Biology Reference
In-Depth Information
limitations in energy sources, and enzyme function over time are obstacles that need to
be addressed.
Beyond proving valuable for exploration of biochemical circuit design principles, continued
developments in cell-free circuits promise to have a variety of applications. Key potential
areas for use include: in situ detection of expression patterns;
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disease detection based on
mRNA levels;
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controlling nanoscale devices; and organizing biological processes in
minimal cells.
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NANOMACHINES
As with nucleic acid circuits, the simplicity, specificity, and predictability of DNA make it an
ideal building block for synthetic nanomachines.
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Nucleic acid nanomachines are synthetic
devices that switch between different molecular conformations based on interactions with
signaling molecules or changes in the environment.
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They have received considerable
attention for their possible applications in molecular-scale electronics and as
biomedicines.
The earliest nanomachines were controlled by environmental factors such as pH and
temperature, but never by a sequence-specific code.
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A breakthrough paper by Yurke et al.
outlined the construction of DNA
using DNA hybridization and strand
displacement technology to create a DNA nanomachine that could repeatedly be opened
and closed.
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More recently, a nucleic acid nanomachine comprising DNA and RNA was
created by researchers using DNA tweezers, as well as another gene that encodes for an
mRNA that closes/changes the conformation of the tweezers. A single-stranded DNA
removal strand can then hybridize with the mRNA and result in opening of the tweezers.
Using this simplified system researchers can create a more complicated and autonomous
nucleobase nanomachine.
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tweezers
'
'
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Researchers also designed DNA nanomachines with integrated instructions into a gene to
establish control of the DNA nanodevice in vitro using gene regulation switches. By
incorporating DNA regulated by regulatory proteins from
E. coli
operons, the researchers
were able to create an independently functioning nanomachine that responds to
environmental cues, such as changes in lactose concentrations. This work paved the way for
development of more complicated nanomachines that are able to respond to environmental
changes.
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Beyond DNA, RNA devices are also being developed.
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DNA ORIGAMI
The field of structural DNA nanotechnology was born in the 1980s with initial work by
Seeman, who proposed building geometric structures with multiple strands of DNA at a
nanoscale level.
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However, complications in synthesis and stoichiometric control left the
field lacking in more promising developments.
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In 2004 the Joyce group demonstrated that
a long single-stranded DNA could be folded into a geometric shape (octahedron) with the
help of synthetic shorter oligomers.
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Taking this further, Paul Rothemund, in a landmark
discovery, demonstrated that long single-stranded DNA could be folded at nanoscale levels
with the help of smaller staple strands to create various shapes.
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Specifically, Rothermund
demonstrated the creation of complex single-layered nanostructures that were 100 nm in
diameter and had a spatial resolution of 6 nm.
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Termed DNA origami, this approach
creates custom nanoscale shapes that are atomically precise by taking advantage of the
specificity of Watson Crick base-pairing.
In recent efforts, there has been a thrust to make 3D DNA origami structures and expand
the dimensionality and functionality of molecularly engineered objects. Douglas et al., for
example, demonstrated the ability to make a variety of 3D shapes from linear DNA
molecules.
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However, proper assembly of the 3D structure required week-long folding
