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A DNA machine is a molecular machine constructed from DNA that exhibits each of the following[1]
- Executes a mechanical process that mimics macroscopic machines
- Requires an energy source in order to carry out its process
- Consumption of the energy source and subsequent generation of waste products
- Machine operation is cyclical, requiring fuel and anti-fuel ingredients
Research into DNA machines was pioneered in the late 1980s by Nadrian Seeman and co-workers from New York University. DNA is used because of the numerous biological tools already found in nature that can affect DNA, and the immense knowledge of how DNA works previously researched by biochemists. There is also a substantial amount of structural information inherent to the four base nucleotides, that makes their utilization as components of larger, more complex nucleic-acid nano-structures appealing. In addition to DNA's selective enzyme reactivity and protein binding, cytosine rich sequences can form i-configurations, 4-stranded DNA secondary structures consisting of two parallel DNA duplexes,[2] and guanine rich sequences can self-assemble into G-quadruplexes, providing initial constructs without intervention. Supra-molecular structures can also be assembled through interactions between metal ions, like T·Hg2+·T, and specific bases.[3] Indeed, the structural information within the four bases has lead to the design of one-dimensional, two-dimensional, and three-dimensional DNA structures.[1] Also, specific methods of sequence amplification of large DNA libraries can yield nucleic acids with specific DNA patterns that have high binding affinities towards low molecular weight substrates, macro-molecules ( cells, aptamers, or catalytic nucleic-acid strands), and proteins.[3]
DNA machines are capable of self assembly due to the strict rules of base pairing that allow portions of the strand to be predictably connected based on their sequence. This "selective stickiness" is a key advantage in the construction of DNA machines.
Examples
[edit]DNA Tweezers
[edit](find non-copyrighted image diagram, re-word)
An example of a DNA machine was reported by Bernard Yurke and co-workers at Lucent Technologies in the year 2000, who constructed molecular tweezers out of DNA. The DNA tweezers contain three strands: A, B and C. Strand A latches onto half of strand B and half of strand C, and so it joins them all together. Strand A acts as a hinge so that the two "arms" — AB and AC — can move. The structure floats with its arms open wide. They can be pulled shut by adding a fourth strand of DNA (D) "programmed" to stick to both of the dangling, unpaired sections of strands B and C. The closing of the tweezers was proven by tagging strand A at either end with light-emitting molecules that do not emit light when they are close together. To re-open the tweezers add a further strand (E) with the right sequence to pair up with strand D. Once paired up, they have no connection to the machine BAC, so float away. The DNA machine can be opened and closed repeatedly by cycling between strands D and E. These tweezers can be used for removing drugs from inside fullerenes as well as from a self assembled DNA tetrahedron. The state of the device can be determined by measuring the separation between donor and acceptor fluorophores using FRET.
DNA Walkers
[edit]DNA walkers are a type of DNA machine that were first theorized in 2003 by John H. Reif, and physically constructed in 2004.[1] Though certain aspects of walker design can change, the basic concept remains the same. Using interconnected one and two-dimensional DNA lattice structures as platforms, DNA "roads" can be developed for DNA Walkers to travel on.[4] The walkers travel along the road, and are capable of continuous translational and rotational movement.[4] Notably, DNA Walkers were the first nucleic acid devices capable of continuous cycles of motion completely anonymously, without the need for environmental changes such as temperature cycling or alteration of the solution's ion composition.[5] In 2004 Yin Peng et. al created DNA Walkers capable of unidirectional linear motion with self-assembling roads, marking a significant step forward in design, as previous walkers traveled bilaterally along the roads at random. Peng's platform was composed of three anchorages, where the six-nucleotide long walker could bind. A step occurs when the walker binds to the next anchorage in the track, and is cut from the previous anchorage by a restriction enzyme. The unidirectional nature of the walker is held due
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References
[edit]- ^ a b c Wang, Fuan; Willner, Bilha; Willner, Itamar (2014). Molecular Machines and Motors. Topics in Current Chemistry. Springer, Cham. pp. 279–338. doi:10.1007/128_2013_515. ISBN 9783319086774.
- ^ "i-Motif DNA: Structure, stability and targeting with ligands". Bioorganic & Medicinal Chemistry. 22 (16): 4407–4418. 2014-08-15. doi:10.1016/j.bmc.2014.05.047. ISSN 0968-0896.
- ^ a b "Functional nucleic acid nanostructures and DNA machines". Current Opinion in Biotechnology. 21 (4): 376–391. 2010-08-01. doi:10.1016/j.copbio.2010.06.001. ISSN 0958-1669.
- ^ a b Reif, John H. (2003-12-01). "The design of autonomous DNA nano-mechanical devices: Walking and rolling DNA". Natural Computing. 2 (4): 439. doi:10.1023/B:NACO.0000006775.03534.92. ISSN 1567-7818.
- ^ Yin, Peng; Yan, Hao; Daniell, Xiaoju G.; Turberfield, Andrew J.; Reif, John H. (2004-09-20). "A Unidirectional DNA Walker That Moves Autonomously along a Track". Angewandte Chemie International Edition. 43 (37): 4906–4911. doi:10.1002/anie.200460522. ISSN 1521-3773.