DNA-based logic
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Bader2018.pdf (11.23Mb)
Date
09/07/2018Item status
Restricted AccessEmbargo end date
31/12/2100Author
Bader, Antoine
Metadata
Abstract
DNA nanotechnology has been developed in order to construct nanostructures and
nanomachines by virtue of the programmable self-assembly properties of DNA
molecules. Although DNA nanotechnology initially focused on spatial arrangement of
DNA strands, new horizons have been explored owing to the development of the
toehold-mediated strand-displacement reaction, conferring new dynamic properties to
previously static and rigid structures. A large variety of DNA reconfigurable
nanostructures, stepped and autonomous nanomachines and circuits have been
operated using the strand-displacement reaction. Biological systems rely on
information processing to guide their behaviour and functions. Molecular computation
is a branch of DNA nanotechnology that aims to construct and operate programmable
computing devices made out of DNA that could interact in a biological context. Similar
to conventional computers, the computational processes involved are based on
Boolean logic, a propositional language that describes statements as being true or false
while connecting them with logic operators. Numerous logic gates and circuits have
been built with DNA that demonstrate information processing at the molecular level.
However, development of new systems is called for in order to perform new tasks of
higher computational complexity and enhanced reliability. The contribution of
secondary structure to the vulnerability of a toehold-sequestered device to undesired
triggering of inputs was examined, giving new approaches for minimizing leakage of
DNA devices. This device was then integrated as a logic component in a DNA-based
computer with a retrievable memory, thus implementing two essential biological
functions in one synthetic device. Additionally, G-quadruplex logic gates were
developed that can be switched between two topological states in a logic fashion. Their
individual responses were detected simultaneously, establishing a new approach for
parallel biological computing. A new AND-NOT logic circuit based on the seesaw
mechanism was constructed that, in combination with the already existing AND and
OR gates, form a now complete basis set that could perform any Boolean computation.
This work introduces a new mode of kinetic control over the operation of such DNA
circuits. Finally, the first example of a transmembrane logic gate being operated at the
single-molecule level is described. This could be used as a potential platform for
biosensing.