An artificial enzyme is a synthetic, organic molecule or ion
that recreates some function of an enzyme. The area promises to deliver
catalysis at rates and selectivity observed in many enzymes.
History
Enzyme
catalysis of chemical reactions occur with high selectivity and rate.
The substrate is activated in a small part of the enzyme's macromolecule
called the active site. There, the binding of a substrate close to functional groups in the enzyme causes catalysis by so-called proximity effects. It is possible to create similar catalysts from small molecule
by combining substrate-binding with catalytic functional groups.
Classically artificial enzymes bind substrates using receptors such as cyclodextrin, crown ethers, and calixarene.
Artificial enzymes based on amino acids or peptides
as characteristic molecular moieties have expanded the field of
artificial enzymes or enzyme mimics. For instance, scaffolded histidine
residues mimics certain metalloproteins and -enzymes such as hemocyanin, tyrosinase, and catechol oxidase).
Artificial enzymes have been designed from scratch via a computational strategy using Rosetta.
In December 2014, it was announced that active enzymes had been
produced that were made from artificial molecules which do not occur
anywhere in nature. In 2016, a book chapter entitled "Artificial Enzymes: The Next Wave" was published.
Nanozymes
Nanozymes are nanomaterials with enzyme-like characteristics.
They have been widely explored for various applications, such as
biosensing, bioimaging, tumor diagnosis and therapy, antibiofouling.
A "short review" article appeared in 2005.
It attributed the term "nanozyme"s to "analogy with the activity of
catalytic polymers (synzymes)", based on the "outstanding catalytic
efficiency of some of the functional nanoparticles synthesized". The
term was coined the previous year by Flavio Manea, Florence Bodar
Houillon, Lucia Pasquato, and Paolo Scrimin. In 2006, nanoceria (i.e., CeO2nanoparticles)
was reported as observed, in rat experiments, preventing retinal
degeneration induced by intracellular peroxides (toxic reactive oxygen
intermediates). This was seen as indicating a possible route to an eventual treatment for causes of blindness. In 2007 intrinsic peroxidase-like activity of ferromagnetic nanoparticles was reported by Yan Xiyun
and coworkers as suggesting a wide range of applications in, for
example, medicine and environmental chemistry, and the authors reported
an immunoassay based on this property.
Hui Wei and Erkang Wang then (2008) used this mimetic property of
easily prepared magnetic nanoparticles (MNP) to demonstrate analytical
applications to bioactive molecules, describing a colorimetric assay for
hydrogen peroxide (H 2O 2) and a sensitive and selective platform for glucose detection.
2010s
As of 2016 review articles are appearing every year, in a range of journals.
A book-length treatment appeared in 2015, described as providing "a
broad portrait of nanozymes in the context of artificial enzyme
research", and a 2016 Chinese book on "Enzyme Engineering" included a chapter on "Nanozymes".
Colorimetric applications of peroxidase mimesis in different
preparations were reported in 2010 and 2011, detecting, respectively,
glucose (via carboxyl‐modified graphene oxide) and single-nucleotide polymorphisms (via hemin−graphene hybrid nanosheets, and without labelling),
with advantages in both cases of cost and convenience. A use of colour
to visualise tumour tissues was reported in 2012, using the peroxidase
mimesis of MNP coated with a protein which recognises cancer cells and
binds to them.
Also in 2012, nanowires of vanadium pentoxide (vanadia, V2O5) were shown to suppress marine biofouling by mimicry of vanadium haloperoxidase, with anticipated ecological benefits. A study at a different centre two years later reported V2O5 showing mimicry of glutathione peroxidase, in in-vitro mammalian cells, suggesting future therapeutic application. The same year, 2014, it was reported that a carboxylated fullerene (C3) was neuroprotective post-injury in an in-vivo primate model of Parkinson's disease.
In 2015, a supramolecular nanodevice was proposed for bioorthogonal
regulation of a transitional-metal nanozyme, based on encapsulating
the nanozyme in a monolayer of hydrophilic gold nanoparticles,
alternatively isolating it from the cytoplasm or allowing access,
according to a gatekeeping receptor molecule controlled by competing guest species; the device is of biomimetic size and was reported as successful within the living cell, controlling pro-fluorophore and prodrug activation processes: it was suggested for imaging and therapeutic applications. A facile process for producing Cu(OH) 2 supercages was reported, and a demonstration of their intrinsic peroxidase-mimicry. A scaffolded "INAzyme" ("integrated nanozyme") arrangement was described, locating hemin (a peroxidase mimic) with glucose oxidase
(GOx) in sub-micron proximity, providing a fast and efficient enzyme
cascade reported as monitoring cerebral brain-cell glucose dynamically in vivo.
A method of ionising hydrophobe-stabilised colloid nanoparticles was
described, with confirmation of their enzyme mimicry in aqueous
dispersion.
Field trials were announced of an MNP-amplified rapid low-cost strip test for Ebola virus, in West Africa. H 2O 2
was reported as displacing label DNA, adsorbed to nanoceria, into
solution, where it fluoresces, providing a highly sensitive glucose
test. Oxidase-like nanoceria has been used for developing self-regulated bioassays. Multi-enzyme mimicking Prussian blue was developed for therapeutics. A review on MOF based enzyme mimics was published. Histidine was used to modulate iron oxide nanoparticles' peroxidase mimicking activities. Gold nanoparticles' peroxidase mimicking activities were modulated via a supramolecular strategy for cascade reactions. A molecular imprinting strategy was developed to improve the selectivity of Fe3O4 nanozymes with peroxidase-like activity. A new strategy was developed to enhance the peroxidase mimicking activity of gold nanoparticles by using hot electrons.
Researchers have designed gold nanoparticles (AuNPs) based integrative
nanozymes with both SERS and peroxidase mimicking activities for
measuring glucose and lactate in living tissues. Cytochrome c oxidase mimicking activity of Cu2O nanoparticles was modulated by receiving electrons from cytochrome c. Fe3O4 NPs were combined with glucose oxidase for tumor therapeutics. Manganese dioxide nanozymes have been used as cytoprotective shells. Mn3O4 Nanozyme for Parkinson's Disease (cellular model) was reported. Heparin elimination in live rats has been monitored with 2D MOF based peroxidase mimics and AG73 peptide.
