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A DNA walker is a class of
nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main ...
nanomachines A molecular machine, nanite, or nanomachine is a molecular component that produces quasi-mechanical movements (output) in response to specific stimuli (input). In cellular biology, macromolecular machines frequently perform tasks essential for ...
where a nucleic acid "walker" is able to move along a nucleic acid "track". The concept of a DNA walker was first defined and named by John H. Reif in 2003. A nonautonomous DNA walker requires external changes for each step, whereas an autonomous DNA walker progresses without any external changes. Various nonautonomous DNA walkers were developed, for example Shin controlled the motion of DNA walker by using 'control strands' which needed to be manually added in a specific order according to the template's sequence in order to get the desired path of motion. In 2004 the first autonomous DNA walker, which did not require external changes for each step, was experimentally demonstrated by the Reif group. DNA walkers have functional properties such as a range of motion extending from linear to 2 and 3-dimensional, the ability to pick up and drop off molecular cargo, performing DNA-templated synthesis, and increased velocity of motion. DNA walkers have potential applications ranging from
nanomedicine Nanomedicine is the medical application of nanotechnology. Nanomedicine ranges from the medical applications of nanomaterials and biological devices, to nanoelectronic biosensors, and even possible future applications of molecular nanotec ...
to
nanorobotics Nanoid robotics, or for short, nanorobotics or nanobotics, is an emerging technology field creating machines or robots whose components are at or near the scale of a nanometer (10−9 meters). More specifically, nanorobotics (as opposed to m ...
. Many different fuel options have been studied including DNA hybridization, hydrolysis of DNA or
ATP ATP may refer to: Companies and organizations * Association of Tennis Professionals, men's professional tennis governing body * American Technical Publishers, employee-owned publishing company * ', a Danish pension * Armenia Tree Project, non ...
, and light. The DNA walker's function is similar to that of the proteins
dynein Dyneins are a family of cytoskeletal motor proteins that move along microtubules in cells. They convert the chemical energy stored in ATP to mechanical work. Dynein transports various cellular cargos, provides forces and displacements importa ...
and
kinesin A kinesin is a protein belonging to a class of motor proteins found in eukaryotic cells. Kinesins move along microtubule (MT) filaments and are powered by the hydrolysis of adenosine triphosphate (ATP) (thus kinesins are ATPases, a type of enz ...
.


Role in DNA nanotechnology

Finding a suitable nanoscale motor capable of autonomous, unidirectional, linear motion is considered important to the development of
DNA nanotechnology DNA nanotechnology is the design and manufacture of artificial nucleic acid structures for technological uses. In this field, nucleic acids are used as non-biological engineering materials for nanotechnology rather than as the carriers of geneti ...
. The walkers have been shown to be capable of autonomous motion over linear, 2-dimensional and 3-dimensional DNA 'tracks' through a large number of schemes. In July 2005, Bath ''et al.'' showed that another way to control DNA walker motion is to use
restriction enzyme A restriction enzyme, restriction endonuclease, REase, ENase or'' restrictase '' is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzymes are one class ...
s to strategically cleave the 'track', causing the forward motion of the walkers. In 2010, two different sets of researchers exhibited the walkers' more complex abilities to selectively pick up and drop off molecular cargo and to perform DNA-templated synthesis as the walker moves along the track. In late 2015, Yehl ''et al.'' showed that three orders of magnitude higher than the speeds of motion seen previously were possible when using DNA-coated spherical particles that would "roll" on a surface modified with
RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
complementary to the nanoparticle's DNA.
RNase H Ribonuclease H (abbreviated RNase H or RNH) is a family of non-sequence-specific endonuclease enzymes that catalyze the cleavage of RNA in an RNA/ DNA substrate via a hydrolytic mechanism. Members of the RNase H family can be found in nearly ...
was used to
hydrolyse Hydrolysis (; ) is any chemical reaction in which a molecule of water breaks one or more chemical bonds. The term is used broadly for substitution, elimination, and solvation reactions in which water is the nucleophile. Biological hydrolysis i ...
the RNA, releasing the bound DNA and allowing the DNA to hybridize to RNA further downstream. In 2018, Valero et al. described a DNA walker based on two interlocked, catenated circular double-stranded DNAs (dsDNAs) and an engineered T7 RNA polymerase (T7RNAP) firmly attached to one of the DNA circles. This
stator The stator is the stationary part of a rotary system, found in electric generators, electric motors, sirens, mud motors or biological rotors. Energy flows through a stator to or from the rotating component of the system. In an electric ...
-ring unidirectionally rotated the interlocked rotor-ring by rolling circle transcription (RCT), driven by nucleotide triphosphate (NTP) hydrolysis, thereby constituting a catenated DNA wheel motor. The wheel motor produces long, repetitive RNA transcripts that remain attached to the DNA-catenane and are used to guide its directional walking along predefined ssDNA tracks arranged on a DNA nanotube.


Applications

The applications of DNA walkers include
nanomedicine Nanomedicine is the medical application of nanotechnology. Nanomedicine ranges from the medical applications of nanomaterials and biological devices, to nanoelectronic biosensors, and even possible future applications of molecular nanotec ...
, diagnostic sensing of biological samples,
nanorobotics Nanoid robotics, or for short, nanorobotics or nanobotics, is an emerging technology field creating machines or robots whose components are at or near the scale of a nanometer (10−9 meters). More specifically, nanorobotics (as opposed to m ...
and much more. In late 2015, Yehl ''et al.'' improved the DNA walker's function by increasing its velocity, and it has been proposed as the basis for a low-cost, low-tech diagnostics machine capable of detecting single nucleotide mutations and heavy-metal contamination in water. In 2018 Nils Walter and his team designed a DNA walker that is capable of moving at a speed of 300 nanometres per minute. This is an order of magnitude faster than the pace of other types of DNA walker.


See also

*
DNA nanotechnology DNA nanotechnology is the design and manufacture of artificial nucleic acid structures for technological uses. In this field, nucleic acids are used as non-biological engineering materials for nanotechnology rather than as the carriers of geneti ...
*
Nanorobotics Nanoid robotics, or for short, nanorobotics or nanobotics, is an emerging technology field creating machines or robots whose components are at or near the scale of a nanometer (10−9 meters). More specifically, nanorobotics (as opposed to m ...
*
Nanomedicine Nanomedicine is the medical application of nanotechnology. Nanomedicine ranges from the medical applications of nanomaterials and biological devices, to nanoelectronic biosensors, and even possible future applications of molecular nanotec ...


References

{{Reflist, 30em DNA nanotechnology Molecular machines