# Structural Biochemistry/DNA as Nanomaterial

DNA’s many properties such as minuscule size, informational element, and amplification provides for the potential of DNA to produce unique materials. As a matter of fact, the DNA molecule is arguably one of the most promising functional nanomaterial to date. DNA’s characteristic trait of self-assembly and molecular recognition makes it a key player in the bottom up construction of nanotechnology. The key factor in DNA’s role as nonmaterial lies in the molecule’s sticky ends. A sticky end is the short single stranded overhang that protrudes from the end of a double stranded DNA molecule. These sticky ends when paired with their complementary counterparts will cohere to form a diverse range of molecular complex. Under lab conditions these sticky end sequences are programmable so that there is control over intermolecular interactions and predictable geometry at the point of cohesion. Such control in formation allows for the construction of artificial DNA structures. Over the years the use of DNA in nanostructures have expanded in three main directions.
* The synthesis of artificial networks using DNA.
* The integration of DNA onto surfaces.
* The formation of metal or semiconductor nanoparticle assemblies along DNA.

## The Fabrication of Artificial Networks

Due to the fact that the DNA double helix runs along a single axis, the molecule is unbranched. This provides a problem with using DNA in the fabrication of nanomaterial because joining DNA molecules by sticky ends can only allow for construction in a single linear direction. However branched DNA does occur naturally in nature as an intermediated formed when chromosomes exchange information during meiosis. This structure is formally known as the Holliday structure. Over the years scientists have been able to feasibly design sequences that leads to stable synthetic variants of the Holliday junction. This allows for the fabrication of artificial networks consisting of native DNA.

## Attachment or Integration of DNA onto Solid State Surfaces.

The first step in DNA technology is to attach the molecule to the surface of interest. There are three different methods that may be used for such attachments.
* Electrostatic interaction between DNA and a substrate.
* Covalent binding of a chemical group attached to the DNA end.
* Binding of a protein attached to the DNA end to the corresponding antibody immobilized at the surface.
Due to the enhanced surface area and high surface free energy, nanoparticles can absorb biomolecules strongly and facilitate attachment. Generally the absorptions of biomolecules onto the naked surface of bulk material will result in their denaturation and loss of bioactivity. However the since nanoparticles have the ability to reduce the distance between the redox site of DNA and the working electrode surface, biomolecules are able to maintain their bioactivity. This is due to the fact that the rate of electron transfer is inversely dependent on the exponential distance between the two molecules.

## Metal Nanoparticles

Metal nanoparticles have the potential to revolutionize convention technology and experimental medicinal industries because of their electrical properties. There has been three main approaches in using DNA to assemble metals or semi-conducting nanoparticles.
* Electrostatic binding of negatively charged DNA to positively charged colloids
* Chemical binding of colloids to DNA
* Formation of nucleation sites along DNA molecules followed by metal or semiconductors deposition to allow for the direct growth of nanoparticles along the DNA.

# Structural DNA Nanotechnology
## Prerequisites for Structural DNA Nanotechnology

Before DNA can be used as nanomaterial it must be structured into the correct form, which can be achieved through three main ideas:
* Hybridization
* Stably branched DNA
* Synthesis of designed sequences.
Hybridization mostly entails the use of sticky-ended cohesion, which combines pieces of linear duplex DNA together through Hydrogen bonding. Sticky-ended cohesion is very useful because we can predict how the sticky ends will cohere with one another due to affinity. The double-helix will be the ultimate structure formed, which helps us to eliminate the need to first establish the crystal structure.
Stably branched DNA in combination with hybridization is what allows for DNA to be construction material. DNA molecules that have branched self-assemble to form larger arrangements. So, where the DNA forms a junction, the sticky ends have come together in a complementary fashion. But, the DNA will have left over sticky ends which it will use to bind to other junctions to “self-assemble” into two-dimensional or three-dimensional lattices.
However, there is one major problem with junctions, they are unstable because of their sequence symmetry. The symmetry exhibited allows for a specific type of isomerization known as branch migration. Branch migration allows the branch point to relocate which makes our entire structure highly unstable. To make it so that DNA is a stable structure we must minimize sequence symmetry. Nature, though, is very symmetrical and we must therefore synthesize DNA molecules of arbitrary sequences. Luckily, we have had laboratories that do just that since the 1980’s and it is now possible to order DNA molecules known as “vanilla” DNA because they lack complexity. So, these DNA molecules are readily synthesized, making it possible to have DNA in a structural form that will aid us in using it as nanomaterial.

