Tunable DNA Origami Motors Translocate Ballistically Over μm Distances at nm/s Speeds

Bazrafshan, Alisina; Meyer, Travis A.; Su, Hanquan; Brockman, Joshua M.; Blanchard, Aaron T.; Piranej, Selma; Duan, Yuxin; Ke, Yonggang; Salaita, Khalid

doi:10.1002/anie.201916281

Cited by 51 publications

(64 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This includes expanding the chemical scope beyond that of base pairing and stacking, for instance through the inclusion of proteins. A recent study combines RNase-based catalytic walkers with steric direction of a DNA nanostructure, where the resulting system converts potential energy from RNA-based fuel into the unidirectional microscale movement of an origami roller 193 . Notably, this motor moves autonomously and without the aid of any external gradient or patterning.…”

Section: Catalysismentioning

confidence: 99%

DNA origami

Dey

Chen

Gothelf

et al. 2021

Nat Rev Methods Primers

527

386

View full text Add to dashboard Cite

Biological materials are self-assembled with near-atomic precision in living cells, whereas synthetic 3D structures generally lack such precision and controllability. Recently, DNA nanotechnology, especially DNA origami technology, has been useful in the bottom-up fabrication of well-defined nanostructures ranging from tens of nanometres to sub-micrometres. In this Primer, we summarize the methodologies of DNA origami technology, including origami design, synthesis, functionalization and characterization. We highlight applications of origami structures in nanofabrication, nanophotonics and nanoelectronics, catalysis, computation, molecular machines, bioimaging, drug delivery and biophysics. We identify challenges for the field, including size limits, stability issues and the scale of production, and discuss their possible solutions. We further provide an outlook on next-generation DNA origami techniques that will allow in vivo synthesis and multiscale manufacturing.

show abstract

Section: Catalysismentioning

confidence: 99%

DNA origami

Dey

Chen

Gothelf

et al. 2021

Nat Rev Methods Primers

527

386

View full text Add to dashboard Cite

show abstract

“…Current walkers can move tens of microns over 10 hours with an average velocity of several nanometers per second. [33][34][35][36] Migrations of these motors on surfaces involve multiple mechanisms and design parameters. [37][38][39][40] Understanding the kinetics of translocation processes is essential to improve the performances of movements.…”

Section: Introductionmentioning

confidence: 99%

Mechanistic Understanding of Surface Migration Dynamics with DNA Walkers

Pan

Qiu

et al. 2021

J. Phys. Chem. B

View full text Add to dashboard Cite

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)

show abstract

“…Some synthetic biomolecular systems, such as molecular spiders [32,33], burnt-bridges ratchets [34], and DNA nanomotors [35][36][37], remodel their tracks as they move and have been engineered to achieve directional motion at the molecular level. This remodeling turns a substrate site into a product site, and where there is a greater affinity to bind to the substrate, motion is biased away from the product wake.…”

Section: Application To Burnt-bridges Ratchetsmentioning

confidence: 99%

Apparent superballistic dynamics in one-dimensional random walks with biased detachment

Korosec

Sivak

Forde

2020

Phys. Rev. Research

View full text Add to dashboard Cite

The mean-squared displacement (MSD) is an averaged quantity widely used to assess anomalous diffusion. In many cases, such as molecular motors with finite processivity, the dynamics of the system of interest produce trajectories of varying duration. Here, we explore the effects of finite processivity on different measures of the MSD. We do so by investigating a deceptively simple dynamical system: a one-dimensional random walk (with equidistant jump lengths, symmetric move probabilities, and constant step duration) with an origin-directed detachment bias. By tuning the time dependence of the detachment bias, we find through analytical calculations and trajectory simulations that the system can exhibit a broad range of anomalous diffusion, extending beyond conventional diffusion to superdiffusion and even superballistic motion. We analytically determine that protocols with a time-increasing detachment lead to an ensemble-averaged velocity increasing in time, thereby providing the effective acceleration that is required to push the system above the ballistic threshold. An MSD analysis of burnt-bridges ratchets similarly reveals superballistic behavior. Because superdiffusive MSDs are often used to infer biased, motorlike dynamics, these findings provide a cautionary tale for dynamical interpretation.

show abstract

Tunable DNA Origami Motors Translocate Ballistically Over μm Distances at nm/s Speeds

Cited by 51 publications

References 51 publications

DNA origami

DNA origami

Mechanistic Understanding of Surface Migration Dynamics with DNA Walkers

Apparent superballistic dynamics in one-dimensional random walks with biased detachment

Contact Info

Product

Resources

About