Glucose oxidase and iron oxide nanozymes were encapsulated within
multi-compartmental hydrogels for incompatible tandem reactions. A cascade nanozyme biosensor was developed for detection of viable Enterobacter sakazakii. An integrated nanozyme of GOx@ZIF-8(NiPd) was developed for tandem catalysis. Charge-switchable nanozymes were developed. Site-selective RNA splicing nanozyme was developed. A nanozymes special issue in Progress in Biochemistry and Biophysics was published. Mn3O4 nanozymes with ROS scavenging activities have been developed for in vivo anti-inflammation. A concept entitled "A Step into the Future – Applications of Nanoparticle Enzyme Mimics" was proposed. Facet-dependent oxidase and peroxidase-like activities of Pd nanoparticles were reported. Au@Pt multibranched nanostructures as bifunctional nanozymes were developed. Ferritin coated carbon nanozymes were developed for tumor catalytic therapy. CuO nanozymes were developed to kill bacteria via a light-controlled manner. Enzymatic activity of oxygenated CNT was studied. Nanozymes were used to catalyze the oxidation of l-Tyrosine and l-Phenylalanine to dopachrome. Nanozyme as an emerging alternative to natural enzyme for biosensing and immunoassay was summarized. Standardized assay was proposed for peroxidase-like nanozymes. Semiconductor QDs as nucleases for site-selective photoinduced cleavage of DNA. 2D-MOF nanozyme-based sensor arrays was constructed for detecting phosphates and probing their enzymatic hydrolysis. N-doped carbon nanomaterials as specific peroxidase mimics were reported. Nanozyme sensor arrays were developed to detect analytes from small Molecules to proteins and cells. Copper oxide nanozyme for Parkinson's Disease was reported. Exosome-like nanozyme vesicles for tumor Imaging was developed. A comprehensive review on nanozymes was published by Chemical Society Reviews. A progress report on nanozymes was published. eg occupancy as an effective descriptor was developed for the catalytic activity of perovskite oxide-based peroxidase mimics. A Chemical Reviews on nanozymes was published. A single-atom strategy was used for developing nanozymes. Nanozyme for metal-free bioinspired cascade photocatalysis was reported. A tutorial review on nanozymes was published by Chemical Society Reviews. Cascade nanozyme reactions to convert CO2 into valuable resources was reported. Renal clearable peroxidase-like gold nanoclusters were used for in vivo disease monitoring. Copper/Carbon hybrid nanozyme was developed for antibacterial therapy. A ferritin nanozyme was developed to treat cerebral malaria. A review on nanozymes was published in Acc. Chem. Res. A new strategy called strain effect was developed to modulate the metal nanozyme activity. Prussian blue nanozymes were used to detect hydrogen sulfide (H2S) in the brains of living rats. Photolyase-like CeO2 was reported. An editorial on nanozymes "Can Nanozymes Have an Impact on Sensing?" was published.
2020s
A single-atom nanozyme was developed for sepsis management. Self-assembled single-atom nanozyme was developed for photodynamic therapy treatment of tumor. An ultrasound-switchable nanozyme against multidrug-resistant bacterial infection was reported. A nanozyme-based H2O2 homeostasis disruptor for chemodynamic tumor therapy was reported. An iridium oxide nanozyme for cascade reaction was developed for tumor therapy. A book entitled Nanozymology was published. Free radical scavenging nanosponge was engineered for ischemic stroke. A minireview on gold-conjugate based nanozymes. SnSe nanosheets as dehydrogenase mimics were developed. Carbon dot-based topoisomerase I mimic was reported to cleave DNA. Nanozyme sensor arrays were developed to detect pesticides. Bioorthogonal nanozymes were used to treat bacterial biofilms. Rhodium nanozyme was used to treat colon diseases. Fe-N-C nanozyme was developed to study drug-drug interaction. Polymeric nanozyme was developed for second near-infrared photothermal ferrotherapy. Cu5.4O nanozyme was reported for anti-inflammation therapy. CeO2@ZIF-8 nanozyme was developed to treat reperfusion-induced injury in ischemic stroke. Peroxidase-like activity of Fe3O4 was explored to study the electrocatalytic kinetics at single-molecule/single-particle level. Cu-TA nanozyme was fabricated to scavenging ROS from cigarette smoke. Metalloenzyme-like copper nanocluster was reported to have anticancer and imaging activities simultaneously. An integrated nanozyme was developed for anti-inflammation therapy. Enhanced enzyme-like catalytic activity was reported under non-equilibrium conditions for gold nanozymes. A DFT method was proposed to predict the activities of peroxidase-like nanozymes. A hydrolytic nanozyme was developed to construct an immunosensor. An orally administered nanozyme was developed for inflammatory bowel disease therapy.
A ligand‐dependent activity engineering strategy was reported to
develop glutathione peroxidase‐mimicking MIL‐47(V) metal–organic
framework nanozyme for therapy. Single site nanozyme was developed for tumor therapy. SOD-like nanozyme was developed to regulate the mitochondria and neural cell function. Pd12 coordination cage as a photoregulated oxidase-like nanozyme was developed. An NADPH oxidase-like nanozyme was developed. A catalase-like nanozyme was developed for tumor therapy. A defect‐rich adhesive molybdenum disulfide/reduced graphene oxide nanozyme was developed for anti-bacterial. A MOF@COF nanozyme was developed for anti-bacterial. Plasmonic nanozymes were reported. Tumor microenvironment responsive nanozyme was developed for tumor therapy. A protein-engineering inspired method was developed to design highly active nanozymes. An editorial on nanozymes definition was published. A nanozyme therapy for hyperuricemia and ischemic stroke was developed. A perspective on artificial enzymes as well as nanozymes was published by Chemistry World. A review on single atom catalysts including single atom nanozymes was published. Peroxidase-like mixed-FeCo-oxide-based surface-textured nanostructures (MTex) were used for biofilm eradication. A nanozyme with better kinetics than natural peroxidase was developed. A self-protecting nanozyme was developed for Alzheimer's Disease. CuSe nanozymes was developed to treat Parkinson's Disease. A nanocluster-based nanozyme was developed. Glucose oxidase-like gold nanoparticles combined with cyclodextran were used for chiral catalysis. An artificial binuclear copper monooxygenase in a MOF was developed. A review on highly efficient design of nanozymes was published. Ni–Pt peroxidase mimics were developed for bioanalysis. A POM-based nanozyme was reported to protect cells from ROS stress. A gating strategy was used to prepare selective nanozymes. A Mn single atom nanozyme was developed for tumor therapy. A pH-responsive oxidase-like graphitic nanozyme was developed for selective killing of Helicobacter pylori. An engineered FeN3P-centred single-atom nanozyme was developed. Peroxidase- and catalase-like activity of gold nanozymes were modulated. Graphdiyne–cerium oxide nanozymes for radiotherapy of esophageal cancer. Defect engineering was used to develop nanozyme for tumor therapy. A book entitled "Nanozymes for Environmental Engineering" was published. Pd single atom nanozyme was developed for tumor therapy. A HRP-like nanozyme was developed for tumor therapy. The mechanism of GOx-like nanozyme was reported. An Account review on nanozymes was published. A mechanism study on nanonuclease-like nanozyme was reported. A perspective on nanozyme definition was published. Aptananozymes were developed. Ceria nanozyme loaded microneedles helped the hair regrowth. Catalase-like Pt nanozyme was used for small extracellular vesicles analysis. A book on Nanozymes: Advances and Applications was published by CRC Press. A review on nanozyme catalytic turnover was published. A nanozyme was developed for ratiometric molecular imaging. A Fe3O4/Ag/Bi2MoO6 photoactivatable nanozyme was developed for cancer therapy. Co/C as NADH oxidase mimic was reported. Iron oxide nanozyme was used to target biofilms causing tooth decay. A new strategey for high performance nanozyme was developed. A high-throughput computational screening strategy was developed to discover SOD-like nanozymes.
