A Light-Triggered Synthetic Nanopore for Controlling Molecular Transport Across Biological Membranes

Controlling biological molecular processes with light is of high interest in biological research and biomedicine, as light allows precise and selective activation in a non-invasive and non-toxic manner. A molecular process benefitting from light control is the transport of cargo across biological membranes, which is conventionally achieved by membrane-puncturing barrel-shaped nanopores. Yet, there is considerable interest to construct more complex gated pores. Here, we pioneer a synthetic light-gated nanostructure which controls transport across membranes via a controllable lid. The light-triggered nanopore is self-assembled from six pore DNA strands and a lid strand carrying light-switchable azobenzene molecules. Exposure to light opens the pore to allow small-molecule transport across membranes. Our light-triggered pore advances biomimetic chemistry and DNA nanotechnology and may be used in biotechnology, biosensing, targeted drug release, or synthetic cells

“Nothing wrong with prejudice and discrimination:” Omaha newspaper coverage of the Civil Rights Movement in 1968

This thesis discusses Omaha newspaper coverage of the Civil Rights Movement from January to April 1968. As the Vietnam War raged, racial tension continued to build in the United States, including Omaha, Nebraska. Despite its desegregation, a primarily white, male government controlled the city. The visit of Alabama Governor George Wallace, a widely known white-supremacist presidential candidate, and the assassination of Dr. Martin Luther King Jr. exacerbated the anger already felt by black communities throughout the city. This thesis examines the accuracy and contrasting content of the Omaha Star, a newspaper created to serve the black community, and the Omaha World-Herald, which mainly published articles written by white men

Exploring the Relationship between BODIPY Structure and Spectroscopic Properties to Design Fluorophores for Bioimaging

Designing chromophores for biological applications requires a fundamental understanding of how the chemical structure of a chromophore influences its photophysical properties. We here describe the synthesis of a library of BODIPY dyes, exploring diversity at various positions around the BODIPY core. The results show that the nature and position of substituents have a dramatic effect on the spectroscopic properties. Substituting in a heavy atom or adjusting the size and orientation of a conjugated system provides a means of altering the spectroscopic profiles with high precision. The insight from the structure–activity relationship was applied to devise a new BODIPY dye with rationally designed photochemical properties including absorption towards the near‐infrared region. The dye also exhibited switch‐on fluorescence to enable visualisation of cells with high signal‐to‐noise ratio without washing‐out of unbound dye. The BODIPY‐based probe is non‐cytotoxic and compatible with staining procedures including cell fixation and immunofluorescence microscopy

Design, assembly, and characterization of membrane-spanning DNA nanopores

DNA nanopores are bio-inspired nanostructures that control molecular transport across lipid bilayer membranes. Researchers can readily engineer the structure and function of DNA nanopores to synergistically combine the strengths of DNA nanotechnology and nanopores. The pores can be harnessed in a wide range of areas, including biosensing, single-molecule chemistry, and single-molecule biophysics, as well as in cell biology and synthetic biology. Here, we provide a protocol for the rational design of nanobarrel-like DNA pores and larger DNA origami nanopores for targeted applications. We discuss strategies for the pores’ chemical modification with lipid anchors to enable them to be inserted into membranes such as small unilamellar vesicles (SUVs) and planar lipid bilayers. The procedure covers the self-assembly of DNA nanopores via thermal annealing, their characterization using gel electrophoresis, purification, and direct visualization with transmission electron microscopy and atomic force microscopy. We also describe a gel assay to determine pore–membrane binding and discuss how to use single-channel current recordings and dye flux assays to confirm transport through the pores. We expect this protocol to take approximately 1 week to complete for DNA nanobarrel pores and 2–3 weeks for DNA origami pores

Solvent-dependent photophysics of a red-shifted, biocompatible coumarin photocage

Controlling the activity of biomolecules with light-triggered photocages is an important research tool in the life sciences. We describe here a coumarin photocage that unusually combines the biocompatible optical properties of strong absorption at a long wavelength close to 500 nm and high photolysis quantum yields. The favourable properties are achieved by synthetically installing on the photocage scaffold a diethyl amino styryl moiety and a thionoester group rather than the lactone typical for coumarins. The photocage's photophysics are analysed with microsecond transient absorption spectroscopy to reveal the nature of the excited state in the photolysis pathway. The excited state is found to be strongly dependent on solvent polarity with a triplet state formed in DMSO and a charge-separated state in water that is likely due to aggregation. A long triplet lifetime is also correlated with a high photolysis quantum yield. Our study on the biocompatible photocage reveals fundamental insight for designing advanced photocages such as longer wavelengths in different solvent conditions tailored for applications in basic and applied research

Light-controlled probes for chemical biology

Controlling the biological activity of chemical probes with light is of interest in many different areas. In research, it allows to selectively probe or perturb biological systems to understand them better. In biomedicine, photocontrol can improve a drug’s activity towards diseased cells. Light is an ideal trigger as it can be focused spatially and temporally. Furthermore, light is non-invasive and non-toxic. The first aim of this thesis was to synthesise new photo-responsive groups which enable the controlled release of small molecules. These light-responsive groups, also termed photocages, are covalently linked to a target molecule to inhibit its activity. Upon application of light, the photocage is excited and released, so that the activity of the target molecule is restored. Existing photocages absorb at wavelengths at around or below 400 nm. However, to apply photocages in biomedicine the wavelength of absorption must be increased in order to achieve sufficient penetration of tissue and create optically orthogonal photocages. This project aimed to overcome this issue and develop a novel coumarin-based photocage that absorbs at longer wavelengths. The spectroscopic and photorelease properties of the new compound were also investigated. In addition, the electronically excited states of the compound were analysed to attain insight into the mechanism of photorelease. This will allow for improved rational design in the future. The photocage could be used for controlled drug release or to study physiological pathways. The second aim was to build a DNA-based membrane channel with a light-controllable molecular valve based on duplex formation and dissociation. This will allow to control when cargo is transported across the channel. Membrane channels are molecular gate keepers that control trans-membrane transport in physiological systems. Recreating and tuning channels is scientifically exciting since it permits to expand the principle into synthetic biology. Rationally designed channels have predictable properties, enabling their use in biomedicine. Naturally occurring membrane channels are usually composed of polypeptides. However, it is challenging to design and build channels with a predictable structure from intricately folded polypeptides. By contrast, DNA as a building material facilitates a simple rational design. To achieve light-control, several light-switchable azobenzene groups were installed in the lid of the molecular valve to tunably alter duplex formation. The artificial channel could be used for controlled drug release or be incorporated into nanoreactors