Date of Award

9-1-2021

Degree Name

Doctor of Philosophy

Department

Chemistry

First Advisor

Shamsi, Mohtashim Hassan

Abstract

TITLE: DNA INTERFACES FOR ELECTROCHEMICAL DETECTION OF NEURODEGENERATIVE REPEAT SEQUENCES DNA repeat sequences in the human genome possess unique biophysical properties due to their sequence-directed structural flexibility. It has been assumed that unique helical flexibility of these sequences forms non-canonical structures inside the cell that disrupts transcription/translation functions and can lead to variety of fatal diseases such as neurodegenerative disorders. Neorodegenerative diseases are caused by certain types of mutations called repeat expansions. Expansion of certain trinucleotide repeat (TNR) sequences have been associated with almost two dozen neurodegenerative and neuromuscular diseases, such as CGG expansion with Fragile X, CAG repeats with Huntington’s disease (HD), CTG repeats with Myotonic Dystrophy, and GAA expansion with Friedreich’s Ataxia depending on their gene location and threshold length. Current diagnosis of repeat expansion disorders includes traditional techniques including two-dimensional gel electrophoresis and various polymerase chain reaction (PCR) based methods. However, these methods are complicated, high cost, frequently generate false negatives, and are time-consuming procedures. Therefore, to develop rapid and sensitive detection tools, a number of researchers have employed electrochemical strategies for detection of TNR sequences and their lengths using electroactive labels and enzyme-linked steps for signal amplification. However, an urgent need exists for further exploration in this area in order to develop label-free, low-cost, and simple biosensing platforms to detect such unique sequences. In this dissertation we investigated the properties of repeat sequences associated with neurodegenerative diseases to characterize and develop low-cost, label-free, and printable electrochemical platforms to detect TNR sequences. First, surface probe microscopy and electrochemical methods were employed for characterization of TNR sequences and showed that the properties of TNRs are sequence dependent rather than by flexibility rank as had been previously reported for them. Then, the interface properties of these repeat sequences were studied on the surface of two-dimensional materials such as graphene and molybdenum disulfide. Finally, we reported a label-free, low-cost, and simple inkjet printable platform to distinguish the CGG expansion associated with Fragile-X disease.

Available for download on Tuesday, September 20, 2022

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