Author ORCID Identifier:
Date of Graduation
5-2026
Document Type
Dissertation
Degree Name
Doctor of Philosophy in Cell & Molecular Biology (PhD)
Degree Level
Graduate
Department
Cell & Molecular Biology
Advisor/Mentor
Li, Jiali
Committee Member
Thallapuranam, Suresh
Second Committee Member
Kral, Timothy
Third Committee Member
Kwon, Young
Keywords
DNA; RNA; solid-state Nanopore
Abstract
This study uses solid-state nanopore technology to investigate the stability and dynamics of RNA molecules under thermal stress and pH fluctuations. Two distinct mRNA samples were analyzed: (1) heat shock protein (HSP)-encoding mRNA extracted from Sulfolobus solfataricus P2, a thermophilic archaeon inhabiting extreme environments such as geothermal sulfuric hot springs (pH < 4, temperature range: 65–90°C), and (2) total RNA extracted from White Leghorn chickens, which thrive under standard physiological conditions. ΦX174 virion single-stranded DNA (ssDNA) were included as a comparative reference. Nanopores, fabricated in silicon nitride membranes, were used to electrically characterize the structural properties of individual RNA molecules in solution, close to their native environments. The nanopore membrane separates two chambers containing salt buffer solution, where ionic current is the primary measurement parameter. When a voltage bias is applied across the membrane, ion flow and an ionic current can be measured. Charged RNA molecules driven translocation through the nanopore induces pore resistance changes, resulting in detectable current blockade events. Variations in these events provide insights into RNA secondary structure and conformational dynamics. By systematically altering pH and temperature, this study elucidates the effects of environmental stressors on RNA stability and structural integrity. The findings reveal distinct responses between thermophilic HSP-encoding mRNA and mesophilic RNA, underscoring the adaptive mechanisms of thermophilic RNA under extreme conditions. These results contribute to a better understanding of RNA behavior under stress and establish a foundation for future applications in RNA-based diagnostics and biotechnology development.
Citation
Li, H. (2026). Sensing RNA’s Conformation with a Solid-State Nanopore Device at Various pH and Temperature. Graduate Theses and Dissertations Retrieved from https://scholarworks.uark.edu/etd/6188