Nanobiotechnology, bionanotechnology, and nanobiology are terms that refer to the intersection of nanotechnology and biology.
Given that the subject is one that has only emerged very recently,
bionanotechnology and nanobiotechnology serve as blanket terms for
various related technologies.
This discipline helps to indicate the merger of biological
research with various fields of nanotechnology. Concepts that are
enhanced through nanobiology include: nanodevices (such as biological machines), nanoparticles,
and nanoscale phenomena that occurs within the discipline of
nanotechnology. This technical approach to biology allows scientists to
imagine and create systems that can be used for biological research.
Biologically inspired nanotechnology uses biological systems as the
inspirations for technologies not yet created. However, as with nanotechnology and biotechnology, bionanotechnology does have many potential ethical issues associated with it.
The most important objectives that are frequently found in
nanobiology involve applying nanotools to relevant medical/biological
problems and refining these applications. Developing new tools, such as
peptoid nanosheets,
for medical and biological purposes is another primary objective in
nanotechnology. New nanotools are often made by refining the
applications of the nanotools that are already being used. The imaging
of native biomolecules, biological membranes, and tissues is also a major topic for nanobiology researchers. Other topics concerning nanobiology include the use of cantilever array sensors and the application of nanophotonics for manipulating molecular processes in living cells.
Recently, the use of microorganisms to synthesize functional nanoparticles has been of great interest. Microorganisms can change the oxidation state of metals.
These microbial processes have opened up new opportunities for us to
explore novel applications, for example, the biosynthesis of metal
nanomaterials. In contrast to chemical and physical methods, microbial
processes for synthesizing nanomaterials can be achieved in aqueous
phase under gentle and environmentally benign conditions. This approach
has become an attractive focus in current green bionanotechnology
research towards sustainable development.
Terminology
The
terms are often used interchangeably. When a distinction is intended,
though, it is based on whether the focus is on applying biological ideas
or on studying biology with nanotechnology. Bionanotechnology generally
refers to the study of how the goals of nanotechnology can be guided by
studying how biological "machines" work and adapting these biological
motifs into improving existing nanotechnologies or creating new ones.
Nanobiotechnology, on the other hand, refers to the ways that
nanotechnology is used to create devices to study biological systems.
In other words, nanobiotechnology is essentially miniaturized biotechnology, whereas bionanotechnology is a specific application of nanotechnology. For example, DNA nanotechnology
or cellular engineering would be classified as bionanotechnology
because they involve working with biomolecules on the nanoscale.
Conversely, many new medical technologies involving nanoparticles
as delivery systems or as sensors would be examples of
nanobiotechnology since they involve using nanotechnology to advance the
goals of biology.
The definitions enumerated above will be utilized whenever a
distinction between nanobio and bionano is made in this article.
However, given the overlapping usage of the terms in modern parlance,
individual technologies may need to be evaluated to determine which term
is more fitting. As such, they are best discussed in parallel.
Most of the scientific concepts in bionanotechnology are derived from
other fields. Biochemical principles that are used to understand the
material properties of biological systems are central in
bionanotechnology because those same principles are to be used to create
new technologies. Material properties and applications studied in
bionanoscience include mechanical properties (e.g. deformation,
adhesion, failure), electrical/electronic (e.g. electromechanical
stimulation, capacitors, energy storage/batteries), optical (e.g. absorption, luminescence, photochemistry),
thermal (e.g. thermomutability, thermal management), biological (e.g.
how cells interact with nanomaterials, molecular flaws/defects,
biosensing, biological mechanisms such as mechanosensation), nanoscience of disease (e.g. genetic disease, cancer, organ/tissue failure), as well as computing (e.g. DNA computing) and agriculture (target delivery of pesticides, hormones and fertilizers.
The impact of bionanoscience, achieved through structural and
mechanistic analyses of biological processes at nanoscale, is their
translation into synthetic and technological applications through
nanotechnology.
Nanobiotechnology takes most of its fundamentals from nanotechnology. Most of the devices designed for nano-biotechnological use are directly based on other existing nanotechnologies. Nanobiotechnology is often used to describe the overlapping
multidisciplinary activities associated with biosensors, particularly
where photonics, chemistry, biology, biophysics, nanomedicine, and engineering converge. Measurement in biology using wave guide techniques, such as dual-polarization interferometry, is another example.
Applications
Applications
of bionanotechnology are extremely widespread. Insofar as the
distinction holds, nanobiotechnology is much more commonplace in that it
simply provides more tools for the study of biology. Bionanotechnology,
on the other hand, promises to recreate biological mechanisms and
pathways in a form that is useful in other ways.
Nanomedicine
Nanomedicine is a field of medical science whose applications are increasing more and more thanks to nanorobots and biological machines,
which constitute a very useful tool to develop this area of knowledge.
In the past years, researchers have made many improvements in the
different devices and systems required to develop nanorobots. This
supposes a new way of treating and dealing with diseases such as cancer;
thanks to nanorobots, side effects of chemotherapy have been
controlled, reduced and even eliminated, so some years from now, cancer
patients will be offered an alternative to treat this disease instead of
chemotherapy,
which causes secondary effects such as hair loss, fatigue or nausea
killing not only cancerous cells but also the healthy ones.
At a clinical level, cancer treatment with nanomedicine will consist of
the supply of nanorobots to the patient through an injection that will
search for cancerous cells while leaving the healthy ones untouched.
Patients that will be treated through nanomedicine will not notice the
presence of these nanomachines inside them; the only thing that is going
to be noticeable is the progressive improvement of their health.
Nanobiotechnology is quite important for medicine formulation. It helps a
lot in making vaccines as well.
Nanobiotechnology
Nanobiotechnology (sometimes referred to as nanobiology) is best described as helping modern medicine progress from treating symptoms to generating cures and regenerating biological tissues. Three American patients have received whole cultured bladders
with the help of doctors who use nanobiology techniques in their
practice. Also, it has been demonstrated in animal studies that a uterus can be grown outside the body and then placed in the body in order to produce a baby. Stem cell treatments have been used to fix diseases that are found in the human heart
and are in clinical trials in the United States. There is also funding
for research into allowing people to have new limbs without having to
resort to prosthesis. Artificial proteins might also become available to manufacture without the need for harsh chemicals and expensive machines. It has even been surmised that by the year 2055, computers may be made out of biochemicals and organic salts.
