Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods

Li, Bingling; Ellington, Andrew D.; Chen, Xi

doi:10.1093/nar/gkr504

Cited by 467 publications

(401 citation statements)

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“…1) were used to monitor the formation of the product of the two CHA reactions, respectively. The performance of each layer was qualitatively similar to that of similar single-layer amplifiers (7), in that it showed robust signal amplification and low leakage (Fig. S2).…”

Section: Resultsmentioning

confidence: 54%

“…The initial trigger C 0 catalyzes the kinetically trapped M 1 to open and hybridize to A 1 , forming M 1 :A 1 , which in turn catalyzes the formation of M 2 :A 2 from hairpins M 2 and A 2 . Each layer used design principles we have previously formalized (7). In particular, all toeholds are 8 nt long and have a 50% GC content.…”

Section: Resultsmentioning

confidence: 99%

“…DNA circuits have been integrated to form complex Boolean networks (1) and molecular neural networks (2). Such programmed circuits have begun to have applications in ordered chemical synthesis (3,4), multiplexed labeling of biomolecules for fluorescent microscopy (5,6), and detection of both nucleic acid and nonnucleic acid analytes (7)(8)(9). The combination of DNA circuitry and DNA nanotechnology (10,11) has given rise to DNA robotics (12) and assembly lines (13).…”

mentioning

confidence: 99%

“…1 (7, 18). Here, we designed two-layer and four-layer amplification cascades based on a particular type of CHA reaction we have optimized before (7). We analyzed the origin and profile of circuit leakage and used a combination of modeling and experiments to reveal that the performance of the CHA cascade, in terms of both fold amplification and sensitivity, depends on the leakage profiles of individual CHA reactions.…”

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confidence: 99%

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Stacking nonenzymatic circuits for high signal gain

Chen

Briggs

McLain

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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231

217

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Signal amplification schemes that do not rely on protein enzymes show great potential in areas as abstruse as DNA computation and as applied as point-of-care molecular diagnostics. Toeholdmediated strand displacement, a programmable form of dynamic DNA hybridization, can be used to design powerful amplification cascades that can achieve polynomial or exponential amplification of input signals. However, experimental implementation of such amplification cascades has been severely hindered by circuit leakage due to catalyst-independent side reactions. In this study, we systematically analyzed the origins, characteristics, and outcomes of circuit leakage in amplification cascades and devised unique methods to obtain high-quality DNA circuits that exhibit minimal leakage. We successfully implemented a two-layer cascade that yielded 7,000-fold signal amplification and a two-stage, four-layer cascade that yielded upward of 600,000-fold signal amplification. Implementation of these unique methods and design principles should greatly empower molecular programming in general and DNA-based molecular diagnostics in particular.amplifier | enzyme-free | DNA circuitry S ignal amplification is a ubiquitous theme in biology and engineering, and the ability to amplify signals at the molecular level in large measure determines the complexity and robustness of the molecular devices and systems that can be built. Over the past decade, DNA has been established as the ultimate "intelligent material" to build complex structures, circuits, and devices. DNA circuits have been integrated to form complex Boolean networks (1) and molecular neural networks (2). Such programmed circuits have begun to have applications in ordered chemical synthesis (3, 4), multiplexed labeling of biomolecules for fluorescent microscopy (5, 6), and detection of both nucleic acid and nonnucleic acid analytes (7-9). The combination of DNA circuitry and DNA nanotechnology (10, 11) has given rise to DNA robotics (12) and assembly lines (13).The signal amplifiers underlying many of these advances are metastable DNA substrates whose conformational transformations can be catalytically triggered by strand displacement. The first amplifier of this class was designed by Turberfield et al. (14) and was later modified by Seelig et al. by using metastable kissingloop structures (15). Since then, many hybridization-based catalytic systems have been developed, including ones based on topologically constrained interactions (16), entropy-driven strand exchange (17), and catalyzed hairpin assembly (CHA) (18). Some of these schemes allow cascading of catalysis wherein the product of one reaction serves as the catalyst of another reaction. Autocatalytic reactions (17, 19) and cross-catalytic reactions (18) may also be constructed and programmed. Such molecular amplifiers can guard against signal damping during serial signal transductions in nucleic acid circuits and are easily adapted to the integration of logical operations (20).Whereas the outcome of these amplifiers, the ampl...

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Section: Resultsmentioning

confidence: 54%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Stacking nonenzymatic circuits for high signal gain

Chen

Briggs

McLain

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

231

217

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“…Since then, many works have contributed to establishing firm strategies based on DNA to conceive and fabricate a wealth of structures and functions. Among them, the most significant are the folding of origami [3] and the DNA motor devices [4] that turn out to be fertile enough to design networks of chemical reactions with a constructed rational approach [5,6,7,8,9,10,11,12]. The combination of DNA origami and DNA motor devices gives the great opportunity to elaborate modular Boolean algorithm based on ordered sequences of chemical reactions confined in an almost perfect topological arrangement [13,14,15,16,17].…”

Section: Introductionmentioning

confidence: 99%

DNA Nanodevices Confined on DNA Origamis: an Isothermal Ratchet Driven by Boundary Conditions

Aimé¹,

Elezgaray²,

Mendoza³

2017

JAN

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In this note we investigate the diffusive behaviour and the boundary conditions of DNA nanodevices using the toe hold mediated strand displacement method. The goal is to extract the basic principles governing the difference observed in diluted solution and in confined environment where the devices are tethered on a DNA Origami. We note that the excluded volume interaction between the two strands running in opposite direction must give a sub diffusive behaviour that can lead to very long waiting times between jumps. When the Boundary Conditions generate a strong asymmetry in the device, the probability to perform the logical operation, thus to remove the output strand, is one. However, we envision unexpected marked differences between diluted solutions and confined environment both for controlling the boundary condition and the sub diffusive behaviour. These differences rise new questions on the interest to use the toe hold mediated strand displacement method on DNA Origamis.

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