TY - JOUR
T1 - Exploring the speed limit of toehold exchange with a cartwheeling DNA acrobat
AU - Li, Jieming
AU - Johnson-Buck, Alexander
AU - Yang, Yuhe Renee
AU - Shih, William M.
AU - Yan, Hao
AU - Walter, Nils G.
N1 - Funding Information:
This work was supported primarily by the US Department of Defense Army Research Office MURI award W911NF-12-1-0420 to N.G.W. and H.Y. The authors thank J. Damon Hoff for technical support, Z. R. Li for graphic design support, and B. Nijholt, E. Krieg, A. M. Bergman and W. Benjamin Rogers for discussions about DNA origami design.
Publisher Copyright:
© 2018, The Author(s).
PY - 2018/8/1
Y1 - 2018/8/1
N2 - Dynamic DNA nanotechnology has yielded nontrivial autonomous behaviours such as stimulus-guided locomotion, computation and programmable molecular assembly. Despite these successes, DNA-based nanomachines suffer from slow kinetics, requiring several minutes or longer to carry out a handful of operations. Here, we pursue the speed limit of an important class of reactions in DNA nanotechnology—toehold exchange—through the single-molecule optimization of a novel class of DNA walker that undergoes cartwheeling movements over a field of complementary oligonucleotides. After optimizing this DNA ‘acrobat’ for rapid movement, we measure a stepping rate constant approaching 1 s−1, which is 10- to 100-fold faster than prior DNA walkers. Finally, we use single-particle tracking to demonstrate movement of the walker over hundreds of nanometres within 10 min, in quantitative agreement with predictions from stepping kinetics. These results suggest that substantial improvements in the operating rates of broad classes of DNA nanomachines utilizing strand displacement are possible.
AB - Dynamic DNA nanotechnology has yielded nontrivial autonomous behaviours such as stimulus-guided locomotion, computation and programmable molecular assembly. Despite these successes, DNA-based nanomachines suffer from slow kinetics, requiring several minutes or longer to carry out a handful of operations. Here, we pursue the speed limit of an important class of reactions in DNA nanotechnology—toehold exchange—through the single-molecule optimization of a novel class of DNA walker that undergoes cartwheeling movements over a field of complementary oligonucleotides. After optimizing this DNA ‘acrobat’ for rapid movement, we measure a stepping rate constant approaching 1 s−1, which is 10- to 100-fold faster than prior DNA walkers. Finally, we use single-particle tracking to demonstrate movement of the walker over hundreds of nanometres within 10 min, in quantitative agreement with predictions from stepping kinetics. These results suggest that substantial improvements in the operating rates of broad classes of DNA nanomachines utilizing strand displacement are possible.
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U2 - 10.1038/s41565-018-0130-2
DO - 10.1038/s41565-018-0130-2
M3 - Article
C2 - 29736034
AN - SCOPUS:85046552043
SN - 1748-3387
VL - 13
SP - 723
EP - 729
JO - Nature nanotechnology
JF - Nature nanotechnology
IS - 8
ER -