Cooperative linear cargo transport with molecular spiders

Semenov, Oleg; Olah, Mark J.; Stefanović, Darko

doi:10.1007/s11047-012-9357-2

Cited by 11 publications

(6 citation statements)

References 14 publications

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“…23,41 Theoretical random motion models such as self-avoiding walk were used to understand migration mechanisms. 42,43 Mechanical models on DNA binding revealed the effects of tensions between walker feet and tracks 44 and force dependence of motors. 45 In terms of thermodynamics, free energy barriers and efficiencies of different DNA motors were compared.…”

Section: Introductionmentioning

confidence: 99%

Mechanistic Understanding of Surface Migration Dynamics with DNA Walkers

Pan

Qiu

et al. 2021

J. Phys. Chem. B

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Dynamic DNA walkers can move cargoes on a surface through various mechanisms including enzymatic reactions and strand displacement. While they have demonstrated high processivity and speed, their motion dynamics are not well understood. Here, we utilize an enzyme-powered DNA walker as a model system and adopt a random walk model to provide new insight on migration dynamics. Four distinct migration modes (ballistic, Lévy, self-avoiding, and diffusive motions) are identified. Each mode shows unique step time and velocity distributions which are related to mean squared displacement (MSD) scaling. Experimental results are in excellent agreement with the theoretical predictions. With a better understanding of the dynamics, we performed a mechanistic study, elucidating the effects of cargo types and sizes, walker sequence designs, and environmental conditions. Finally, this study provides a set of design principles for tuning the behaviors of DNA walkers. The DNA walkers from this work could serve as a versatile platform for mathematical studies and open new opportunities for bioengineering. File list (2) download file view on ChemRxiv MS_FIN.pdf (1.05 MiB) download file view on ChemRxiv SI_FIN.pdf (451.43 KiB)

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Section: Introductionmentioning

confidence: 99%

Mechanistic Understanding of Surface Migration Dynamics with DNA Walkers

Pan

Qiu

et al. 2021

J. Phys. Chem. B

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“…Subsequent simulations [14] have shown this AK spider model to exhibit transient superdiffusive behavior as the walkers move between periods of ballistic and diffusive motion depending on the walker's position with respect to the boundary between visited and unvisited sites [14]. Other work has extended the AK model to study mathematical properties of AK spider walks in 1D [15][16][17] and 2D [18]; the collective and cooperative behavior of multi-spider systems in 1D [19][20][21]; and the effect of a load force on the rigid 1D walking gaits of AK-like spiders under the kinetic rates specific to deoxyribozymes [22,23].…”

Section: Introductionmentioning

confidence: 99%

Superdiffusive transport by multivalent molecular walkers moving under load

Olah

Stefanović

2013

Phys. Rev. E

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We introduce a model for translational molecular motors to demonstrate that a multivalent catalytic walker with flexible, uncoordinated legs can transform the free energy of surface-bound substrate sites into mechanical work and undergo biased, superdiffusive motion, even in opposition to an external load force. The walker in the model lacks any inherent orientation of body or track, and its legs have no chemomechanical coupling other than the passive constraint imposed by their connection to a common body. Yet, under appropriate kinetic conditions, the walker's motion is biased in the direction of unvisited sites, which allows the walker to move nearly ballistically away from the origin as long as a local supply of unmodified substrate sites is available. The multivalent random walker model is mathematically formulated as a continuous-time Markov process and is studied numerically. We use Monte Carlo simulations to generate ensemble estimates of the mean squared displacement and mean work done for this nonergodic system. Our results show that a residence time bias between visited and unvisited sites leads to superdiffusive motion over significant times and distances. This mechanism can be used to adapt any enzyme-substrate system with appropriate kinetics for use as a functional chemical implementation of a molecular motor, without the need for structural anisotropy or conformationally mediated chemomechanical coordination.

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“…Samii et al investigated various gaits and numbers of legs (Samii et al, 2010(Samii et al, , 2011, emphasizing the possibility of detachment from a 1D track. We studied the behavior of multiple spiders continuously released onto a 1D track (Semenov et al, 2011b(Semenov et al, , 2012) from a point source. Related to the present topic, Antal and Krapivsky evaluated the diffusion constant and the amplitude describing the asymptotic behavior of the number of visited sites (i.e., released products) for a single simplified spider on an infinite square Figure 2: The general multivalent random walker model describes the motion of multipedal walkers acting as molecular motors as they move over tracks of surface-bound substrate fuel.…”

Section: Molecular Spiders and Their Modelsmentioning

confidence: 99%

Catalytic Molecular Walkers: Aspects of Product Release

Stefanović¹,

Stojanović²,

Olah³

et al. 2013

Advances in Artificial Life, ECAL 2013

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We study a model of multi-legged catalytic molecular walkers that abstract a class of recently developed synthetic molecular motors. We focus on their kinetics of release of catalytic product, delineating the influence of chemical kinetic parameters, geometric configuration, and loss from surface, and also contrast with bulk kinetics of product release. We show that molecular walkers can achieve a uniform rate of release over long time scales, which can be exploited in applications.

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Cooperative linear cargo transport with molecular spiders

Cited by 11 publications

References 14 publications

Mechanistic Understanding of Surface Migration Dynamics with DNA Walkers

Mechanistic Understanding of Surface Migration Dynamics with DNA Walkers

Superdiffusive transport by multivalent molecular walkers moving under load

Catalytic Molecular Walkers: Aspects of Product Release

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