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An experimental study of the putative mechanism of a synthetic autonomous rotary DNA nanomotor

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ABSTRACT

DNA has been used to construct a wide variety of nanoscale molecular devices. Inspiration for such synthetic molecular machines is frequently drawn from protein motors, which are naturally occurring and ubiquitous. However, despite the fact that rotary motors such as ATP synthase and the bacterial flagellar motor play extremely important roles in nature, very few rotary devices have been constructed using DNA. This paper describes an experimental study of the putative mechanism of a rotary DNA nanomotor, which is based on strand displacement, the phenomenon that powers many synthetic linear DNA motors. Unlike other examples of rotary DNA machines, the device described here is designed to be capable of autonomous operation after it is triggered. The experimental results are consistent with operation of the motor as expected, and future work on an enhanced motor design may allow rotation to be observed at the single-molecule level. The rotary motor concept presented here has potential applications in molecular processing, DNA computing, biosensing and photonics.

No MeSH data available.


Related in: MedlinePlus

(a) Toehold-mediated strand displacement. An invader binds to the toehold (blue) and displaces the shorter incumbent via branch migration. (b) The underlying principle of the rotary motor concept described in this paper. The motor consists of two ‘wheels’ (grey squares); each wheel has a ‘tape’ wrapped round it. The two tapes are mainly complementary and are designed to displace each other from the wheels. This is intended to exert torque on the wheels, causing them to turn. (c) The DNA structures and devices studied in this paper. From left to right: linear construct, triangle, rotary motor (based on two squares). The motor is shown with the brake applied. The brake consists of a pair of blocking strands (bright blue) and it is released through displacement of the blocking strands by the unblocking strands (lilac). For clarity, parts of the motor that are irrelevant to the operating mechanism are not shown. The motor is illustrated in more detail in figure 4 and the electronic supplementary material. (d) Operation of a quartz crystal microbalance with dissipation monitoring. The piezoelectric crystal oscillates, driven by an applied voltage. The generated acoustic wave propagates into solution through a layer of surface-immobilized molecules. The frequency and energy dissipation of the wave reflect the mass and structure of the layer.
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RSOS160767F1: (a) Toehold-mediated strand displacement. An invader binds to the toehold (blue) and displaces the shorter incumbent via branch migration. (b) The underlying principle of the rotary motor concept described in this paper. The motor consists of two ‘wheels’ (grey squares); each wheel has a ‘tape’ wrapped round it. The two tapes are mainly complementary and are designed to displace each other from the wheels. This is intended to exert torque on the wheels, causing them to turn. (c) The DNA structures and devices studied in this paper. From left to right: linear construct, triangle, rotary motor (based on two squares). The motor is shown with the brake applied. The brake consists of a pair of blocking strands (bright blue) and it is released through displacement of the blocking strands by the unblocking strands (lilac). For clarity, parts of the motor that are irrelevant to the operating mechanism are not shown. The motor is illustrated in more detail in figure 4 and the electronic supplementary material. (d) Operation of a quartz crystal microbalance with dissipation monitoring. The piezoelectric crystal oscillates, driven by an applied voltage. The generated acoustic wave propagates into solution through a layer of surface-immobilized molecules. The frequency and energy dissipation of the wave reflect the mass and structure of the layer.

Mentions: It was first suggested in the 1980s that DNA could be used to build nanostructures through self-assembly of oligonucleotides by complementary base pairing [1]. In a DNA nanostructure, the base sequence of each DNA strand is designed to ensure that it binds in the correct position and performs its intended function. Static DNA nanostructures described in the literature include polyhedra [2–4], tiles [5], solid blocks [6] and twisted or curved shapes [7]. DNA can also be used to make dynamic nanomachines that are capable of undergoing a change of state or conformation. Many such devices are driven by toehold-mediated strand displacement [8–10]. For this process, the initial state (figure 1a) consists of a double-stranded DNA construct with a short single-stranded toehold domain, and a single-stranded DNA invader that is complementary to the longer of the two strands in the main construct. The toehold-binding domain of the invader binds to the toehold, and then branch migration occurs. Eventually, the invading strand displaces the incumbent, leading to a final state that consists of a complete double helix and a shorter single-stranded molecule.Figure 1.


