Degree
Doctor of Philosophy (PhD)
Department
Department of Mechanical and Industrial Engineering
Document Type
Dissertation
Abstract
Mechanically robust Solid-state nanopores that enable a label-free, long read, high throughput, and low-cost sequencing have the potential to be served as the next-generation DNA sequencing platforms. However, the challenges of mass production and limited accuracy in nucleobases separation pose significant obstacles to solid-state nanopore-based DNA sensing. To address these challenges, we propose a novel lab-on-a-chip device composed of dual in-plane nanopores made into polymer substrates that can be fabricated using high throughput nanoimprint lithography (NIL), capable of discriminating DNA and RNA nucleobases by measuring time-of-flight (TOF). In this study, we present a proof of concept by demonstrating the ability of the dual nanopore TOF sensor to discriminate between mononucleotides via their TOF.
First, the fabrication process for creating the dual nanopore TOF sensors in polyethylene glycol diacrylate (PEGDA) substrate was discussed. Then, an active compression-based pore size tuning was used to regulate the size of the in-plane nanopores at the sensor and manipulate the translocation mechanism of biomolecules. The results demonstrate that while the size of in-plane nanopores significantly determines the characteristics of electronic signals, the TOF values do not change with the dimension of nanopores.
The PEGDA-made dual nanopore TOF sensor with different nanocolumn lengths was utilized to demonstrate exonuclease DNA and RNA sequencing under various experimental conditions. A higher identification accuracy of mononucleotide was achieved at longer nanocolumns. Also, the results indicate that increasing the driving voltages improves the sensor's performance in terms of event frequency, signal-to-noise ratio, and TOF-based separation accuracy. In addition, the effect of alkali cations on the sensor's performance, including event frequency, noise level, dwelling time, current blockade, and TOF of mononucleotides, was investigated. The results showed that KCl solutions yielded higher current blockade and event rates, leading to better identification accuracy. The study also demonstrated that higher electrolyte pH improved the identification accuracy of RNA nucleobases. Finally, in addition to the specific geometry of in-plane nanopores, a significantly low ion diffusion coefficient measured inside the nanochannel confined with nanopores at the sensor could contribute to the unprecedented electronic signals observed for mononucleotides.
Date
4-5-2023
Recommended Citation
Riahipour, Ramin, "Bio NEMS: Studying Resistive Pulse Sensing Technique to Discriminate Mononucleotides Using In-Plane Solid-State Nanopore Configuration" (2023). LSU Doctoral Dissertations. 6132.
https://repository.lsu.edu/gradschool_dissertations/6132
Committee Chair
Park, Sunggook
DOI
10.31390/gradschool_dissertations.6132
Included in
Biology and Biomimetic Materials Commons, Mechanical Engineering Commons, Semiconductor and Optical Materials Commons