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

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

Observing strand displacement in a folded nanostructure. (a) Schematic diagram of the triangle structure. The long strand T had six domains (t, d, c, b, a, RC-CS), separated with T triplets where necessary. The long strand T was folded into a triangular conformation by means of two shorter strands (bd-staple) and (ac-staple) and the triangle could be immobilized through attachment to the CS strand. (b) QCM-D data which illustrate immobilization of strand CS and either isothermal on-surface assembly of triangles (T+S) or attachment of pre-folded triangles (F(T)). Control strands were used to test whether the triangle had assembled correctly. (c) Strand displacement in the nanotriangles. The immobilized triangles were exposed to unfolded or folded reverse complements, which bound to their targets and induced displacement. Red lines: smoothed data (50 point adjacent average filter). (d) Dissipation changes as a function of frequency changes for the time period shown in part (c). A 20 point adjacent-averaging smoothing filter was used.
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RSOS160767F3: Observing strand displacement in a folded nanostructure. (a) Schematic diagram of the triangle structure. The long strand T had six domains (t, d, c, b, a, RC-CS), separated with T triplets where necessary. The long strand T was folded into a triangular conformation by means of two shorter strands (bd-staple) and (ac-staple) and the triangle could be immobilized through attachment to the CS strand. (b) QCM-D data which illustrate immobilization of strand CS and either isothermal on-surface assembly of triangles (T+S) or attachment of pre-folded triangles (F(T)). Control strands were used to test whether the triangle had assembled correctly. (c) Strand displacement in the nanotriangles. The immobilized triangles were exposed to unfolded or folded reverse complements, which bound to their targets and induced displacement. Red lines: smoothed data (50 point adjacent average filter). (d) Dissipation changes as a function of frequency changes for the time period shown in part (c). A 20 point adjacent-averaging smoothing filter was used.

Mentions: QCM-D experiments were also performed on a geometrically constrained structure, formed by using two 23 nt oligonucleotides to fold a 73 nt oligonucleotide (T) into a triangular configuration (figure 3a). The shorter strands were named ‘staples’, following the convention of DNA origami [5]. Surface-immobilization of this structure was achieved via hybridization of the triangle strand with a pre-immobilized capture strand (CS), as shown in figure 3a.Figure 3.


An experimental study of the putative mechanism of a synthetic autonomous rotary DNA nanomotor
Observing strand displacement in a folded nanostructure. (a) Schematic diagram of the triangle structure. The long strand T had six domains (t, d, c, b, a, RC-CS), separated with T triplets where necessary. The long strand T was folded into a triangular conformation by means of two shorter strands (bd-staple) and (ac-staple) and the triangle could be immobilized through attachment to the CS strand. (b) QCM-D data which illustrate immobilization of strand CS and either isothermal on-surface assembly of triangles (T+S) or attachment of pre-folded triangles (F(T)). Control strands were used to test whether the triangle had assembled correctly. (c) Strand displacement in the nanotriangles. The immobilized triangles were exposed to unfolded or folded reverse complements, which bound to their targets and induced displacement. Red lines: smoothed data (50 point adjacent average filter). (d) Dissipation changes as a function of frequency changes for the time period shown in part (c). A 20 point adjacent-averaging smoothing filter was used.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5383820&req=5

RSOS160767F3: Observing strand displacement in a folded nanostructure. (a) Schematic diagram of the triangle structure. The long strand T had six domains (t, d, c, b, a, RC-CS), separated with T triplets where necessary. The long strand T was folded into a triangular conformation by means of two shorter strands (bd-staple) and (ac-staple) and the triangle could be immobilized through attachment to the CS strand. (b) QCM-D data which illustrate immobilization of strand CS and either isothermal on-surface assembly of triangles (T+S) or attachment of pre-folded triangles (F(T)). Control strands were used to test whether the triangle had assembled correctly. (c) Strand displacement in the nanotriangles. The immobilized triangles were exposed to unfolded or folded reverse complements, which bound to their targets and induced displacement. Red lines: smoothed data (50 point adjacent average filter). (d) Dissipation changes as a function of frequency changes for the time period shown in part (c). A 20 point adjacent-averaging smoothing filter was used.
Mentions: QCM-D experiments were also performed on a geometrically constrained structure, formed by using two 23 nt oligonucleotides to fold a 73 nt oligonucleotide (T) into a triangular configuration (figure 3a). The shorter strands were named ‘staples’, following the convention of DNA origami [5]. Surface-immobilization of this structure was achieved via hybridization of the triangle strand with a pre-immobilized capture strand (CS), as shown in figure 3a.Figure 3.

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