Folding‐upon‐Repair DNA Nanoswitches for Monitoring the Activity of DNA Repair Enzymes

DNA as an informational polymer has, for the past 30 years, progressively become an essential molecule to rationally build chemical reaction networks endowed with powerful signal‐processing capabilities. Whether influenced by the silicon world or inspired by natural computation, molecular programming has gained attention for diagnosis applications. Of particular interest for this review, molecular classifiers have shown promising results for disease pattern recognition and sample classification. Because both input integration and computation are performed in a single tube, at the molecular level, this low‐cost approach may come as a complementary tool to molecular profiling strategies, where all biomarkers are quantified independently using high‐tech instrumentation. After introducing the elementary components of molecular classifiers, some of their experimental implementations are discussed either using digital Boolean logic or analog neural network architectures.

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“…Enzymes themselves may be used as inputs of DNA circuits using modified nucleic acid substrates. [ 39 ]…”

Section: Elementary Modules Of Molecular Classifiersmentioning

confidence: 99%

Molecular Computation for Molecular Classification

et al. 2023

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“…4 Most mechanisms use chemical 'fuel' (e.g., DNA, redox, pH) to exert stimulus-specific control over DNA nanostructures. [5][6][7][8][9][10] However, these approaches require precise and repeated addition of reagents directly into the system, which accumulate over many on-off cycles, leading to contamination of the microenvironment that can potentially limit the lifetime of these devices. 11 As such, it is highly desirable to design nanostructures that can rapidly and reversibly respond to non-invasive stimuli.…”

Section: Introductionmentioning

confidence: 99%

A modular intramolecular triplex photo-switching motif that enables rapid and reversible control of aptamer binding activity

Trinh

Thompson

Clark

et al. 2022

Preprint

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DNA switches that can change conformation in response to certain wavelengths of light could enable rapid and non-invasive control of chemical processes for a wide range of applications. However, most current photo-responsive DNA switches are limited either by irreversible switching or reversible switching with impractically slow kinetics. Here, we report the design of an intramolecular triplex photoswitch (TPS) design based on single-stranded DNA that undergoes rapid and reversible photoswitching between folded and unfolded states through isomerization of internal azobenzene modifications. After optimizing the performance of our photoswitch design, we used molecular dynamics (MD) simulations to reveal how individual azobenzenes contribute to the stabilization or destabilization of the triplex depending on their photoisomerization state. By coupling our TPS to an existing aptamer, we can reversibly modulate its binding affinity with less than 15 seconds of UV light exposure. We further demonstrate reproducible shifting in affinity over multiple cycles of UV and blue light irradiation without substantial photobleaching. Given that our TPS can introduce switching functionality to aptamers without manipulating the aptamer sequence itself, we believe our design methodology should offer a versatile means for integrating photo-responsive properties into DNA nanostructures.

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“…We can experience nano sensors, nano actuators, nanoresonators, and nanofluid carriers with new physical properties that we can describe as completely different and perfect. (see [1], [2], [3], [4], and [5]).…”

mentioning

confidence: 98%

Free Vibrations Analysis of Stepped Nanobeams Using Nonlocal Elasticity Theory

Nalbant,

Bagdatli,

Tekin

2023

Scientia Iranica

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Free vibration of stepped nanobeams was investigated using Eringen's nonlocal elasticity theory. Beam analysis is based on Bernoulli-Euler theory and nanoscale analysis is based on Eringen's nonlocal elasticity theory. The system boundary conditions were determined as simplesimple. The equations of motion of the system were obtained using Hamilton's principle. For the solution of the obtained state equations, a multi-time scale, which is one of the perturbation methods, was used. The results part of the study, it is aimed to observe the nano-size effect and the effects of the step state. For this purpose, the natural frequency values of the first three modes of the system were obtained for different non-local parameter values, step rates, and step positions. When the results were examined, it was determined that the non-local parameter value, step ratio, and natural frequency were inversely proportional to each other. In addition, to strengthen the accuracy of the results, the results obtained were compared with the results of other studies in the literature conducted under the specified conditions, and a perfect agreement was observed. The current beam model, on the other hand, could help design and manufacture ICs such as nano-sensors and nanoactuators.

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Folding‐upon‐Repair DNA Nanoswitches for Monitoring the Activity of DNA Repair Enzymes

Cited by 12 publications

References 44 publications

Molecular Computation for Molecular Classification

Molecular Computation for Molecular Classification

A modular intramolecular triplex photo-switching motif that enables rapid and reversible control of aptamer binding activity

Free Vibrations Analysis of Stepped Nanobeams Using Nonlocal Elasticity Theory

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