Research ArticleChemistry

DNA-assembled nanoarchitectures with multiple components in regulated and coordinated motion

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Science Advances  29 Nov 2019:
Vol. 5, no. 11, eaax6023
DOI: 10.1126/sciadv.aax6023
  • Fig. 1 Schematic of the macroscopic and nanoscopic systems with regulated and coordinated motion.

    (A) Macroscopic elements such as gears, shafts, and racks are assembled together to form gear trains. (B) Nanoscopic elements including DNA origami filaments, fluorophores, and metallic nanocrystals are assembled together to form the technomimetic analogs of the gear trains for executing independent, synchronous, or joint motion.

  • Fig. 2 Independent revolution.

    (A) Epicyclic gearset, in which two planet gears (A and B; gray) of different diameters mounted on a sun gear (brown) using two shafts can independently revolve around the sun gear. (B) DNA-assembled hybrid nanosystem, in which two origami filaments (A, 13 helices; B, 23 helices) anchored on the side surface of an AuNR through DNA hybridization can independently revolve around the AuNR. Two fluorophores (ATTO 550 and ATTO 647 N) are tethered on filaments A and B, respectively, allowing for in situ optically monitoring the revolution process. (C) Cross-sectional view of the system. Three rows of footholds (coded 1 to 3) evenly separated by 120° and six rows of footholds (coded 4 to 9) evenly separated by 60° are extended from filaments A and B, respectively. Upon addition of blocking and removal strands, toehold-mediated strand displacement reactions enable counterclockwise revolution of filament A around the AuNR by rotation, while filament B keeps its anchoring position on the AuNR. (D) Transmission electron microscopy (TEM) image of the AuNR-origami structures before rotation. Scale bar, 50 nm. Inset: Averaged TEM image. Scale bar, 20 nm. (E) Representative route for an independent revolution process, comprising nine distinct states (I to IX). The positions of the two fluorophores and their relative distances to the AuNR surface along the respective radial directions are given for each state. Experimental measurements (F) and theoretical calculations (G) of the fluorescence intensities of ATTO 550 (blue) and ATTO 647 N (red) during the independent revolution process from I to IX. Kinks in fluorescence are observed when filament A revolves around the AuNR, transiting from IV to V and from VII to VIII, respectively, as highlighted by the black dashed frames. a.u., arbitrary units.

  • Fig. 3 Synchronous revolution.

    (A) Epicyclic gearset, in which two planet gears (A and B; gray) of the same diameter mounted on a sun gear (brown) using one single shaft can synchronously revolve around the sun gear. (B) DNA-assembled hybrid nanosystem, in which two origami filaments (A and B, 23 helices) anchored on the side surface of an AuNR through DNA hybridization can synchronously revolve around the AuNR. Two fluorophores (ATTO 550 and ATTO 647 N) are tethered on filaments A and B, respectively. (C) Cross-sectional view of the system. Six rows of footholds (coded 1 to 6) evenly separated by 60° are extended from each filament. Upon addition of the same set of the DNA fuels, toehold-mediated strand displacement reactions enable synchronous revolution of the two filaments around the AuNR. (D) TEM image of the AuNR-origami structures before rotation. Scale bar, 50 nm. Inset: Averaged TEM image. Scale bar, 20 nm. (E) Representative route for a synchronous revolution process, comprising six distinct states (I to VI). The positions of the two fluorophores and their relative distances to the AuNR surface along the respective radial directions are given for each state. Experimental measurements (F) and theoretical calculations (G) of the fluorescence intensities of ATTO 550 and ATTO 647 N, respectively, during the synchronous revolution process from I to VI.

  • Fig. 4 Joint motion.

    (A) Combination of relative sliding from rack-and-pinion gearing and synchronous revolution from epicyclic gearing. (B) DNA-assembled hybrid nanosystem, in which two origami filaments (A and B, 23 helices) anchored on an AuNP (10 nm) through DNA hybridization. Twelve rows of footholds are extended from the filaments. (C) Relative sliding and synchronous revolution enabled by toehold-mediated strand displacement reactions upon addition of corresponding DNA fuels. (D) Representative route for joint motion, comprising seven distinct states (I to VII). The positions of the two fluorophores and their relative distances to the AuNP surface along the respective radial directions are given for each state. The two different double racks for relative sliding are indicated by parallel planes in red and gray, respectively. (E) TEM image of the AuNP-origami structures at state I. Scale bar, 50 nm. (F) Experimental measurements of the fluorescence intensities of ATTO 550 and ATTO 647 N, respectively, during the joint motion process from I to VII.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/5/11/eaax6023/DC1

    Fig. S1. DNA origami design for the independent revolution.

    Fig. S2. TEM images of the DNA origami filaments without Au nanocrystals.

