Enzyme-Free Nucleic Acid Logic Circuits

@article{Seelig2006EnzymeFreeNA,
  title={Enzyme-Free Nucleic Acid Logic Circuits},
  author={Georg Seelig and David Soloveichik and David Yu Zhang and Erik Winfree},
  journal={Science},
  year={2006},
  volume={314},
  pages={1585 - 1588}
}
Biological organisms perform complex information processing and control tasks using sophisticated biochemical circuits, yet the engineering of such circuits remains ineffective compared with that of electronic circuits. To systematically create complex yet reliable circuits, electrical engineers use digital logic, wherein gates and subcircuits are composed modularly and signal restoration prevents signal degradation. We report the design and experimental implementation of DNA-based digital… Expand
Catalytic nucleic acids (DNAzymes) as functional units for logic gates and computing circuits: from basic principles to practical applications.
This feature article addresses the implementation of catalytic nucleic acids as functional units for the construction of logic gates and computing circuits, and discusses the future applications ofExpand
Interfacing synthetic DNA logic operations with protein outputs.
TLDR
By using zinc-finger proteins, AND, OR, and NOR logic gates were created that respond to short oligonucleotide inputs and lead to the activation or deactivation of a split-luciferase enzyme. Expand
DNA computing circuits using libraries of DNAzyme subunits.
TLDR
The construction of a DNA-based computational platform that uses a library of catalytic nucleic acids, and their substrates, for the input-guided dynamic assembly of a universal set of logic gates and a half-adder/half-subtractor system is reported. Expand
Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades
TLDR
This work experimentally demonstrated several digital logic circuits, culminating in a four-bit square-root circuit that comprises 130 DNA strands, which enables fast and reliable function in large circuits with roughly constant switching time and linear signal propagation delays. Expand
Analog Computation by DNA Strand Displacement Circuits.
TLDR
This work proposes an architecture for the systematic construction of DNA circuits for analog computation based on DNA strand displacement, and describes how DNA circuits to compute polynomial functions of inputs can be built. Expand
Design and application of cotranscriptional non-enzymatic RNA circuits and signal transducers
TLDR
This work implemented a particular nucleic acid circuit, catalytic hairpin assembly, using RNA for both information storage and processing and demonstrated that the design principles developed for DNA circuits could be readily translated to engineering RNA circuits that operated with similar kinetics and sensitivities of detection. Expand
Fast and compact DNA logic circuits based on single-stranded gates using strand-displacing polymerase
TLDR
A new DNA logic circuits architecture based on single-stranded logic gates and strand-displacing DNA polymerase requires less computation time and fewer DNA strands. Expand
Programmable DNA Nanoindicator-Based Platform for Large-Scale Square Root Logic Biocomputing.
TLDR
A high-capacity DNA biocomputing system can calculate the square root of a 10 bit binary number by designing DNA sequences and programming DNA strand displacement reactions, and the input signals are optimized through the output feedback to improve performance in more complex logical operations. Expand
A Simple DNA Gate Motif for Synthesizing Large-Scale Circuits
TLDR
A DNA catalytic gate architecture that appears suitable for practical synthesis of large-scale circuits involving possibly thousands of gates is proposed. Expand
Simultaneous G-Quadruplex DNA Logic.
TLDR
Three G- quadruplex-based logic gates that operate simultaneously in a single reaction vessel are reported that respond to unique Boolean DNA inputs by undergoing topological conversion from duplex to G-quadruplex states that were resolved using a thioflavin T dye and gel electrophoresis. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 49 REFERENCES
Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes
TLDR
A computational approach for designing allosteric ribozymes triggered by binding oligonucleotides was described, and four universal types of RNA switches possessing AND, OR, YES and NOT Boolean logic functions were created in modular form, which allows ligand specificity to be changed without altering the catalytic core of the ribozyme. Expand
Deoxyribozyme-based logic gates.
TLDR
A set of deoxyribozyme-based logic gates capable of generating any Boolean function, constructed through a modular design that combines molecular beacon stem-loops with hammerhead-type deoxy ribozymes, open the possibility of communication between various computation elements in solution. Expand
RNA synthetic biology
TLDR
Challenges for this emerging field include determining how computational and directed-evolution techniques can be implemented to increase the complexity of engineered RNA systems, as well as determining how such systems can be broadly extended to mammalian systems. Expand
An autonomous molecular computer for logical control of gene expression
TLDR
An autonomous biomolecular computer is described that, at least in vitro, logically analyses the levels of messenger RNA species, and in response produces a molecule capable of affecting levels of gene expression. Expand
Programmable ligand-controlled riboregulators of eukaryotic gene expression
TLDR
The design of a class of small trans-acting RNAs that directly regulate gene expression in a ligand-dependent manner, called antiswitches, are described, made fully tunable and modular by rational design. Expand
Engineered allosteric ribozymes as biosensor components.
  • R. Breaker
  • Biology, Medicine
  • Current opinion in biotechnology
  • 2002
TLDR
RNA and DNA molecules can be engineered to function as molecular switches that trigger catalytic events when a specific target molecule becomes bound, making possible the creation of new types of biosensor devices and genetic control elements. Expand
A DNA-fuelled molecular machine made of DNA
TLDR
The construction of a DNA machine in which the DNA is used not only as a structural material, but also as ‘fuel’; each cycle produces a duplex DNA waste product. Expand
Reconstruction of genetic circuits
TLDR
Recent progress in this area of synthetic biology is described, highlighting newly developed genetic components and biological lessons learned from this approach. Expand
Catalyzed relaxation of a metastable DNA fuel.
TLDR
A metastable DNA "fuel" and a corresponding DNA "catalyst" that improve upon the original hybridization-based catalyst system and becomes a viable component enabling future DNA-based synthetic molecular machines and logic circuits. Expand
Engineered riboregulators enable post-transcriptional control of gene expression
TLDR
A post-transcriptional regulation system in Escherichia coli that uses RNA to both silence and activate gene expression is presented, inserting a complementary cis sequence directly upstream of the ribosome binding site in a target gene. Expand
...
1
2
3
4
5
...