Another example of current nanobiotechnological research involves
nanospheres coated with fluorescent polymers. Researchers are seeking
to design polymers whose fluorescence is quenched when they encounter
specific molecules. Different polymers would detect different
metabolites. The polymer-coated spheres could become part of new
biological assays, and the technology might someday lead to particles
which could be introduced into the human body to track down metabolites
associated with tumors and other health problems. Another example, from a
different perspective, would be evaluation and therapy at the
nanoscopic level, i.e. the treatment of Nanobacteria (25-200 nm sized)
as is done by NanoBiotech Pharma.
While nanobiology is in its infancy, there are a lot of promising
methods that will rely on nanobiology in the future. Biological systems
are inherently nano in scale; nanoscience must merge with biology in
order to deliver biomacromolecules
and molecular machines that are similar to nature. Controlling and
mimicking the devices and processes that are constructed from molecules
is a tremendous challenge to face for the converging disciplines of
nanobiotechnology. All living things, including humans, can be considered to be nanofoundries.
Natural evolution has optimized the "natural" form of nanobiology over
millions of years. In the 21st century, humans have developed the
technology to artificially tap into nanobiology. This process is best
described as "organic merging with synthetic." Colonies of live neurons can live together on a biochip device; according to research from Dr. Gunther Gross at the University of North Texas. Self-assembling nanotubes have the ability to be used as a structural system. They would be composed together with rhodopsins; which would facilitate the optical computing process and help with the storage of biological materials. DNA (as the software
for all living things) can be used as a structural proteomic system - a
logical component for molecular computing. Ned Seeman - a researcher at
New York University - along with other researchers are currently researching concepts that are similar to each other.
Bionanotechnology
DNA nanotechnology is one important example of bionanotechnology. The utilization of the inherent properties of nucleic acids like DNA
to create useful materials is a promising area of modern research.
Another important area of research involves taking advantage of membrane properties to generate synthetic membranes. Proteins that self-assemble
to generate functional materials could be used as a novel approach for
the large-scale production of programmable nanomaterials. One example is
the development of amyloids found in bacterial biofilms as engineered nanomaterials that can be programmed genetically to have different properties. Protein folding
studies provide a third important avenue of research, but one that has
been largely inhibited by our inability to predict protein folding with a
sufficiently high degree of accuracy. Given the myriad uses that
biological systems have for proteins, though, research into
understanding protein folding is of high importance and could prove
fruitful for bionanotechnology in the future.
Lipid nanotechnology
is another major area of research in bionanotechnology, where
physico-chemical properties of lipids such as their antifouling and
self-assembly is exploited to build nanodevices with applications in
medicine and engineering.
Lipid nanotechnology approaches can also be used to develop
next-generation emulsion methods to maximize both absorption of
fat-soluble nutrients and the ability to incorporate them into popular
beverages.
Agriculture
In
the agriculture industry, engineered nanoparticles have been serving as
nano carriers, containing herbicides, chemicals, or genes, which target
particular plant parts to release their content.
Previously nanocapsules containing herbicides have been reported to
effectively penetrate through cuticles and tissues, allowing the slow
and constant release of the active substances. Likewise, other
literature describes that nano-encapsulated slow release of fertilizers
has also become a trend to save fertilizer consumption and to minimize
environmental pollution through precision farming. These are only a few
examples from numerous research works which might open up exciting
opportunities for nanobiotechnology application in agriculture. Also,
application of this kind of engineered nanoparticles to plants should be
considered the level of amicability before it is employed in
agriculture practices. Based on a thorough literature survey, it was
understood that there is only limited authentic information available to
explain the biological consequence of engineered nanoparticles on
treated plants. Certain reports underline the phytotoxicity of various
origin of engineered nanoparticles to the plant caused by the subject of
concentrations and sizes . At the same time, however, an equal number
of studies were reported with a positive outcome of nanoparticles, which
facilitate growth promoting nature to treat plant.
In particular, compared to other nanoparticles, silver and gold
nanoparticles based applications elicited beneficial results on various
plant species with less and/or no toxicity.
Silver nanoparticles (AgNPs) treated leaves of Asparagus showed the
increased content of ascorbate and chlorophyll. Similarly, AgNPs-treated
common bean and corn has increased shoot and root length, leaf surface
area, chlorophyll, carbohydrate and protein contents reported earlier. The gold nanoparticle has been used to induce growth and seed yield in Brassica juncea.
Tools
This field relies on a variety of research methods, including experimental tools (e.g. imaging, characterization via AFM/optical tweezers etc.), x-ray diffraction based tools, synthesis via self-assembly, characterization of self-assembly (using e.g. MP-SPR, DPI, recombinant DNA methods, etc.), theory (e.g. statistical mechanics, nanomechanics, etc.), as well as computational approaches (bottom-up multi-scale simulation, supercomputing).
DNA nanotechnology involves forming artificial, designed nanostructures out of nucleic acids, such as this DNA tetrahedron. Each edge of the tetrahedron is a 20 base pair DNA double helix, and each vertex is a three-arm junction. The 4 DNA strands that form the 4 tetrahedral faces are color-coded.
The conceptual foundation for DNA nanotechnology was first laid out by Nadrian Seeman
in the early 1980s, and the field began to attract widespread interest
in the mid-2000s. This use of nucleic acids is enabled by their strict base pairing rules, which cause only portions of strands with complementarybase sequences to bind together to form strong, rigid double helix structures. This allows for the rational design of base sequences that will selectively assemble to form complex target structures with precisely controlled nanoscale
features. Several assembly methods are used to make these structures,
including tile-based structures that assemble from smaller structures,
folding structures using the DNA origami method, and dynamically reconfigurable structures using strand displacement methods. The field's name specifically references DNA,
but the same principles have been used with other types of nucleic
acids as well, leading to the occasional use of the alternative name nucleic acid nanotechnology.
Fundamental concepts
These four strands associate into a DNA four-arm junction because this structure maximizes the number of correct base pairs, with A matched to T and C matched to G. See this image for a more realistic model of the four-arm junction showing its tertiary structure.
This double-crossover (DX) supramolecular complex consists of five DNA single strands that form two double-helical
domains, on the top and the bottom in this image. There are two
crossover points where the strands cross from one domain into the other.
Properties of nucleic acids
Nanotechnology is often defined as the study of materials and devices with features on a scale below 100 nanometers. DNA nanotechnology, specifically, is an example of bottom-upmolecular self-assembly,
in which molecular components spontaneously organize into stable
structures; the particular form of these structures is induced by the
physical and chemical properties of the components selected by the
designers.
In DNA nanotechnology, the component materials are strands of nucleic
acids such as DNA; these strands are often synthetic and are almost
always used outside the context of a living cell. DNA is well-suited to
nanoscale construction because the binding between two nucleic acid
strands depends on simple base pairing rules which are well understood, and form the specific nanoscale structure of the nucleic acid double helix. These qualities make the assembly of nucleic acid structures easy to control through nucleic acid design. This property is absent in other materials used in nanotechnology, including proteins, for which protein design is very difficult, and nanoparticles, which lack the capability for specific assembly on their own.
