Probabilistic Analysis of Localized DNA Hybridization Circuits.

@article{Dalchau2015ProbabilisticAO,
  title={Probabilistic Analysis of Localized DNA Hybridization Circuits.},
  author={Neil Dalchau and Harish Chandran and Nikhil Gopalkrishnan and Andrew Phillips and John H. Reif},
  journal={ACS synthetic biology},
  year={2015},
  volume={4 8},
  pages={
          898-913
        }
}
Molecular devices made of nucleic acids can perform complex information processing tasks at the nanoscale, with potential applications in biofabrication and smart therapeutics. However, limitations in the speed and scalability of such devices in a well-mixed setting can significantly affect their performance. In this article, we propose designs for localized circuits involving DNA molecules that are arranged on addressable substrates and interact via hybridization reactions. We propose designs… 
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28 Citations
Background Citations
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Methods Citations
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28 Citations

Citation Type

Citation Type

DNA Hybridization Reactions Using DNA Hairpins
TLDR
This article proposes designs for localized elementary logic circuits involving DNA molecules that are arranged on addressable substrates and interact via hybridization reactions, and develops an efficient method for probabilistic model checking of localized circuits, which is implemented within the Visual DSD design tool.
Structure sampling for computational estimation of localized DNA interaction rates
TLDR
This paper presents an automated method for estimating reaction rates in tethered molecular circuits that takes the geometry of the tethered species into account, and probabilistically generate samples of structure distributions based on simple biophysical models and use these to estimate important parameters for kinetic models.
A spatially localized architecture for fast and modular DNA computing.
TLDR
This work creates logic gates and signal transmission lines by spatially arranging reactive DNA hairpins on a DNA origami and expects this approach will motivate using spatial constraints for future molecular control circuit designs.
Localized DNA Hybridization Chain Reactions on DNA Origami.
TLDR
Chains of localized DNA hybridization reactions on the surface of a self-assembled DNA origami rectangle are demonstrated, providing faster reaction kinetics and considerable increased scalability.
A Spatially Localized Architecture for Fast and Modular Computation at the Molecular Scale
TLDR
This work creates logic gates and signal transmission lines by spatially arranging reactive DNA hairpins on a DNA origami to motivate the use of spatial constraints in molecular engineering more broadly, bringing embedded molecular control circuits closer to applications.
Localized DNA circuit design with majority gates
TLDR
A localized DNA majority gate is proposed in this paper to exploit the compact logic representation of majority logic, thereby achieving smaller circuit footprint and addressing how DNA molecules have to be arranged in order to ensure correct functionality.
Nucleic Acid Databases and Molecular-Scale Computing.
TLDR
Various implications and challenges of DNA-based storage and computing are discussed, and innovative work on bridging these two areas of research is encouraged to further explore molecular parallelism and near-data processing.
Automated analysis of tethered DNA nanostructures using constraint solving
TLDR
This paper uses a satisfaction modulo theories solver to determine whether the constraint problem associated with a given structure is satisfiable, which corresponds to whether that structure is physically realizable given the constraints imposed by the tether geometry.
Accelerating DNA-Based Computing on a Supramolecular Polymer
TLDR
Supramolecular BTA polymers are established as an efficient platform for DNA-based molecular operations, paving the way for the construction of autonomous bionanomolecular systems that confine and combine molecular sensing, computation, and actuation.
G-Quadruplexes Light up Localized DNA Circuits.
TLDR
This new protocol generates nanoplatforms that no longer requires protective-deprotective systems and is therefore completely neutral to the sample, enlarging the potential applications from biosensors devices to metal detector sensors.
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