18,380 research outputs found
Towards spatial computing and chemical information storage in soft materials using DNA programming
Living organisms possess the ability to form and recover complex patterns in prescribed locations at length scales of hundreds of microns. During the past 15 years, experimentalists within the fields of DNA nanotechnology and synthetic biology have developed a variety of systems capable of self-assembly and reorganization at the nanoscale using synthetic oligonucleotide building blocks to mimic the functions of biological tissues and to provide new routes of manipulating materials with molecular programs. Programming āsmart and responsiveā nano- and micromaterials using DNA circuits has the potential to impact numerous applications including molecular diagnostics, biodefense, drug delivery systems, and low-energy information storage. In this thesis, I present and develop computational and experimental systems that leverage oligonucleotide strand displacement reaction networks, digital maskless photolithographic technology, and microfluidic delivery methods to design DNA-functionalized micro-materials that process and store chemical information spatiotemporally. These systems couple reactions, transport, and feedback control to achieve specific temporal concentration profiles at specific points in hydrogel substrates. First, I developed a reaction-diffusion waveguide designed to coordinate spatiotemporal sensing and regulation of synthetic DNA- based materials using autocatalysis. I discuss the design requirements for this architecture and the results of in silico and experimental analyses of the components of this system. Based on the operational requirements of this system, I then designed a DNA-compatible hydrogel microfabrication method that accommodates UV photo-directed release of oligonucleotides from defined regions of a hydrogel, which can be used to initiate downstream reaction-diffusion processes in materials. Building on this platform, I constructed a reaction-diffusion system that enables shape programming of biomolecular attractor patterns in photopatterned poly(ethylene-glycol) diacrylate microgels. These patterns were able to heal their structure in response to spatial perturbation. Finally, I develop and discuss a model of a reaction-diffusion associative memory, consisting of a distributed network of nodes that store and repair spatial chemical patterns
DNA as a universal substrate for chemical kinetics
Molecular programming aims to systematically engineer molecular and chemical systems of autonomous function and ever-increasing complexity. A key goal is to develop embedded control circuitry within a chemical system to direct molecular events. Here we show that systems of DNA molecules can be constructed that closely approximate the dynamic behavior of arbitrary systems of coupled chemical reactions. By using strand displacement reactions as a primitive, we construct reaction cascades with effectively unimolecular and bimolecular kinetics. Our construction allows individual reactions to be coupled in arbitrary ways such that reactants can participate in multiple reactions simultaneously, reproducing the desired dynamical properties. Thus arbitrary systems of chemical equations can be compiled into real chemical systems. We illustrate our method on the LotkaāVolterra oscillator, a limit-cycle oscillator, a chaotic system, and systems implementing feedback digital logic and algorithmic behavior
Programmable interactions with biomimetic DNA linkers at fluid membranes and interfaces
At the heart of the structured architecture and complex dynamics of
biological systems are specific and timely interactions operated by
biomolecules. In many instances, biomolecular agents are spatially confined to
flexible lipid membranes where, among other functions, they control cell
adhesion, motility and tissue formation. Besides being central to several
biological processes, \emph{multivalent interactions} mediated by reactive
linkers confined to deformable substrates underpin the design of
synthetic-biological platforms and advanced biomimetic materials. Here we
review recent advances on the experimental study and theoretical modelling of a
heterogeneous class of biomimetic systems in which synthetic linkers mediate
multivalent interactions between fluid and deformable colloidal units,
including lipid vesicles and emulsion droplets. Linkers are often prepared from
synthetic DNA nanostructures, enabling full programmability of the
thermodynamic and kinetic properties of their mutual interactions. The coupling
of the statistical effects of multivalent interactions with substrate fluidity
and deformability gives rise to a rich emerging phenomenology that, in the
context of self-assembled soft materials, has been shown to produce exotic
phase behaviour, stimuli-responsiveness, and kinetic programmability of the
self-assembly process. Applications to (synthetic) biology will also be
reviewed.Comment: 63 pages, revie
Communication and quorum sensing in non-living mimics of eukaryotic cells.
Cells in tissues or biofilms communicate with one another through chemical and mechanical signals to coordinate collective behaviors. Non-living cell mimics provide simplified models of natural systems; however, it has remained challenging to implement communication capabilities comparable to living cells. Here we present a porous artificial cell-mimic containing a nucleus-like DNA-hydrogel compartment that is able to express and display proteins, and communicate with neighboring cell-mimics through diffusive protein signals. We show that communication between cell-mimics allows distribution of tasks, quorum sensing, and cellular differentiation according to local environment. Cell-mimics can be manufactured in large quantities, easily stored, chemically modified, and spatially organized into diffusively connected tissue-like arrangements, offering a means for studying communication in large ensembles of artificial cells
Remote Toehold: A Mechanism for Flexible Control of DNA Hybridization Kinetics
Hybridization of DNA strands can be used to build molecular devices, and control of the kinetics of DNA hybridization is a crucial element
in the design and construction of functional and autonomous devices.
Toehold-mediated strand displacement has proved to be a powerful
mechanism that allows programmable control of DNA hybridization. So
far, attempts to control hybridization kinetics have mainly focused on
the length and binding strength of toehold sequences. Here we show that
insertion of a spacer between the toehold and displacement domains
provides additional control: modulation of the nature and length of the
spacer can be used to control strand-displacement rates over at least 3
orders of magnitude. We apply this mechanism to operate displacement
reactions in potentially useful kinetic regimes: the kinetic
proofreading and concentration-robust regimes
Experimental Biological Protocols with Formal Semantics
Both experimental and computational biology is becoming increasingly
automated. Laboratory experiments are now performed automatically on
high-throughput machinery, while computational models are synthesized or
inferred automatically from data. However, integration between automated tasks
in the process of biological discovery is still lacking, largely due to
incompatible or missing formal representations. While theories are expressed
formally as computational models, existing languages for encoding and
automating experimental protocols often lack formal semantics. This makes it
challenging to extract novel understanding by identifying when theory and
experimental evidence disagree due to errors in the models or the protocols
used to validate them. To address this, we formalize the syntax of a core
protocol language, which provides a unified description for the models of
biochemical systems being experimented on, together with the discrete events
representing the liquid-handling steps of biological protocols. We present both
a deterministic and a stochastic semantics to this language, both defined in
terms of hybrid processes. In particular, the stochastic semantics captures
uncertainties in equipment tolerances, making it a suitable tool for both
experimental and computational biologists. We illustrate how the proposed
protocol language can be used for automated verification and synthesis of
laboratory experiments on case studies from the fields of chemistry and
molecular programming
Chaste: a test-driven approach to software development for biological modelling
Chaste (āCancer, heart and soft-tissue environmentā) is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence.\ud
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Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling
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