    Fig. S3. Additional TEM images of the DNA origami–AuNR structures for independent revolution.

    Fig. S4. Structure gallery for the averaged TEM image in Fig. 2D.

    Fig. S5. Fluorophore design for the independent revolution.

    Fig. S6. Detailed structural parameters for independent revolution.

    Fig. S7. Kink formation in fluorescence.

    Fig. S8. Reversibility of independent revolution.

    Fig. S9. Control experiment to directly probe the intermediate states.

    Fig. S10. Fit of rate constants from the control experiment.

    Fig. S11. Calculated time-dependent fluorescence intensity for the intermediate state I.

    Fig. S12. DNA origami design for the synchronous revolution and joint system.

    Fig. S13. Fluorophore design for the synchronous revolution.

    Fig. S14. Structure gallery for the averaged TEM image in Fig. 3D.

    Fig. S15. Additional TEM images of the DNA origami–AuNR structures for synchronous revolution.

    Fig. S16. Structure gallery for the average TEM image.

    Fig. S17. Additional TEM images of the DNA origami–AuNR structures for synchronous revolution.

    Fig. S18. In situ fluorescence intensity changes of ATTO 550 (blue) and ATTO 647 N (red) during synchronous revolution in two cycles.

    Fig. S19. Design details of the footholds for joint motion.

    Fig. S20. Additional TEM images of the DNA origami–AuNP structures for joint motion.

    Fig. S21. Theoretical calculations of the fluorescence intensities of ATTO 550 and ATTO 647 N for the joint motion.

    Table S1. Detailed sequences of the 12 foothold rows for independent revolution, synchronous revolution, and joint motion.

    Table S2. Blocking strands (B) and removal strands (R).

    Table S3. Samples added to drive the independent rotation for in situ fluorescence detection.

    Table S4. Samples added to drive the synchronous motion for in situ fluorescence detection.

    Table S5. Samples added to drive the joint motion for in situ fluorescence detection.

    Supplementary Notes

    Data S1. Strands for the independent rotation.

    Data S2. Strands for the synchronous motion.

    Data S3. Strands for the joint motion.

    Reference (40)

  • Supplementary Materials

    The PDFset includes:

    • Fig. S1. DNA origami design for the independent revolution.
    • Fig. S2. TEM images of the DNA origami filaments without Au nanocrystals.
    • Fig. S3. Additional TEM images of the DNA origami–AuNR structures for independent revolution.
    • Fig. S4. Structure gallery for the averaged TEM image in Fig. 2D.
    • Fig. S5. Fluorophore design for the independent revolution.
    • Fig. S6. Detailed structural parameters for independent revolution.
    • Fig. S7. Kink formation in fluorescence.
    • Fig. S8. Reversibility of independent revolution.
    • Fig. S9. Control experiment to directly probe the intermediate states.
    • Fig. S10. Fit of rate constants from the control experiment.
    • Fig. S11. Calculated time-dependent fluorescence intensity for the intermediate state I.
    • Fig. S12. DNA origami design for the synchronous revolution and joint system.
    • Fig. S13. Fluorophore design for the synchronous revolution.
    • Fig. S14. Structure gallery for the averaged TEM image in Fig. 3D.
    • Fig. S15. Additional TEM images of the DNA origami–AuNR structures for synchronous revolution.
    • Fig. S16. Structure gallery for the average TEM image.
    • Fig. S17. Additional TEM images of the DNA origami–AuNR structures for synchronous revolution.
    • Fig. S18. In situ fluorescence intensity changes of ATTO 550 (blue) and ATTO 647 N (red) during synchronous revolution in two cycles.
    • Fig. S19. Design details of the footholds for joint motion.
    • Fig. S20. Additional TEM images of the DNA origami–AuNP structures for joint motion.
    • Fig. S21. Theoretical calculations of the fluorescence intensities of ATTO 550 and ATTO 647 N for the joint motion.
    • Table S1. Detailed sequences of the 12 foothold rows for independent revolution, synchronous revolution, and joint motion.
    • Table S2. Blocking strands (B) and removal strands (R).
    • Table S3. Samples added to drive the independent rotation for in situ fluorescence detection.
    • Table S4. Samples added to drive the synchronous motion for in situ fluorescence detection.
    • Table S5. Samples added to drive the joint motion for in situ fluorescence detection.
    • Supplementary Notes
    • Reference (40)

    Download PDF

    Other Supplementary Material for this manuscript includes the following:

    • Data S1 (Microsoft Excel format). Strands for the independent rotation.
    • Data S2 (Microsoft Excel format). Strands for the synchronous motion.
    • Data S3 (Microsoft Excel format). Strands for the joint motion.

    Files in this Data Supplement:

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