DNA Nanotechnology

Ashang Luwang Laiva *

This is a model of the ligated version of a DNA tetrahedron with six 20bp edges, as described in Goodman, R.P.; Schaap, I.A.T.; Tardin, C.F.; Erben, C.M.; Berry, R.M.; Schmidt, C.F.; Turberfield, A.J. (9 December 2005)
Pix - Wikipedia/Antony-22

What we know of DNA so far is, a hereditary material that contains coded genetic sequences. Now, what could be DNA Nanotechnology? To begin with, let's stress upon a little on what exactly is Nanotechnology. The term "Nanotechnology" itself is self-explanatory. "Nano" meaning a unit of 10-9 meters (nanometer) and "technology" meaning engineering and manipulation of materials. In brief, Nanotechnology can be defined as a science of engineering and manipulation of nanoscale materials.

Now, the question is whether DNA is a nanomaterial? Yes, it is and more precisely, a nanobiomolecule. Structurally, a typical double stranded DNA (dsDNA) molecule has a diameter of approximately 2 nm with its length extending from micrometers to few millimeters. In general, people visualize a nanomaterial as a spherical particle with a diameter of few nanometers, which is not entirely true. However, a nanomaterial is a material with atleast one dimension in the nanometer range. Depending on the dimensional parameters, a nanomaterial could be one dimensional (1-D), two dimensional (2-D) or three dimensional (3-D). This is explained by the "Quantum confinement" effect. Therefore, a dsDNA molecule with one dimension (diameter) in the nanometer range is a nanomaterial.

Now, what makes a nanoparticle unique from its bulk counterparts? Nanoparticles have a high surface to volume ratio which provide sites for introducing functionalities. It is because of its surface properties that allow nanoparticles to be used in wide range of applications. Similarly, besides the nano-structured dimension of dsDNA, the dsDNA has a negatively charged phosphate backbone. This allows for the deposition of cations and positively charged molecules on the phosphate backbone. Also, the terminal ends of a dsDNA nucleotide can be functionalized with various functional groups. Such possibilities makes it useful in the fabrication of biomolecule based MEMS (micro electro mechanical system) devices.

DNA Nanotechnology, proposed by Seeman in 1982, has been growing extremely in the last decade. The DNA Nanotechnology is expected to play an important role in bridging the gap between nanoscale components and the microscale MEMS. To understand the role of DNA in this field, we should first be clear about the self-driven hybridization process of DNA. This is in general, termed "self-assembly" and it leads to a thermodynamically stable structure. However, according to the definition of Halley and Winkler, it is better to call assemble process for a nanosystem in micro to nanoscale region as self-organization, since self-organization implies a non-equilibrium process. Considering these features, we can now possibly think of its applications in Nanotechnology.

How about stretching a supercoiled DNA? How do we stretch it? How would DNA be useful in nanotechnology? The answers to these questions have been realized with the development of advanced scientific tools and techniques. The use of micro total analysis system (µTAS) based on microfluidics and nanofluidics has made possible for DNA sequencing, protein separation, single cell analysis, biomolecular sorting and even single molecule detection. The nanoscale pores or nanofluidic channels form a very narrow path for the passage of biomolecules.

Such nanofluidic system have high surface to volume ratio, thus the surface effects are dominant and the interaction between the inner surface of the fluidic device and the molecules can be easily controlled. DNA molecules because of their negative surface charges are easily stretched out while passing through these channels. Besides the dsDNA, single stranded DNA or RNA can also be sieved and sorted through these channels. These DNA strands play an important role in molecular electronics. Molecular electronics is a subfield of nanotechnology that envisions the use of single molecules, or small groups of molecules, as components in electronic applications.

Recent researches in charge transport phenomenon of biological molecules have shown potential applications in the development of next generation transistors, sensors and circuits. Considering DNA, it is surprising to learn that DNA itself has an intrinsic conducting property. Experiments have shown that DNA has metallic, semiconducting and even insulating properties. This wide range of characteristics can be attributed to the complexity of the DNA structure such as base sequence, length, orientation, structure fluctuations and the experimental conditions such as temperature, electrode contact and so on. In some experiments, DNA is believed to conduct by tunneling (quantum mechanical effect) of holes between the guanine bases. This DNA could be used to bridge as nanowires between two microelectrodes.

As discussed earlier, the terminal ends of DNA can be functionalized with various linkers or functional groups. This functionalized DNA can be either physically or chemically adsorbed on a suitable electrode surface. In this way, a DNA nucleotide strand of suitable length can be used to connect between two microelectrodes. The negatively charged backbone of the DNA interconnect can be neutralized by binding with counter-ions like silver or gold. Further, metals can be electrochemically deposited along the DNA to create very thin wires. The latter process is termed "metallization".

