New Ways to Look through Nanopores

New Ways to Look through Nanopores

Klughammer, N. (TU Delft BN/Cees Dekker Lab)

Dekker, C. (promotor)
Joo, C. (copromotor)

Delft University of Technology

2023-11-17

In this thesis, we have introduced palladium zero-mode waveguides (Pd ZMWs) as a valuable tool for biophysics research and have showcased several applications thereof. We started by using them as single-molecule sensors for free translocations of fluorophores, proteins, and voltage-driven translocations of DNA. By studying salt-gradient driven DNA translocations we could investigate the effect of diffusiophoresis on nanopore translocations. Next, we attached nucleoporins to Pd ZMWs, which allowed us to mimic the transport occurring through the nuclear-pore complex. Here, we found that the pore diameter plays a crucial role for the selectivity of NPC mimics. To explore this effect further, we developed a new method making the structure of NPC mimics visible using cryo-EM. In a last application, we could enable observations of single membrane-bound fluorophores despite a high-cytoplasmic fluorescence background in live-cells by letting them grow into Pd ZMW nanowells.

Single-molecule Biophysics
Single-molecule Fluorescence
Solid-state Nanopores
Nanofabrication
Nanotechnology
Zero-mode Waveguides
Subwavelength Apertures
Palladium Nanopores
Live-cell Imaging
Nuclear Pore Complex
Nuclear Transport
Cryo-EM
Diffusiophoresis
Free Diffusion

https://doi.org/10.4233/uuid:b43633d1-5722-4457-8603-8396ff34181e

978-90-8593-577-3

Casimir PhD series, 2023 (30)

Institutional Repository

doctoral thesis

© 2023 N. Klughammer