dna catalysts have been developed as methods of amplifying single-stranded nucleic acid signals. the maximum turnover (gain) of these systems, however, often varies based on strand and complex purities, and has so far...
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ISBN:
(纸本)9783642183041
dna catalysts have been developed as methods of amplifying single-stranded nucleic acid signals. the maximum turnover (gain) of these systems, however, often varies based on strand and complex purities, and has so far not been well-controlled. Here we introduce methods for controlling the asymptotic turnover of strand displacement-based dna catalysts and show how these could be used to construct linear classifier systems.
dna strand displacement has been used to construct a variety of components, devices, and circuits. the sequences of involved nucleic acid molecules can greatly influence the kinetics and function of strand displacemen...
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ISBN:
(纸本)9783642183041
dna strand displacement has been used to construct a variety of components, devices, and circuits. the sequences of involved nucleic acid molecules can greatly influence the kinetics and function of strand displacement reactions. To facilitate consideration of spurious reactions during the design process, one common strategy is to subdivide dna strands into domains, continuous nucleic acid bases that can be abstracted to act as a unit in hybridization and dissociation. Here, considerations for domain-based sequence design are discussed, and heuristics are presented for the sequence design of domains. Based on these heuristics, a randomized algorithm is implemented for sequence design.
Process algebras are widely used to define the formal semantics of concurrent communicating processes. In this paper, we implement a particularly expressive form of process algebra, known as stochastic pi-calculus;at ...
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ISBN:
(纸本)9783642106033
Process algebras are widely used to define the formal semantics of concurrent communicating processes. In this paper, we implement a particularly expressive form of process algebra, known as stochastic pi-calculus;at the molecular scale by providing a design for a dna-based biomolecular device that simulates a process algebraic machine. Our design of the molecular stochastic pi-calculus system makes use of a modified form of Whiplash-PCR (WPCR) machines. In this design, we connect (via a tethering dna nanostructure) a number of dna strands, each of which corresponds to a WPCR. machine. this collection of WPCR machines are used to execute distinct concurrent processes, each with its own distinct program. Furthermore, their close proximity enables computation to proceed via communication.
We consider the problem of characterizing nontrivial languages D that are maximal withthe property that D*, the Kleene closure of D, is contained in the subword closure of a given set S of words of some fixed length ...
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ISBN:
(纸本)9783642236372
We consider the problem of characterizing nontrivial languages D that are maximal withthe property that D*, the Kleene closure of D, is contained in the subword closure of a given set S of words of some fixed length k. the subword closure of S is simply the set of words for which all subwords of length k are in S. We provide a deep structural characterization of these languages D, which leads to polynomial time algorithms for computing such languages. this work is motivated by the problem of encoding arbitrary data into a set of dna molecules such that all blocks of length k in these molecules satisfy the constraint S - eg, they can form no stable bonds between them, or they have a desired g-c ratio.
the potential for inferring the presence of cancer by the detection of miRNA in human blood has motivated research into the design and operation of dna-based chemical amplifiers that can operate in bodily fluids. As a...
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ISBN:
(纸本)9783642183041
the potential for inferring the presence of cancer by the detection of miRNA in human blood has motivated research into the design and operation of dna-based chemical amplifiers that can operate in bodily fluids. As a first step toward this goal, we have tested the operation of a dna-based autocatalytic network in human serum and mouse serum. Withthe addition of sodium dodecyl sulfate to prevent degradation by nuclease activity, the network was found to operate successfully with bothdna and RNA catalysts.
Sticker complexes are a formal graph-based data model for a restricted class of dna complexes, motivated by potential applications to databases. this data model allows for a purely declarative definition of hybridizat...
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Sticker complexes are a formal graph-based data model for a restricted class of dna complexes, motivated by potential applications to databases. this data model allows for a purely declarative definition of hybridization. We introduce the notion of terminating hybridization, which intuitively means that only a finite number of different products can be generated. We characterize this notion in purely graph-theoretic terms. Under a finite alphabet, each product is shown to be of polynomial size. Yet, terminating hybridization can still produce results of exponential size, in that there may be exponentially many different (nonisomorphic) finished products. We indicate a class of complexes where hybridization is guaranteed to be polynomially bounded.
Chemical reaction networks (CRNs) and dna strand displacement systems (DSDs) are widely-studied and useful models of molecularprogramming. In this tutorial, we introduce the models, illustrating the expressive power ...
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the hybridization of complementary nucleic acid strands is the most basic of all reactions involving nucleic acids, but has a major limitation: the specificity of hybridization reactions depends critically on the leng...
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ISBN:
(纸本)9783642183041
the hybridization of complementary nucleic acid strands is the most basic of all reactions involving nucleic acids, but has a major limitation: the specificity of hybridization reactions depends critically on the lengths of the complementary pairs of strands and can drop to very low values for sufficiently long strands. this reduction in specificity occurs especially in the presence of noise in the form of other competing strands that have sequence segments identical to the target. this limits the scale and accuracy of biotechnology and nanotechnology applications which depend on hybridization reactions. Our paper develops techniques for ensuring specific high-fidelity dna hybridization reactions for target strands of arbitrary length. Our protocol is executed autonomously, without external mediation and driven by a series of conversions of single stranded dna into duplex dnathat help overcome kinetic energy traps, similar to dna walkers.
Algorithmic dna tile systems have the potential to allow the construction by self-assembly of large structures with complex nanometer-scale details out of relatively few monomer types, but are constrained by errors in...
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ISBN:
(数字)9783030000301
ISBN:
(纸本)9783030000301;9783030000295
Algorithmic dna tile systems have the potential to allow the construction by self-assembly of large structures with complex nanometer-scale details out of relatively few monomer types, but are constrained by errors in growth and the limited sequence space of orthogonal dna sticky ends that program tile interactions. We present a tile set optimization technique that, through analysis of algorithmic growth equivalence, potentially sensitive error pathways, and potential lattice defects, can significantly reduce the size of tile systems while preserving proofreading behavior that is essential for obtaining low error rates. Applied to systems implementing multiple algorithms that are far beyond the size of currently feasible implementations, the optimization technique results in systems that are comparable in size to already-implemented experimental systems.
dna nanomachines are assemblies that rely on molecular inputs that are processed or transduced into measurable outputs. though dna nanotechnology has created a gamut of molecular devices, an outstanding challenge has ...
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ISBN:
(纸本)9783642236372
dna nanomachines are assemblies that rely on molecular inputs that are processed or transduced into measurable outputs. though dna nanotechnology has created a gamut of molecular devices, an outstanding challenge has been the demonstration of functionality and relevance of these devices in living systems. the I-switch is a dna nanodevice that, in response to protons, changes its conformation to produce a fluorescence resonance energy transfer (FRET) signal. We show that this rationally designed molecular device is capable of measuring spatiotemporal pH changes associated with endosomes as they undergo maturation in living cells in culture. Furthermore, we show that the nanomachine retains its autonomous functionality as it maps the same biological process in cells of a living organism like C. elegans. this demonstration of the quantitative functionality of an artificially designed scaffold positions dna nanodevices as powerful tools to interrogate biological phenomena.
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