Here, DNA serves as a template for the growth of nanowire. Similarly, single stranded DNA (ssDNA) can be hybridized with a complementary linker strand and serve as linkers to construct nanoparticle multilayers on surfaces. In another application, thiol derivatized ssDNA nucleotides are adsorbed on gold nanoparticles where they are used as linkers to complete bio-affinity based nanocircuits of biotin and streptavidin. At the nano level, self-assembly plays a major role in the interaction of the molecular species.

What we have discussed so far is the use of DNA as a template and a linker in the development of nanocircuits. Now, let's think about if DNA can work as a nanomechanical device? Firstly, we should know that our body is a factory of nanomotors. Biological motor proteins such as myosin and kinesin are also nanomechanical devices. From an engineering perspective, motor proteins are an attractive alternative to current MEMS devices because of their small sizes, high speeds, high efficiencies and ease of mass production. Why we look into the biological components as an alternative to purely inorganic devices is because of its superior functions and design flexibilities.

Like the motor proteins, DNA can also work as a nanomechanical device, however their working mechanisms are different. Molecular tweezers and molecular beacons work entirely on the hybridization of one or more single stranded oligonucleotide with a complementary ssDNA strand. In molecular beacons, the two ends of a specially designed single stranded oligonucleotide are initially labeled with a fluorophore and a quencher respectively. Prior to hybridization with a target nucleotide, the beacon forms an intramolecular hair-pin like structure and keeps the fluorophore and quencher in close proximity, which results in minimal fluorescence signal due to static quenching of the fuorophore by the quencher.

After introducing the target, loop sequence of the molecular beacon hybridizes to the target and opens up the stem duplex. Consequently, the two moieties are spatially separated, leading to the restoration of the fluorescence. Molecular tweezers also work on the same principle except that multiple DNA molecules are involved in hybridization.

Now, the question is, what application can it serve? We have seen that ssDNA hybridizes only with a complementary strand. Hybridization is a self-assembly process and it is very specific. Therefore, we can use this concept to develop a bio-affinity based DNA sensor. Fluorophore labeled molecules can be used to develop photo-switchable devices as in the case of molecular beacons and tweezers. If we look into gene therapy, the negatively charged phosphate backbone of the DNA has provided a good option for cationic ligands and polymers to be used as the gene delivery vehicle. This DNA-polymer conjugate mimics a biological system. Such conjugates can be called "bio-mimetic nanostructures"

No engineering methodology has been realized to assemble multiple functional nanocomponents to specific positions on MEMS/LSI (large scale integration) in a specific sequence. This is a challenging goal to address, namely controlling assembly position and sequence of multiple nanoscale functional components made of a variety of nanomaterials to realize a high functional nanosystem. DNA origami proposed by Rothemund in 2006 opened up a gate to various researchers to use DNA nanotechnology as their scientific tool.

DNA origami uses long scaffold, typically 7,249-nucleotide long circular single strand M13 phage genome and more than 200 short staple strands, to fold the M13 scaffold into an arbitrary two dimensional (2-D) or three-dimensional (3-D) shape with size of a few tens to a few hundreds of nanometer scale. It is believed that scaffolded DNA origami can be adapted to create more complex or larger structures. An obvious application of patterned DNA origami would be the creation of a 'nano breadboard', to which diverse components could be added. The concept of scaffolded DNA origami could find use in fields as diverse as molecular biology and device physics.

The process of Nanotechnology exist in nature for over the centuries. This came into light when Richard Feynman put forward the concept of Nanotechnology as a new scientific field in one of his lectures in 1959. There are naturally occurring magnetotactic bacterias that are known to synthesize magnetite nanoparticles, however the exact mechanism is still not clear. It is only through the development of highly sophisticated instruments that we are now able to harness this technology and manipulate it.

Now, Nanotechnology has become the core to the new era of science. In recent researches, scientists have developed different techniques to incorporate bio-components in the development of nanodevices. The use of bio-components would lead to hybrid devices. As mentioned before, incorporation of bio-components provide design flexibilities and superior functions. Methods based on self-assembly are considered as promising alternatives that offer inexpensive and parallel synthesis of nanostructures under mild conditions.

DNA Nanotechnology works solely on the process of self-assembly. The field of DNA Nanotechnology has exploited the combinatorial specificity property of the nucleotide sequence of DNA to create a number of more complex nanostructures.