UC Irvine

In the past five decades, several landmark discoveries have demonstrated that nucleic acids are a multi-talented class of biomolecules. These discoveries include naturally occurring ribozymes (RNA enzymes), man-made ribozymes and deoxyribozymes (DNA enzymes), and DNA and RNA aptamers (nucleic acid-based molecular binders). These advancements have increased the popularity of nucleic acid molecules as potential biorecognition elements for analytical and biosensor applications. The studies presented here focuses on the in vitro selection of a rational deigned functional aptamer molecules capable of identifying bladder cancer urine samples by recognizing the urinary molecular compositions, or urine biomarkers, associated with bladder cancer. To achieve the aforementioned, I described the different in vitro selection strategies designed to identify aptamer molecules that recognize various target molecules with high specificity and affinity. This is followed by a more detailed focus on the in vitro selection of structure-switching aptamer scheme where I reported the designing and testing of a diverse DNA library. I provided three different selections that were performed utilizing the custom DNA library to demonstrate the feasibility of the library design and the structure-switching in vitro selection platform. Lastly, I performed a complex selection to isolate bladder cancer specific structure-switching aptamers. The complex selection yield specific-aptamers that can distinguish bladder cancer urine samples from hematuria, or blood in urine, urine samples.