discovery of Aptamers for Pesticides

By

Zhe Song

Master of Science, Graduate Program in Environmental Toxicology

University of California, Riverside, December 2016

Dr. Wenwan Zhong, Chairperson

DNA aptamers has been established as powerful molecular tools in wide range of applications in bio-analytical studies. Their unique properties including high binding affinity towards different classes of targets and stability make DNA aptamers became a reliable alternative biosensors in addition to antibody. In this thesis, we explored the binding affinity between two reported pesticides and their selected DNA aptamers with the combination of two Capillary Electrophoresis running modes: Affinity Capillary Electrophoresis (ACE) and Non-equilibrium Capillary Electrophoresis of Equilibrium Mixtures (NECEEM). We also developed a novel separation strategy to improve the on-column enrichment efficiency of target bound aptamers in CE.

In chapter 1, we introduced and discussed the basic concept of Capillary Electrophoresis , the application and selection of DNA aptamers and the rationale why further modification of CE-SELEX method is required to improve the quality and efficiency of aptamer isolation.

In chapter 2, we explored the binding affinity of two reported pesticides targets-DNA aptamer system: N-Methyl Mesoporphyrin IX (NMM)-Clone3.5 and Tebuconazole-T2 with the aid of ACE and NECEEM based on their characterized dissociation kinetics. We also investigate the effects of binding buffer component on binding affinity between N-Methyl Mesoporphyrin IX (NMM) target and Clone3.5 aptamer.

In chapter 3, we developed a novel gold nanoparticle assisted sweeping CE strategy to improve the isolation efficiency of both of the target bound Clone3.5 and T2 aptamers. Preliminary on-column enrichment of target bound aptamers had been successfully observed. In addition, we demonstrated the excellent selectivity of our method for free single-stranded DNA over target bound aptamers, meaning that the strategy developed by us own great potential in CE-SELEX method.

Finally, in chapter 4, we summarized the exciting progress we made first and then, we laid out the challenges in separation method development and provided outlooks in future investigation in this field.