In a new study, researchers from Shanghai Jiao Tong University in China, Emory University and Purdue University in the United States used DNA to construct simple machines that consist of DNA arrays made up of DNA Modular DNA structural units that switch between two different shapes. They said that these DNA machines could be used to make nanosensors or amplifiers. Potentially, they may be combined to form a logic gate, a part of a molecular computer. Relevant findings were published online in the journal Science on June 22, 2017, and the paper was titled "Reconfiguration of DNA molecular arrays driven by information relay." The paper was written by Emerson University - Assistant Professor Yongkang Ke, Department of Biomedical Engineering, Georgia Institute of Technology, Jie Song, Scientist, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University and Chengde Mao, Department of Chemistry, Purdue University.
Ke said that these DNA machines can transmit discrete bits of information in space or amplify signals. "In the DNA-based computing world, DNA contains information, but these DNA molecules float in solution," said Ke, "The novelty of this new research is that we are joining together these DNA parts in a real machine. "
Similarly, several laboratories have used DNA to make nanomachines, such as tweezers and wheelchairs. Ke says his team's research on DNA arrays illustrates how to make structures that have more complex dynamics.
The structure of these DNA arrays looks like an accordion retractable security door. Extending or contracting a structural unit can also cause the attached structural unit to change shape, acting like a domino.
The structural elements of these DNA arrays utilize the energy obtained when DNA duplexes are stacked together to maintain stability. In order to be stable, the four segments of these structural units can be arranged side-by-side in two different directions. By extending a DNA strand on the edge of a DNA array, the researchers constructed an external trigger. When this DNA chain is added, it squeezes the structural units at the edges, changing its shape.
To visualize these DNA arrays, these researchers used atomic force microscopy. They constructed rectangular 11x4 DNA arrays and 11x7 DNA arrays that joined the trigger chain and subsequently observed that this domino effect was propagated from the structural units located at the corners to the rest of the DNA array.
By designing breakpoints on these DNA arrays, it is possible to stop or restart their domino effect at selected sites. The shape conversion of these structural units can be adjusted by temperature or chemical denaturants.
For reference, these rectangular arrays of DNA are about 50 nanometers wide, hundreds of nanometers long, and are slightly smaller than an HIV or influenza virus particle.
To construct these DNA array structures, these researchers used origami and modular brick methods. The two rectangular arrays of DNA are self-assembled by looking for their complementary strands of DNA in solution. This paper folding resulted in more stable structure formation at elevated temperatures or presence of denaturant.
In the new study, the researchers confirmed that they were able to construct rectangular arrays of DNA and tubular DNA arrays using structural units of DNA arrays. They are also able to construct a rectangular array of DNA arrays with three basic conformations, and these two-dimensional DNA array building blocks have only two conformations. Ke said his team is working hard to make use of these same foundational principles to make larger, more complex machines with three-dimensional shapes.
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