Explorations of DNA-Single-Walled Carbon Nanotube Interactions to Develop Multiplexed Molecularly Specific Biosensors for Inflammation

Author

Amelia K. Ryan, CUNY City CollegeFollow

Date of Award

2025

Document Type

Dissertation

Department

Biomedical Engineering

First Advisor

Ryan Williams

Keywords

nanoparticles, biosensors, single-walled carbon nanotubes, interleukin-6, interleukin-12

Abstract

Inflammatory cytokines such as interleukin-6 (IL-6) and interleukin-12 (IL-12) are central regulators of immune signaling and key biomarkers of disease, yet existing assays for their detection remain slow, invasive, and lack multiplexing ability. This dissertation advances the development of single-walled carbon nanotube (SWCNT) optical nanosensors capable of real-time, multiplexed, and molecularly specific cytokine detection through innovative use of single-stranded DNA (ssDNA) interfaces.

First, an IL-6-specific DNA aptamer was employed as both a dispersing agent and recognition probe for SWCNT fluorescence sensing. Sequence modifications, including anchor domains, truncations, and thermally induced refolding, were systematically tested to optimize sensitivity and selectivity. The resulting nanosensor exhibited reproducible, selective quenching in response to IL-6 while showing no response to random DNA controls, validating the aptamer’s dual role in solubilization and target recognition. This streamlined strategy simplified sensor fabrication and provided a generalizable framework for designing aptamer-based SWCNT sensors.

The next studies introduced an amine-functionalized ssDNA (DNA-NH₂) to unify SWCNT chirality sorting and biomolecular conjugation. DNA-NH₂ demonstrated sorting ability in aqueous two-phase extraction (ATPE) while enabling subsequent covalent attachment of antibodies to the SWCNT. This dual-function approach yielded chirality-sorted, antibody-conjugated SWCNT with distinct near-infrared emission peaks corresponding to different cytokine targets. These constructs demonstrated independent optical responses to IL-6 and IL-12, representing the first realization of spectrally multiplexed SWCNT sensors. The use of chemically modified DNA as a bridge between ATPE sorting and molecular recognition marks a significant advance in sensor scalability and versatility.

Finally, the multiplexed sensors were immobilized on APTES-coated glass substrates and integrated into a microglia-neuroblast co-culture model of neuroinflammation. Upon lipopolysaccharide stimulation, spatially heterogeneous wavelength shifts were observed by hyperspectral microscopy, suggesting localized cytokine release and immune activation. This chip-based sensor platform enables non-invasive, spatially resolved monitoring of extracellular signaling in living cell systems – an essential step toward functional imaging of neuroimmune dynamics.

Collectively, these studies establish efficient routes to specific and multiplexed SWCNT sensors by exploiting ssDNA as a multifunctional interface for dispersion, sorting, bioconjugation, and recognition. The resulting nanosensors expand the toolkit for studying inflammatory biology and lay the groundwork for translational biosensing applications. Future work will focus on enhancing chiral purity and reversibility, coupling nanosensor readouts with conventional microscopy methods, and extending these platforms to further in vitro and in vivo disease models. This research moves nanoscale optical sensing closer to real-time molecular diagnostics and spatiotemporal mapping of immune signaling.

Recommended Citation

Ryan, Amelia K., "Explorations of DNA-Single-Walled Carbon Nanotube Interactions to Develop Multiplexed Molecularly Specific Biosensors for Inflammation" (2025). CUNY Academic Works.
https://academicworks.cuny.edu/cc_etds_theses/1246