DNA Strand-Displacement Timer Circuits

We demonstrate reaction-diffusion systems that generate stable patterns of DNA oligonucleotide concentrations within agarose gels, including linear and "hill" (i.e. increasing then decreasing) shapes in one and two dimensions. The reaction networks that produce these patterns are driven by enzyme-free DNA strand-displacement reactions, in which reactant DNA complexes continuously release and recapture target strands of DNA in the gel; a balance of these reactions produces stable patterns. The reactant complexes are maintained at high concentrations by liquid reservoirs along the gel boundary. We monitor our patterns using time-lapse fluorescence microscopy and show that the shape of our patterns can be easily tuned by manipulating the boundary reservoirs. Finally, we show that two overlapping, stable gradients can be generated by designing two sets of non-interacting release and recapture reactions with DNA strand-displacement systems. This paper represents a step toward the generation of scalable, complex reaction-diffusion patterns for programming the spatiotemporal behavior of synthetic materials.

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“…55 for more details). The bands corresponding to the complexes were identied using UV-shadowing at a wavelength of 254 nm.…”

Section: Dna Complex Preparationmentioning

confidence: 99%

Stable DNA-based reaction–diffusion patterns

et al. 2017

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“…Systems of synthetic oligonucleotides have been successfully designed as switches, amplifiers, logic gates, and oscillators. [24][25][26][27] By programming these circuits to produce specific TF sequences as outputs, they can function as embedded controllers for programming gene-expression dynamics under our framework. This use of nucleic-acid computing for the active, on-demand synthesis of functional RNAs could find applications in biological analysis, directed evolution, and molecular information processing.…”

Section: Discussionmentioning

confidence: 99%

Cell-free transcriptional regulation via nucleic-acid-based transcription factors

Chou

Shih

2019

Preprint

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Cells execute complex transcriptional programs by deploying distinct protein regulatory assemblies that interact with cis-regulatory elements throughout the genome. Using concepts from DNA nanotechnology, we synthetically recapitulated this feature in cell-free gene networks actuated by T7 RNA polymerase (RNAP). Our approach involves engineering nucleic-acid hybridization interactions between a T7 RNAP site-specifically functionalized with single-stranded DNA (ssDNA), templates displaying cis-regulatory ssDNA domains, and auxiliary nucleic-acid assemblies acting as artificial transcription factors (TFs). By relying on nucleic-acid hybridization, de novo regulatory assemblies can be computationally designed to emulate features of proteinbased TFs, such as cooperativity and combinatorial binding, while offering unique advantages such as programmability, chemical stability, and scalability. We illustrate the use of nucleic-acid TFs to implement transcriptional logic, cascading, feedback, and multiplexing. This framework will enable rapid prototyping of increasingly complex in vitro genetic devices for applications such as portable diagnostics, bio-analysis, and the design of adaptive materials.

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“…Analog computing with transients Recognizing temporal patterns can be interpreted as an analog operation that is naturally suited for molecular computation. While molecular circuits of digital gates have solved remarkable problems [12][13][14] and even mimicked deep neural networks [15], several recent papers [16][17][18][19][20][21][22][23][24][25] have shown that analog computations are naturally suited for molecular circuits. Analog operations represent information directly in continuous physical variables like concentration or time intervals [26,27].…”

mentioning

confidence: 99%

Temporal Pattern Recognition through Analog Molecular Computation

O’Brien

Murugan

2019

ACS Synth. Biol.

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Living cells communicate information about physiological conditions by producing signaling molecules in a specific timed manner. Different conditions can result in the same total amount of a signaling molecule, differing only in the pattern of the molecular concentration over time. Such temporally coded information can be completely invisible to even state-of-the-art molecular sensors with high chemical specificity that respond only to the total amount of the signaling molecule. Here, we demonstrate design principles for circuits with temporal specificity, that is, molecular circuits that respond to specific temporal patterns in a molecular concentration. We consider pulsatile patterns in a molecular concentration characterized by three fundamental temporal features -time period, duty fraction and number of pulses. We develop circuits that respond to each one of these features while being insensitive to the others. We demonstrate our design principles using abstract Chemical Reaction Networks and with explicit simulations of DNA strand displacement reactions. In this way, our work develops building blocks for temporal pattern recognition through molecular computation.

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DNA Strand-Displacement Timer Circuits

Cited by 75 publications

References 32 publications

Stable DNA-based reaction–diffusion patterns

Stable DNA-based reaction–diffusion patterns

Cell-free transcriptional regulation via nucleic-acid-based transcription factors

Temporal Pattern Recognition through Analog Molecular Computation

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