Date of Award

Spring 5-2022

Document Type

Honors Thesis

Degree Name

Bachelor of Science

Department

Biological Science

Advisor/Committee Chair

Arun Richard Chandrasekaran

Committee Member

Ken Halvorsen

Committee Member

Gabriele Fuchs

Abstract

Long non-coding RNAs (lncRNAs) are transcripts that are over 200 nucleotides and do not encode proteins. LncRNAs are involved in a wide spectrum of biological processes ranging from cell proliferation, apoptosis, and nutrient sensing to cell differentiation. Further, lncRNAs have been reported to play an important role in a wide range of pathophysiological processes and are linked to diseases such as cancer. Thus, lncRNAs are becoming increasingly important as biomarkers to study biological and disease processes. In our work, we develop a DNA nanoswitch-based assay for detecting long RNAs. The DNA nanoswitch is a reconfigurable device that undergoes a conformational change from a linear “off” state to a looped “on” state upon interaction with the target molecule. The two states can be easily identified on an agarose gel. Using in vitro transcribed RNA controls, we optimize the assay for detecting different lengths of target RNAs, validate the sensitivity and specificity of the assay, and detection of target RNA in the presence of total RNA extract. Our work aims to create a lncRNA detection assay that will be useful in the early treatment of diseases and in screening potential biomarkers (for example, in Duchenne Muscular Dystrophy). The DNA nanoswitch-based assay is low-cost, highly sensitive and specific, and easily adaptable in any laboratory for detecting various biomarkers.

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