The structure of a nucleic acid molecule consists of a sequence of nucleotides distinguished by which nucleobase they contain. In DNA, the four bases present are adenine (A), cytosine (C), guanine (G), and thymine
(T). Nucleic acids have the property that two molecules will only bind
to each other to form a double helix if the two sequences are complementary, meaning that they form matching sequences of base pairs, with A only binding to T, and C only to G. Because the formation of correctly matched base pairs is energetically favorable,
nucleic acid strands are expected in most cases to bind to each other
in the conformation that maximizes the number of correctly paired bases.
The sequences of bases in a system of strands thus determine the
pattern of binding and the overall structure in an easily controllable
way. In DNA nanotechnology, the base sequences of strands are
rationally designed by researchers so that the base pairing interactions
cause the strands to assemble in the desired conformation. While DNA is the dominant material used, structures incorporating other nucleic acids such as RNA and peptide nucleic acid (PNA) have also been constructed.
Subfields
DNA
nanotechnology is sometimes divided into two overlapping subfields:
structural DNA nanotechnology and dynamic DNA nanotechnology.
Structural DNA nanotechnology, sometimes abbreviated as SDN, focuses on
synthesizing and characterizing nucleic acid complexes and materials
that assemble into a static, equilibrium
end state. On the other hand, dynamic DNA nanotechnology focuses on
complexes with useful non-equilibrium behavior such as the ability to
reconfigure based on a chemical or physical stimulus. Some complexes,
such as nucleic acid nanomechanical devices, combine features of both
the structural and dynamic subfields.
The complexes constructed in structural DNA nanotechnology use
topologically branched nucleic acid structures containing junctions. (In
contrast, most biological DNA exists as an unbranched double helix.)
One of the simplest branched structures is a four-arm junction that
consists of four individual DNA strands, portions of which are
complementary in a specific pattern. Unlike in natural Holliday junctions, each arm in the artificial immobile four-arm junction has a different base sequence,
causing the junction point to be fixed at a certain position. Multiple
junctions can be combined in the same complex, such as in the widely
used double-crossover (DX) structural motif,
which contains two parallel double helical domains with individual
strands crossing between the domains at two crossover points. Each
crossover point is, topologically, a four-arm junction, but is
constrained to one orientation, in contrast to the flexible single
four-arm junction, providing a rigidity that makes the DX motif suitable
as a structural building block for larger DNA complexes.
Dynamic DNA nanotechnology uses a mechanism called toehold-mediated strand displacement
to allow the nucleic acid complexes to reconfigure in response to the
addition of a new nucleic acid strand. In this reaction, the incoming
strand binds to a single-stranded toehold region of a double-stranded complex, and then displaces one of the strands bound in the original complex through a branch migration process. The overall effect is that one of the strands in the complex is replaced with another one. In addition, reconfigurable structures and devices can be made using functional nucleic acids such as deoxyribozymes and ribozymes, which can perform chemical reactions, and aptamers, which can bind to specific proteins or small molecules.
Structural DNA nanotechnology
Structural
DNA nanotechnology, sometimes abbreviated as SDN, focuses on
synthesizing and characterizing nucleic acid complexes and materials
where the assembly has a static, equilibrium endpoint. The nucleic acid double helix has a robust, defined three-dimensional geometry that makes it possible to simulate,
predict and design the structures of more complicated nucleic acid
complexes. Many such structures have been created, including two- and
three-dimensional structures, and periodic, aperiodic, and discrete
structures.
Extended lattices
The assembly of a DX array. Left, schematic diagram. Each bar represents a double-helical domain of DNA, with the shapes representing complementarysticky ends. The DX complex at top will combine with other DX complexes into the two-dimensional array shown at bottom. Right, an atomic force microscopy image of the assembled array. The individual DX tiles are clearly visible within the assembled structure. The field is 150 nm across.
Left, a model of a DNA tile used to make another two-dimensional periodic lattice. Right, an atomic force micrograph of the assembled lattice.
An example of an aperiodic two-dimensional lattice that assembles into a fractal pattern. Left, the Sierpinski gasket fractal. Right, DNA arrays that display a representation of the Sierpinski gasket on their surfaces
Small nucleic acid complexes can be equipped with sticky ends and combined into larger two-dimensional periodic lattices containing a specific tessellated pattern of the individual molecular tiles.
The earliest example of this used double-crossover (DX) complexes as
the basic tiles, each containing four sticky ends designed with
sequences that caused the DX units to combine into periodic
two-dimensional flat sheets that are essentially rigid two-dimensional
crystals of DNA. Two-dimensional arrays have been made from other motifs as well, including the Holliday junctionrhombus lattice, and various DX-based arrays making use of a double-cohesion scheme. The top two images at right show examples of tile-based periodic lattices.
Two-dimensional arrays can be made to exhibit aperiodic
structures whose assembly implements a specific algorithm, exhibiting
one form of DNA computing. The DX tiles can have their sticky end sequences chosen so that they act as Wang tiles, allowing them to perform computation. A DX array whose assembly encodes an XOR operation has been demonstrated; this allows the DNA array to implement a cellular automaton that generates a fractal known as the Sierpinski gasket. The third image at right shows this type of array. Another system has the function of a binary counter,
displaying a representation of increasing binary numbers as it grows.
These results show that computation can be incorporated into the
assembly of DNA arrays.
DX arrays have been made to form hollow nanotubes 4–20 nm in diameter, essentially two-dimensional lattices which curve back upon themselves. These DNA nanotubes are somewhat similar in size and shape to carbon nanotubes,
and while they lack the electrical conductance of carbon nanotubes, DNA
nanotubes are more easily modified and connected to other structures.
One of many schemes for constructing DNA nanotubes uses a lattice of
curved DX tiles that curls around itself and closes into a tube.
In an alternative method that allows the circumference to be specified
in a simple, modular fashion using single-stranded tiles, the rigidity
of the tube is an emergent property.
Forming three-dimensional lattices of DNA was the earliest goal
of DNA nanotechnology, but this proved to be one of the most difficult
to realize. Success using a motif based on the concept of tensegrity, a balance between tension and compression forces, was finally reported in 2009.
Discrete structures
Researchers have synthesized many three-dimensional DNA complexes that each have the connectivity of a polyhedron, such as a cube or octahedron, meaning that the DNA duplexes trace the edges of a polyhedron with a DNA junction at each vertex. The earliest demonstrations of DNA polyhedra were very work-intensive, requiring multiple ligations and solid-phase synthesis steps to create catenated polyhedra.
Subsequent work yielded polyhedra whose synthesis was much easier.
These include a DNA octahedron made from a long single strand designed
to fold into the correct conformation, and a tetrahedron that can be produced from four DNA strands in one step, pictured at the top of this article.