## Individual Steps
### Motif Design

This step involves the switching of the connections between DNA strands, it is very similar to recombinant DNA in that we do something close to crossing over by switching connections between two different DNA double helices, this ultimately gives us a new connectivity. It is important to note that this step is purely theoretical, it is a type of drawing stage similar to blue prints for the later sequence design. Motif design is carried out through an operation called reciprocal exchange, if only a single reciprocal exchange is performed a conformer has just been made, and there is no difference. There must be at least two operations carried out for there to be a result of different topologies. There are a few key motifs that have been generated:
* DX motif: has exchanges between strands of opposite polarity and is known for its length which is twice that of a conventional linear duplex DNA
* DX + J motif: has an extra domain which is usually perpendicular to the plane of the two helix axes which allows the domain to be a topographic marker, easy to distinguish through a atomic force microscope.
* TX motif: has three domains that are joined in a particular pattern known as 1-3 fashion (where the top helical domain of one is joined at the bottom domain of another). These three domains are useful because in 2D arrays created there will be useful cavities.
* PX motif: happens everywhere that two double helices can be juxtaposed
* JX2 motif: is the topoisomer of the PX motif and it lacks two of the exchanges that the PX has

### Sequence Design and Symmetry Minimization

This step is where we use the motifs designed previously, and we go to the lab and literally design. The main goal is to get the molecules we are working with to become excited states. One effective method for achieving this is based on minimization of sequence symmetry, which of course has worked very well for the design of branched molecules.
There are a few helpful guidelines to follow to avoid getting unstable molecules:
* prevent long stretches of Guanine, because these could form other structures near crossover points
* avoid certain tracts that look like they might be symmetric, such as: homopolymer tracts, polyprimidine tracts, alternating purine-pyrimidine tracts, or polypurine tracts
There are some situations where these previous tips don’t necessarily work, in the case of a 12-arm junction for example. Here it is impossible to flank the branch points with different base pairs. So instead of attempting to eliminate symmetry around the center of the junction, we take identical nucleotide pairs and space them at four-step intervals around the junction.
There are a few situations where scientists have completely ignored sequence symmetry and have managed to design structures, such as with DNA origami. Scientists used a long single strand of viral DNA to scaffold a couple hundred shorter strands to produce a two-dimensional or three-dimensional shape. Two astonishing DNA origami pieces that they were able to create include a smiley face, and a map of the Western Hemisphere.

## Uses of DNA as a Nanomaterial

DNA has a variety of amazing uses, one such use of this tiny molecule is that it can be used to make nanomechanical devices that are extremely unique in and of themselves. Such nanomechanical devices include molecules that self-assemble, change their own shapes, and walk along a DNA sidewalk. DNA can also be used to organize other cellular species, DNA can help to organize or move proteins, enzymes, and nanoelectronic components. Such remarkable uses for this dynamic molecule has spurred on others to begin investigating the possibilities for programming the information in DNA beyond the use of just its genetic code.

# Other Types of DNA-based Nanomaterials

DNA species is not only used for organizing, but can be used also with DNA-based systems. Some of these systems are periodic assembly, using DNA to organize proteins and nanoelectronic components, algorithmic assembly, derived from DNA-based computation, and seminatural components.

## Organization of proteins and nanoelectric components using Periodic Assembly

DNA can be used to organize protein structures. Protein to proteins can be bound using structural DNA nanotechnology. For example, biotin groups can be attached to DNA arrays and then it was bounded to streptavidin. Another focus of structural DNA nanotechnology is organizing nanoelectronic and nanophotonic component. Multiple components can be used to organize metallic nanoparticles, such as gold.

## Algorithmic Assembly

Structural DNA nanotechnology can be used to organize aperiodic matter, although it is not as simple, using algorithmic assembly. One advantage of algorithmic assembly is its ability to generate complex algorithmic patterns using only a few tiles. However, its disadvantage is that algorithmic assembly is extremely sensitive to errors, and it is more prone to error than periodic assembly.

## Seminatural Constructs

It is also possible to combine other chemical species with DNA in nanoconstructs. Metallo-organic complexes were placed in junction sites, which led to different properties in presence or absence of metal. It is also possible to stimulate G-tetrad formation by use of a square-shaped organometallic molecule.

# DNA-Based Nanomechanical Devices

Because DNA can be combined with other molecular synthesized species, it is extremely valuable. Therefore, it is also questioned whether the arrangement can be changed per time. A fourth dimension is used in structural DNA nanotechnology.
Devices can be based on Structural Transitions. However, this system is limited to two states, as they ignore the programmability of DNA. Also there are transitions that are sequence dependet, so many individually addressable devices can be in the same solution.

## Reference

Seeman, Nadrian C. "Nanomaterials Based on DNA". Annual Review of Biochemistry 2010. Vol. 79: 65-87. 03/11/2010. DOI: 10.1146/annurev-biochem-060308-102244
Abu-Salah, Khalid M., Ansari, Anees A., Alrokayan, Salman A. “DNA-Based Applications in Nanobiotechnology”. Journal of Biomedicine and Biotechnology 2010. 2010:15. 12/1/2001