3 research outputs found
Transmembrane molecular machines
Transmembrane molecular machines are ubiquitous in nature. These evolved systems
demonstrate superlative elegance and efficiency of operation. Imitation and hijacking of
biological components such as proteins and DNA has emerged as a means of imparting
desirable characteristics to rationally designed synthetic molecular machines. This thesis
presents work towards various synthetic transmembrane molecular machines based on alpha-haemolysin (α-HL).
Chapter One reviews progress towards synthetic transmembrane machines, introducing
natural examples, defining criteria for being ‘a molecular machine’ cataloguing examples and
trends in synthetic molecular machines in solution, on surfaces and in membranes. Examples
are evaluated in terms of their machine like behaviour and α-HL emerges as a particularly
promising component in the development of synthetic transmembrane molecular machines.
Chapter Two examines solvent isotope effects resulting from substitution of hydrogen by
deuterium in water at the nanoscale – on the rates of transmembrane ion transport and
transmembrane translocation of ssDNA through α-HL, both of which are of concern in the
context of building molecular machines which use α-HL as a component.
Chapters Three to Six look at different machine applications of related transmembrane
architectures based on individual transmembrane rotaxanes constructed in α-HL from
DNA/PEG copolymer ‘thread’ strands and DNA ‘primer’ strands.
Chapter Three uses this approach to observe translational motion of the thread strand in
both directions along the z-axis due to nucleotide incorporation and pyrophosphorolysis in
real-time with single-nucleotide resolution.
Chapter Four provides the first demonstration of asymmetrical, hysteretic cyclical
behaviour in the translational motion of the thread strand by incorporation of a nicking site
which resets the system after nucleotide incorporations have occurred.
Chapter Five introduces a novel variant of the rotaxane architecture using a circularised
primer strand which allows real time observation of rolling circle amplification at the single
molecule level by coupling the process to the unidirectional translocation of the thread strand.
Chapter Six considers the use of the vestibule of α-HL as a transmembrane DNA ligase
mimic with the DNA thread/primer complex as substrate