Nanostructures of arbitrary, non-regular shapes are usually made using the DNA origami
method. These structures consist of a long, natural virus strand as a
"scaffold", which is made to fold into the desired shape by
computationally designed short "staple" strands. This method has the
advantages of being easy to design, as the base sequence is predetermined by the scaffold strand sequence, and not requiring high strand purity and accurate stoichiometry, as most other DNA nanotechnology methods do. DNA origami was first demonstrated for two-dimensional shapes, such as a smiley face, a coarse map of the Western Hemisphere, and the Mona Lisa painting. Solid three-dimensional structures can be made by using parallel DNA helices arranged in a honeycomb pattern,
and structures with two-dimensional faces can be made to fold into a
hollow overall three-dimensional shape, akin to a cardboard box. These
can be programmed to open and reveal or release a molecular cargo in
response to a stimulus, making them potentially useful as programmable molecular cages.
Templated assembly
Nucleic
acid structures can be made to incorporate molecules other than nucleic
acids, sometimes called heteroelements, including proteins, metallic
nanoparticles, quantum dots, and fullerenes.
This allows the construction of materials and devices with a range of
functionalities much greater than is possible with nucleic acids alone.
The goal is to use the self-assembly of the nucleic acid structures to
template the assembly of the nanoparticles hosted on them, controlling
their position and in some cases orientation.
Many of these schemes use a covalent attachment scheme, using oligonucleotides with amide or thiol functional groups as a chemical handle to bind the heteroelements. This covalent binding scheme has been used to arrange gold nanoparticles on a DX-based array,
and to arrange streptavidin protein molecules into specific patterns on a DX array.
A non-covalent hosting scheme using Dervan polyamides on a DX array was used to arrange streptavidin proteins in a specific pattern on a DX array. Carbon nanotubes have been hosted on DNA arrays in a pattern allowing the assembly to act as a molecular electronic device, a carbon nanotube field-effect transistor.
In addition, there are nucleic acid metallization methods, in which
the nucleic acid is replaced by a metal which assumes the general shape
of the original nucleic acid structure, and schemes for using nucleic acid nanostructures as lithography masks, transferring their pattern into a solid surface.
Dynamic DNA nanotechnology
Dynamic
DNA nanotechnology often makes use of toehold-mediated strand
displacement reactions. In this example, the red strand binds to the
single stranded toehold region on the green strand (region 1), and then
in a branch migration
process across region 2, the blue strand is displaced and freed from
the complex. Reactions like these are used to dynamically reconfigure
or assemble nucleic acid nanostructures. In addition, the red and blue
strands can be used as signals in a molecular logic gate.
Dynamic DNA nanotechnology focuses on forming nucleic acid systems
with designed dynamic functionalities related to their overall
structures, such as computation and mechanical motion. There is some
overlap between structural and dynamic DNA nanotechnology, as structures
can be formed through annealing and then reconfigured dynamically, or
can be made to form dynamically in the first place.
DNA complexes have been made that change their conformation upon some stimulus, making them one form of nanorobotics.
These structures are initially formed in the same way as the static
structures made in structural DNA nanotechnology, but are designed so
that dynamic reconfiguration is possible after the initial assembly. The earliest such device made use of the transition between the B-DNA and Z-DNA forms to respond to a change in buffer conditions by undergoing a twisting motion.
This reliance on buffer conditions caused all devices to change state at
the same time. Subsequent systems could change states based upon the
presence of control strands, allowing multiple devices to be
independently operated in solution. Some examples of such systems are a
"molecular tweezers" design that has an open and a closed state,
a device that could switch from a paranemic-crossover (PX) conformation
to a double-junction (JX2) conformation, undergoing rotational motion
in the process, and a two-dimensional array that could dynamically expand and contract in response to control strands.
Structures have also been made that dynamically open or close,
potentially acting as a molecular cage to release or reveal a functional
cargo upon opening.
DNA walkers
are a class of nucleic acid nanomachines that exhibit directional
motion along a linear track. A large number of schemes have been
demonstrated.
One strategy is to control the motion of the walker along the track
using control strands that need to be manually added in sequence. Another approach is to make use of restriction enzymes or deoxyribozymes to cleave the strands and cause the walker to move forward, which has the advantage of running autonomously.
A later system could walk upon a two-dimensional surface rather than a
linear track, and demonstrated the ability to selectively pick up and
move molecular cargo. Additionally, a linear walker has been demonstrated that performs DNA-templated synthesis as the walker advances along the track, allowing autonomous multistep chemical synthesis directed by the walker. The synthetic DNA walkers' function is similar to that of the proteins dynein and kinesin.
Strand displacement cascades
Cascades
of strand displacement reactions can be used for either computational
or structural purposes. An individual strand displacement reaction
involves revealing a new sequence in response to the presence of some
initiator strand. Many such reactions can be linked into a cascade
where the newly revealed output sequence of one reaction can initiate
another strand displacement reaction elsewhere. This in turn allows for
the construction of chemical reaction networks with many components,
exhibiting complex computational and information processing abilities.
These cascades are made energetically favorable through the formation of
new base pairs, and the entropy
gain from disassembly reactions. Strand displacement cascades allow
isothermal operation of the assembly or computational process, in
contrast to traditional nucleic acid assembly's requirement for a
thermal annealing step, where the temperature is raised and then slowly
lowered to ensure proper formation of the desired structure. They can
also support catalytic function of the initiator species, where less than one equivalent of the initiator can cause the reaction to go to completion.
Strand displacement complexes can be used to make molecular logic gates capable of complex computation. Unlike traditional electronic computers, which use electric current
as inputs and outputs, molecular computers use the concentrations of
specific chemical species as signals. In the case of nucleic acid
strand displacement circuits, the signal is the presence of nucleic acid
strands that are released or consumed by binding and unbinding events
to other strands in displacement complexes. This approach has been used
to make logic gates such as AND, OR, and NOT gates. More recently, a four-bit circuit was demonstrated that can compute the square root of the integers 0–15, using a system of gates containing 130 DNA strands.
Another use of strand displacement cascades is to make dynamically assembled structures. These use a hairpin
structure for the reactants, so that when the input strand binds, the
newly revealed sequence is on the same molecule rather than
disassembling. This allows new opened hairpins to be added to a growing
complex. This approach has been used to make simple structures such as
three- and four-arm junctions and dendrimers.
Applications
DNA
nanotechnology provides one of the few ways to form designed, complex
structures with precise control over nanoscale features. The field is
beginning to see application to solve basic science problems in structural biology and biophysics. The earliest such application envisaged for the field, and one still in development, is in crystallography,
where molecules that are difficult to crystallize in isolation could be
arranged within a three-dimensional nucleic acid lattice, allowing
determination of their structure. Another application is the use of DNA origami rods to replace liquid crystals in residual dipolar coupling experiments in protein NMR spectroscopy; using DNA origami is advantageous because, unlike liquid crystals, they are tolerant of the detergents needed to suspend membrane proteins in solution. DNA walkers have been used as nanoscale assembly lines to move nanoparticles and direct chemical synthesis. Further, DNA origami structures have aided in the biophysical studies of enzyme function and protein folding.
