doi: 10.1126/sciadv.adi8444. Epub 2023 Sep 22.
Autonomous DNA molecular motor tailor-designed to navigate DNA origami surface for fast complex motion and advanced nanorobotics
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- PMID:37738343
- PMCID: PMC10516491
- DOI: 10.1126/sciadv.adi8444
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Autonomous DNA molecular motor tailor-designed to navigate DNA origami surface for fast complex motion and advanced nanorobotics
Winna Siti et al. Sci Adv..
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Abstract
Nanorobots powered by designed DNA molecular motors on DNA origami platforms are vigorously pursued but still short of fully autonomous and sustainable operation, as the reported systems rely on manually operated or autonomous but bridge-burning molecular motors. Expanding DNA nanorobotics requires origami-based autonomous non-bridge-burning motors, but such advanced artificial molecular motors are rare, and their integration with DNA origami remains a challenge. Here, we report an autonomous non-bridge-burning DNA motor tailor-designed for a triangle DNA origami substrate. This is a translational bipedal molecular motor but demonstrates effective translocation on both straight and curved segments of a self-closed circular track on the origami, including sharp ~90° turns by a single hand-over-hand step. The motor is highly directional and attains a record-high speed among the autonomous artificial molecular motors reported to date. The resultant DNA motor-origami system, with its complex translational-rotational motion and big nanorobotic capacity, potentially offers a self-contained "seed" nanorobotic platform to automate or scale up many applications.
Figures
(A toC) Schematic illustration of the motor (A) and its fuel (B), with all the tested motor versions listed in (C). (D) Schematic illustration of the motor’s stepping mechanisms on an origami-based periodic track with identical bi-overhang sites (i.e., F1 and F2 with a 32-bp gap). The dye-labeling scheme for a bi-overhang site is shown for the purpose of fluorescence motility detection. The asterisk (*) indicates complementary sequences, “nt” stands for nucleotides, and “bp” stands for base pairs.
(A) Design of the origami-based circular track (origami’s staple-folded scaffold shown by the gray line). (B andC) Atomic force microscopy (AFM) images of the equilateral triangular DNA origami (B) and amplified views (C). Scale bars, 100 nm. (D toF) A truncated linear three-site track [illustrated in (D)] and typical fluorescence change by the motor’s operation on the track (relative to the fluorescence at the time of fuel/enzyme supply, i.e., zero time). The remaining panels are all the same as (D) to (F) except for different truncated tracks: (H andI) are data for the curved three-site track illustrated in (G); (K andL) are data for the second curved three-site track in (J); (N andO) are data for the eight-site track in (M); (Q andR) are data for another eight-site track in (P). The amplified details of early fluorescence change in (F) and (O) are shown in two insets. The data for motor version 1 (all panels in the third column of the figure) are obtained with st1-st2 spacers below F1 and F2 overhangs as 9dT-3dT and at 12.5 mM MgCl2. The data for motor version 2 (all panels in the fourth column) are obtained with st1-st2 spacers as 5dT-5dT and at 5.0 mM MgCl2. The motors used are all for the 25–base pair (bp) bridge [except (K), (L), (N), and (O) for the 30-bp bridge]. All the data are obtained for 1:1 motor-origami ratio at 25°C, 10 nM motor, 1.0 μM fuel, and 200 nM nicking enzyme [except 30°C for (H) and (I), and 30 nM motor, 300 nM enzyme, and 1.5 μM fuel for (N) and (O)].
(A toE) The enzyme-triggered partial motility experiments for motor version M25V2 on the linear three-site track [(A) to (C) for motor-origami system illustration, fluorescence during the motor-origami binding, and later enzyme-induced fluorescence change, respectively] and on the curved three-site track around corner A (D and E). As shown in (A) and (D), the motor’s track-bound leg is mutated froma andb segments tof ande segments, respectively. The middle bi-overhang site is mutated accordingly froma*′ andb* segments tof* ande*, respectively, to allow intra-site cartwheeling of the mutated leg. The green arrowhead indicates the cutting site for the elongated fuel. (F) The average leg binding bias for motor version 2 at the 25–base pair (bp) bridge (i.e., M25V2) on the two truncated three-site tracks at different temperatures. The data in (B), (C), and (E) are for 25°C. The data in (B), (C), (E), and (F) are all obtained using st1-st2 spacers as 5dT-5dT below the F1 and F2 overhangs (including the mutated ones) at 5.0 mM MgCl2 (using 7 nM motor and 10 nM origami for motor-origami mix and 200 nM enzyme for fuel hydrolysis and ensuing leg binding).
(A toF) The fuel-triggered enzyme-free partial motility experiments for motor version M25V2 on the truncated linear three-site track [(A) to (C) for system illustration, fluorescence during motor-origami binding, and later fuel-induced fluorescence change] and on a minimal two-site track (D to F). The yellow dashed curves in (A) and (D) indicate the motor’s inter-site binding state. (G) The average dissociation bias for motor versions 1 and 2 with different bridge lengths. In the histogram, each bar (for a combination of motor version/bridge length) is obtained by averaging over nine partial motility experiments [for three three-site tracks as shown in Fig. 2 (D, G, and J) and for three temperatures per track at 25°, 30°, and 37°C]. The data are all obtained for 1:1 motor-origami ratio at 10 nM motor and 1.0 μM fuel. The data in (B), (C), (E), and (F) are for 25°C.
(A andB) Typical raw speed data for motor version 1 on a truncated linear three-site track as shown in Fig. 2D (A), and for motor version 2 on a curved three-site track as shown in Fig. 2J (B). The peak values from the rapidly dropping raw speed data are taken as the motor’s measured speed and used to produce the speed histograms in (C) and (D). (C andD) Average speed for motor versions 1 and 2. Each bar in the two histograms is obtained by equal-weight average over three different three-site tracks as illustrated in Fig. 2 (D, G, and J). (E) The motor’s speed obtained by further averaging the speed data in (C) and (D) over the three operational temperatures 25°, 30°, and 37°C by equal weightage. All the data are obtained at 1:1 motor-origami ratio at 10 nM motor, 1.0 μM fuel, and 200 nM enzyme (st1-st2 spacers as 9dT-3dT and 12.5 mM MgCl2 for motor version 1; 5dT-5dT and 5.0 mM MgCl2 for motor version 2).
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