A Bipedal DNA Motor that Travels Back and Forth between Two DNA Origami Tiles

Liber, Miran; Tomov, Toma E.; Tsukanov, Roman; Berger, Yaron; Nir, Eyal

doi:10.1002/smll.201402028

Cited by 64 publications

(63 citation statements)

References 30 publications

(38 reference statements)

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“…The results suggest that the walkers can operate on longer tracks for real applications, especially when the tracks are embedded in a larger, rigid platform such as a DNA origami scaffold. 25,26…”

Section: Direction-dissociation Anti-correlationmentioning

confidence: 99%

A DNA bipedal nanowalker with a piston-like expulsion stroke

et al. 2017

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Artificial molecular walkers beyond burn-bridge designs are important for nanotechnology, but their systematic development remains difficult. Herein, we have reported a new rationally designed DNA walker-track system and experimentally verified a previously proposed general expulsion regime for implementing non-burn-bridge nanowalkers. The DNA walker has an optically powered engine motif that reversibly extends and contracts the walker via a quadruplex-duplex conformational change. The walker's extension is an energy-absorbing and force-generating process, which drives the walker's leg dissociation off-track in a piston-like expulsion stroke. The unzipping-shearing asymmetry provides the expulsion stroke a bias, which decides the direction of the walker. Moreover, three candidate walkers of different sizes were fabricated. Fluorescence motility experiments indicated two of them as successful walkers and revealed a distinctive size dependence that was expected for these expulsive walkers, but was not observed in previously reported walkers. This study identifies unique technical requirements for expulsive nanowalkers. The present DNA design is readily adapted for making similar walkers from other molecules since the unzipping-shearing asymmetry is common.

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Section: Direction-dissociation Anti-correlationmentioning

confidence: 99%

A DNA bipedal nanowalker with a piston-like expulsion stroke

et al. 2017

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“…The invader can then be viewed as an input signal while the incumbent can be seen as an output signal. At this level of abstraction, DNA strand displacement can be idealized into "tinker toys" that fit together to form complex, interactive networks in the field of nanotechnology (4)(5)(6)(7) with applications in diverse areas such as biosensing (8,9), DNA construction (10)(11)(12), DNA motors (13)(14)(15)(16)(17), and DNA computation (18)(19)(20)(21)(22)(23).…”

Section: Introductionmentioning

confidence: 99%

The Effect of Basepair Mismatch on DNA Strand Displacement

Broadwater

Kim

2016

Biophysical Journal

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DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent effects of displacement kinetics have not been extensively characterized. Here, we measured toehold-mediated strand displacement kinetics using single-molecule fluorescence in the presence of a single basepair mismatch. The apparent displacement rate varied significantly when the mismatch was introduced in the invading DNA strand. The rate generally decreased as the mismatch in the invader was encountered earlier in displacement. Our data indicate that a single base pair mismatch in the invader stalls branch migration and displacement occurs via direct dissociation of the destabilized incumbent strand from the substrate strand. We combined both branch migration and direct dissociation into a model, which we term the concurrent displacement model, and used the first passage time approach to quantitatively explain the salient features of the observed relationship. We also introduce the concept of splitting probabilities to justify that the concurrent model can be simplified into a three-step sequential model in the presence of an invader mismatch. We expect our model to become a powerful tool to design DNA-based reaction schemes with broad functionality.

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“…Their work demonstrated that single-molecule uorescence constituted an excellent tool for chaperoning the development of DNA-based technology, which was used appropriately and efficiently in another paper reported by them three years later. 69 The singlemolecule uorescence characterization showed the successful operation of a dynamic DNA walking device, striding back and forth between two origami tiles (Fig. 2c).…”

Section: Bipedal Walking Devicesmentioning

confidence: 99%