DNA nanotechnology is moving toward potential real-world
applications. The ability of nucleic acid arrays to arrange other
molecules indicates its potential applications in molecular scale
electronics. The assembly of a nucleic acid structure could be used to
template the assembly of molecular electronic elements such as molecular wires,
providing a method for nanometer-scale control of the placement and
overall architecture of the device analogous to a molecular breadboard. DNA nanotechnology has been compared to the concept of programmable matter because of the coupling of computation to its material properties.
In a study conducted by a group of scientists from iNANO and CDNA centers in Aarhus University,
researchers were able to construct a small multi-switchable 3D DNA Box
Origami. The proposed nanoparticle was characterized by atomic force microscopy (AFM), transmission electron microscopy (TEM) and Förster resonance energy transfer
(FRET). The constructed box was shown to have a unique reclosing
mechanism, which enabled it to repeatedly open and close in response to a
unique set of DNA or RNA keys. The authors proposed that this "DNA
device can potentially be used for a broad range of applications such as
controlling the function of single molecules, controlled drug delivery,
and molecular computing."
There are potential applications for DNA nanotechnology in nanomedicine, making use of its ability to perform computation in a biocompatible format to make "smart drugs" for targeted drug delivery, as well as for diagnostic applications. One such system being investigated uses a hollow DNA box containing proteins that induce apoptosis, or cell death, that will only open when in proximity to a cancer cell.
There has additionally been interest in expressing these artificial
structures in engineered living bacterial cells, most likely using the transcribed
RNA for the assembly, although it is unknown whether these complex
structures are able to efficiently fold or assemble in the cell's cytoplasm. If successful, this could enable directed evolution of nucleic acid nanostructures.
Scientists at Oxford University
reported the self-assembly of four short strands of synthetic DNA into a
cage which can enter cells and survive for at least 48 hours. The
fluorescently labeled DNA tetrahedra were found to remain intact in the laboratory cultured human kidney cells despite the attack by cellular enzymes after two days. This experiment showed the potential of drug delivery inside the living cells using the DNA ‘cage’. A DNA tetrahedron was used to deliver RNA Interference (RNAi) in a mouse model, reported a team of researchers in MIT. Delivery of the interfering RNA for treatment has showed some success using polymer or lipid,
but there are limits of safety and imprecise targeting, in addition to
short shelf life in the blood stream. The DNA nanostructure created by
the team consists of six strands of DNA to form a tetrahedron, with one
strand of RNA affixed to each of the six edges. The tetrahedron is
further equipped with targeting protein, three folate molecules, which lead the DNA nanoparticles to the abundant folate receptors found on some tumors. The result showed that the gene expression targeted by the RNAi, luciferase,
dropped by more than half. This study shows promise in using DNA
nanotechnology as an effective tool to deliver treatment using the
emerging RNA Interference technology. The DNA tetrahedron was also used in an effort to overcome the phenomena multidrug resistance. Doxorubicin (DOX) was conjugated with the tetrahedron and was loaded into MCF-7 breast cancer cells that contained the P-glycoprotein
drug efflux pump. The results of the experiment showed the DOX was not
being pumped out and apoptosis of the cancer cells was achieved. The
tetrahedron without DOX was loaded into cells to test its
biocompatibility, and the structure showed no cytotoxicity itself.
The DNA tetrahedron was also used as barcode for profiling the
subcellular expression and distribution of proteins in cells for
diagnostic purposes. The tetrahedral-nanostructured showed enhanced
signal due to higher labeling efficiency and stability.
Applications for DNA nanotechnology in nanomedicine also focus on mimicking the structure and function of naturally occurring membrane proteins with designed DNA nanostructures. In 2012, Langecker et al. introduced a pore-shaped DNA origami structure that can self-insert into lipid membranes via hydrophobic cholesterol
modifications and induce ionic currents across the membrane. This first
demonstration of a synthetic DNA ion channel was followed by a variety
of pore-inducing designs ranging from a single DNA duplex, to small tile-based structures, and large DNA origami transmembrane porins. Similar to naturally occurring protein ion channels,
this ensemble of synthetic DNA-made counterparts thereby spans multiple
orders of magnitude in conductance. The study of the membrane-inserting
single DNA duplex
showed that current must also flow on the DNA-lipid interface as no
central channel lumen is present in the design that lets ions pass
across the lipid bilayer. This indicated that the DNA-induced lipid pore has a toroidal shape, rather than cylindrical, as lipid headgroups reorient to face towards the membrane-inserted part of the DNA. Researchers from the University of Cambridge and the University of Illinois at Urbana-Champaign then demonstrated that such a DNA-induced toroidal pore can facilitate rapid lipid flip-flop between the lipid bilayer leaflets. Utilizing this effect, they designed a synthetic DNA-built enzyme that flips lipids in biological membranes orders of magnitudes faster than naturally occurring proteins called scramblases. This development highlights the potential of synthetic DNA nanostructures for personalized drugs and therapeutics.
Design
DNA nanostructures must be rationally designed
so that individual nucleic acid strands will assemble into the desired
structures. This process usually begins with specification of a desired target structure or function. Then, the overall secondary structure
of the target complex is determined, specifying the arrangement of
nucleic acid strands within the structure, and which portions of those
strands should be bound to each other. The last step is the primary structure design, which is the specification of the actual base sequences of each nucleic acid strand.
Structural design
The
first step in designing a nucleic acid nanostructure is to decide how a
given structure should be represented by a specific arrangement of
nucleic acid strands. This design step determines the secondary
structure, or the positions of the base pairs that hold the individual
strands together in the desired shape. Several approaches have been demonstrated:
Tile-based structures. This approach breaks the target
structure into smaller units with strong binding between the strands
contained in each unit, and weaker interactions between the units. It is
often used to make periodic lattices, but can also be used to implement
algorithmic self-assembly, making them a platform for DNA computing.
This was the dominant design strategy used from the mid-1990s until the
mid-2000s, when the DNA origami methodology was developed.
Folding structures. An alternative to the tile-based
approach, folding approaches make the nanostructure from one long
strand, which can either have a designed sequence that folds due to its
interactions with itself, or it can be folded into the desired shape by
using shorter, "staple" strands. This latter method is called DNA origami, which allows forming nanoscale two- and three-dimensional shapes (see Discrete structures above).
Dynamic assembly. This approach directly controls the kinetics of DNA self-assembly, specifying all of the intermediate steps in the reaction mechanism in addition to the final product. This is done using starting materials which adopt a hairpin structure; these then assemble into the final conformation in a cascade reaction, in a specific order (see Strand displacement cascades below). This approach has the advantage of proceeding isothermally, at a constant temperature. This is in contrast to the thermodynamic approaches, which require a thermal annealing step where a temperature change is required to trigger the assembly and favor proper formation of the desired structure.
