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Engineering Transport through Biological and Synthetic Nanopores

  • Author(s): Buchsbaum, Steven
  • Advisor(s): Siwy, Zuzanna S
  • et al.
Abstract

Biological nanopores are an essential element to the success of the lipid bilayer that makes life possible on the cellular level. Protein based pores are responsible for the transport of specific ions and molecules across the bilayer and can accomplish their jobs with incredible variety. Some pores, such as those from bacteria have relatively simple structures and allow for many types of transport. Others, like those found in neurons have very high specificity as well as the ability to respond to different cues in the surrounding environment. The vast number of biological ion channels and their complex structures make it difficult to study and understand the nanofluidic phenomena they exhibit. Inspired by the pores seen in nature, scientists have begun to create their own synthetic versions which are usually simpler in structure. These man made pores have been fabricated through a variety of techniques and materials and provide well controlled systems capable of isolating and testing specific transport phenomena. Additionally, these pores provide the building blocks with which more complicated and truly biomimetic pores can be made.

In this thesis, three very different types of nanopores will be examined. First, an alpha hemolysin pore will be isolated and the physics governing transport time will be studied. The diameter and charge of single stranded DNA molecule is modified before being electrophoretically driven through the pores inner constriction. These translocation events are monitored via current measurements across the pore and a biological model is formulated to explain the behavior. This work has the potential to improve DNA sequencing technologies which are dependent on slowing down DNA translocation speed for accurate reads. Next, a synthetic conical nanopore etched in a polymer film will be used as the foundation for a biomimetic nanopore gate. Through the attachment of ssDNA to the pore walls, a pH and voltage responsive nanochannel is created. This is done through the careful selection of the DNA sequence to contain protonatable nucleotides which enable the formation of a transport blocking mesh. Synthetic gated channels that can respond to multiple stimuli as well as have a robust and reversible closing mechanism have been historically difficult to design and are essential to advancing the nanopore field. Finally, a different type of synthetic nanochannel is made from the inner volume of a carbon nanotube. We present a platform that allows for the isolation and study of a single nanotube and use it to examine the underlying transport properties. Carbon nanotube based nanochannels show several unique behaviors which the current literature has not been able to completely explain. Several questions such as the magnitude and origin of enhanced flow and even what carries the current remain open, motivating additional studies, such as ours, which aim to help provide much needed answers.

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