An experimental study of the putative mechanism of a synthetic autonomous rotary DNA nanomotor
(a) Toehold-mediated strand displacement. An invader binds to the toehold (blue) and displaces the shorter incumbent via branch migration. (b) The underlying principle of the rotary motor concept described in this paper. The motor consists of two ‘wheels’ (grey squares); each wheel has a ‘tape’ wrapped round it. The two tapes are mainly complementary and are designed to displace each other from the wheels. This is intended to exert torque on the wheels, causing them to turn. (c) The DNA structures and devices studied in this paper. From left to right: linear construct, triangle, rotary motor (based on two squares). The motor is shown with the brake applied. The brake consists of a pair of blocking strands (bright blue) and it is released through displacement of the blocking strands by the unblocking strands (lilac). For clarity, parts of the motor that are irrelevant to the operating mechanism are not shown. The motor is illustrated in more detail in figure 4 and the electronic supplementary material. (d) Operation of a quartz crystal microbalance with dissipation monitoring. The piezoelectric crystal oscillates, driven by an applied voltage. The generated acoustic wave propagates into solution through a layer of surface-immobilized molecules. The frequency and energy dissipation of the wave reflect the mass and structure of the layer.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5383820&req=5

RSOS160767F1: (a) Toehold-mediated strand displacement. An invader binds to the toehold (blue) and displaces the shorter incumbent via branch migration. (b) The underlying principle of the rotary motor concept described in this paper. The motor consists of two ‘wheels’ (grey squares); each wheel has a ‘tape’ wrapped round it. The two tapes are mainly complementary and are designed to displace each other from the wheels. This is intended to exert torque on the wheels, causing them to turn. (c) The DNA structures and devices studied in this paper. From left to right: linear construct, triangle, rotary motor (based on two squares). The motor is shown with the brake applied. The brake consists of a pair of blocking strands (bright blue) and it is released through displacement of the blocking strands by the unblocking strands (lilac). For clarity, parts of the motor that are irrelevant to the operating mechanism are not shown. The motor is illustrated in more detail in figure 4 and the electronic supplementary material. (d) Operation of a quartz crystal microbalance with dissipation monitoring. The piezoelectric crystal oscillates, driven by an applied voltage. The generated acoustic wave propagates into solution through a layer of surface-immobilized molecules. The frequency and energy dissipation of the wave reflect the mass and structure of the layer.
Mentions: It was first suggested in the 1980s that DNA could be used to build nanostructures through self-assembly of oligonucleotides by complementary base pairing [1]. In a DNA nanostructure, the base sequence of each DNA strand is designed to ensure that it binds in the correct position and performs its intended function. Static DNA nanostructures described in the literature include polyhedra [2–4], tiles [5], solid blocks [6] and twisted or curved shapes [7]. DNA can also be used to make dynamic nanomachines that are capable of undergoing a change of state or conformation. Many such devices are driven by toehold-mediated strand displacement [8–10]. For this process, the initial state (figure 1a) consists of a double-stranded DNA construct with a short single-stranded toehold domain, and a single-stranded DNA invader that is complementary to the longer of the two strands in the main construct. The toehold-binding domain of the invader binds to the toehold, and then branch migration occurs. Eventually, the invading strand displaces the incumbent, leading to a final state that consists of a complete double helix and a shorter single-stranded molecule.Figure 1.

View Article: PubMed Central - PubMed

ABSTRACT

DNA has been used to construct a wide variety of nanoscale molecular devices. Inspiration for such synthetic molecular machines is frequently drawn from protein motors, which are naturally occurring and ubiquitous. However, despite the fact that rotary motors such as ATP synthase and the bacterial flagellar motor play extremely important roles in nature, very few rotary devices have been constructed using DNA. This paper describes an experimental study of the putative mechanism of a rotary DNA nanomotor, which is based on strand displacement, the phenomenon that powers many synthetic linear DNA motors. Unlike other examples of rotary DNA machines, the device described here is designed to be capable of autonomous operation after it is triggered. The experimental results are consistent with operation of the motor as expected, and future work on an enhanced motor design may allow rotation to be observed at the single-molecule level. The rotary motor concept presented here has potential applications in molecular processing, DNA computing, biosensing and photonics.

No MeSH data available.


Related in: MedlinePlus