After any of the above approaches are used to design the secondary
structure of a target complex, an actual sequence of nucleotides that
will form into the desired structure must be devised. Nucleic acid
design is the process of assigning a specific nucleic acid base sequence
to each of a structure's constituent strands so that they will
associate into a desired conformation. Most methods have the goal of
designing sequences so that the target structure has the lowest energy,
and is thus the most thermodynamically favorable, while incorrectly
assembled structures have higher energies and are thus disfavored. This
is done either through simple, faster heuristic methods such as sequence symmetry minimization, or by using a full nearest-neighbor
thermodynamic model, which is more accurate but slower and more
computationally intensive. Geometric models are used to examine tertiary structure of the nanostructures and to ensure that the complexes are not overly strained.
Nucleic acid design has similar goals to protein design.
In both, the sequence of monomers is designed to favor the desired
target structure and to disfavor other structures. Nucleic acid design
has the advantage of being much computationally easier than protein
design, because the simple base pairing rules are sufficient to predict a
structure's energetic favorability, and detailed information about the
overall three-dimensional folding of the structure is not required. This
allows the use of simple heuristic methods that yield experimentally
robust designs. Nucleic acid structures are less versatile than proteins
in their function because of proteins' increased ability to fold into
complex structures, and the limited chemical diversity of the four nucleotides as compared to the twenty proteinogenic amino acids.
Materials and methods
Gel electrophoresis methods, such as this formation assay
on a DX complex, are used to ascertain whether the desired structures
are forming properly. Each vertical lane contains a series of bands,
where each band is characteristic of a particular reaction intermediate.
The fully formed target structures can be verified using native gel electrophoresis, which gives size and shape information for the nucleic acid complexes. An electrophoretic mobility shift assay can assess whether a structure incorporates all desired strands. Fluorescent labeling and Förster resonance energy transfer (FRET) are sometimes used to characterize the structure of the complexes.
Nucleic acid structures can be directly imaged by atomic force microscopy,
which is well suited to extended two-dimensional structures, but less
useful for discrete three-dimensional structures because of the
microscope tip's interaction with the fragile nucleic acid structure; transmission electron microscopy and cryo-electron microscopy are often used in this case. Extended three-dimensional lattices are analyzed by X-ray crystallography.
History
The woodcut Depth (pictured) by M. C. Escher
reportedly inspired Nadrian Seeman to consider using three-dimensional
lattices of DNA to orient hard-to-crystallize molecules. This led to the
beginning of the field of DNA nanotechnology.
The conceptual foundation for DNA nanotechnology was first laid out by Nadrian Seeman in the early 1980s.
Seeman's original motivation was to create a three-dimensional DNA
lattice for orienting other large molecules, which would simplify their crystallographic study
by eliminating the difficult process of obtaining pure crystals. This
idea had reportedly come to him in late 1980, after realizing the
similarity between the woodcut Depth by M. C. Escher and an array of DNA six-arm junctions. Several natural branched DNA structures were known at the time, including the DNA replication fork and the mobile Holliday junction,
but Seeman's insight was that immobile nucleic acid junctions could be
created by properly designing the strand sequences to remove symmetry in
the assembled molecule, and that these immobile junctions could in
principle be combined into rigid crystalline lattices. The first
theoretical paper proposing this scheme was published in 1982, and the
first experimental demonstration of an immobile DNA junction was
published the following year.
In 1991, Seeman's laboratory published a report on the synthesis
of a cube made of DNA, the first synthetic three-dimensional nucleic
acid nanostructure, for which he received the 1995 Feynman Prize in Nanotechnology. This was followed by a DNA truncated octahedron. It soon became clear that these structures, polygonal shapes with flexible junctions as their vertices, were not rigid enough to form extended three-dimensional lattices. Seeman developed the more rigid double-crossover (DX) structural motif, and in 1998, in collaboration with Erik Winfree, published the creation of two-dimensional lattices of DX tiles.
These tile-based structures had the advantage that they provided the
ability to implement DNA computing, which was demonstrated by Winfree
and Paul Rothemund
in their 2004 paper on the algorithmic self-assembly of a Sierpinski
gasket structure, and for which they shared the 2006 Feynman Prize in
Nanotechnology. Winfree's key insight was that the DX tiles could be
used as Wang tiles, meaning that their assembly could perform computation.
The synthesis of a three-dimensional lattice was finally published by
Seeman in 2009, nearly thirty years after he had set out to achieve it.
New abilities continued to be discovered for designed DNA structures throughout the 2000s. The first DNA nanomachine—a
motif that changes its structure in response to an input—was
demonstrated in 1999 by Seeman. An improved system, which was the first
nucleic acid device to make use of toehold-mediated strand
displacement, was demonstrated by Bernard Yurke
the following year. The next advance was to translate this into
mechanical motion, and in 2004 and 2005, several DNA walker systems were
demonstrated by the groups of Seeman, Niles Pierce, Andrew Turberfield, and Chengde Mao.
The idea of using DNA arrays to template the assembly of other
molecules such as nanoparticles and proteins, first suggested by Bruche
Robinson and Seeman in 1987, was demonstrated in 2002 by Seeman, Kiehl et al. and subsequently by many other groups.
In 2006, Rothemund first demonstrated the DNA origami
method for easily and robustly forming folded DNA structures of
arbitrary shape. Rothemund had conceived of this method as being
conceptually intermediate between Seeman's DX lattices, which used many
short strands, and William Shih's
DNA octahedron, which consisted mostly of one very long strand.
Rothemund's DNA origami contains a long strand which folding is assisted
by several short strands. This method allowed forming much larger
structures than formerly possible, and which are less technically
demanding to design and synthesize. DNA origami was the cover story of Nature on March 15, 2006.
Rothemund's research demonstrating two-dimensional DNA origami
structures was followed by the demonstration of solid three-dimensional
DNA origami by Douglas et al. in 2009, while the labs of Jørgen Kjems and Yan demonstrated hollow three-dimensional structures made out of two-dimensional faces.
DNA nanotechnology was initially met with some skepticism due to
the unusual non-biological use of nucleic acids as materials for
building structures and doing computation, and the preponderance of proof of principle
experiments that extended the abilities of the field but were far from
actual applications. Seeman's 1991 paper on the synthesis of the DNA
cube was rejected by the journal Science after one reviewer praised its originality while another criticized it for its lack of biological relevance.
By the early 2010s the field was considered to have increased its
abilities to the point that applications for basic science research were
beginning to be realized, and practical applications in medicine and
other fields were beginning to be considered feasible.
The field had grown from very few active laboratories in 2001 to at
least 60 in 2010, which increased the talent pool and thus the number of
scientific advances in the field during that decade.
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