Folding the DNA

DNA nanotechnology which is like paper folding was developed around 30 years back. In 2006, Paul Rothemund of the California Institute of Technology demonstrated folding long strands of DNA into a wide range of predetermined shapes. The resulting nanostructures can be used as scaffolding or as miniature circuit boards for precisely assembling components such as carbon nanotubes and nanowires.

But to make DNA  structure of several folds, several hundred "staples" must be added to the regions surrounding the single DNA strands, and for making new nanostructures a new set of staples are requires. Moreover, the DNA structures tend to arrange themselves randomly onto a substrate surface making it difficult to integrate them into electronic circuits subsequently.

DNA brick

To overcome the above difficulty researchers at Harvard University in the US have developed a technique to make highly complex 3D nanostructures by assembling together synthetic DNA "bricks". The bricks, which are like tiny pieces of LEGO, can be assembled into a wide variety of shapes and configurations to build elaborately designed nanostructures. Researchers made DNA-bricks by self-assembly technique starting with long DNA strands by interlocking short, synthetic strands of DNA together to make larger structures by suitably controlling the local interactions between the strands. The technique relies on DNA self-assembly method using the four base pairs in DNA – adenosine, thymine, cytosine and guanine which can naturally join in specific ways to fabricate a collection of 2D structures.

Technique

The technique to make 3D structure starts with a smaller DNA-brick strand of only 32 bases long having four regions to bind to four neighbouring DNA-brick strands which are connected through 90° and built in space for creating a DNA molecular cube containing hundreds of bricks. Each DNA structure self-assembles to a brick encoded with an individual sequence that determines its final position in the nanostructure. Each sequence will only be attracted to a complementary sequence so that specific shapes can be created through the selection of different sequences.

Applications

Using DNA-brick technique any number of structures can be made very easily from the same master cube by simply selecting subsets of specific DNA bricks. Many complex shapes can be made containing intricate cavities, surface features and channels which are more complex than any 3D DNA structure constructed so far. Also modifications can be made by adding or removing DNA bricks without changing the main structure. The researchers claim that many appropriate technologically relevant guest molecules can be incorporated into functional devices that might serve as programmable molecular probes, instruments for biological imaging and drug-delivery vehicles and to fabricate high-throughput complex inorganic devices for electronics and photonics applications. They further claim that by using synthetic polymers rather than the natural form of DNA, it may be possible to create functional structures that are stable in a wider variety of different environments. The researchers say that the structures made using DNA-brick technique might find use in a wide variety of applications such as in smart medical devices for targeted drug delivery in the body, programmable imaging probes and even in the manufacture of speedier and more powerful computer-chip circuits.

DNA microchip

Microchips are used in computers, cell phones and other electronic devices. IBM is building DNA microchips using DNA nanostructures. This is an effort for using biological molecules to help with processing in the semiconductor industry, because biological structures like DNA actually offer some very reproducible, repetitive kinds of patterns. It will be the structure of next-generation and chipmakers are competing to develop smallest chips at cheaper price.

Gene detection

A gene detection platform made from self-assembled DNA nanostructures has been made using 100 trillion reactive and functional DNA components. By scanning attached differentiated labels on mass a clear reading of the molecular composition of a solution can be obtained. This method will allow for the bar coding of individual molecules for easy identification and analysis.

Bio sensing

Investigation of US researchers has resulted in nanostructures made entirely out of graphene and DNA. When the interactions between the two components were tracked using a fluorescent protein it was found that single-stranded DNA interacts with the carbon compound much stronger than its double-stranded sibling.

When complementary DNA was added to strands already on grapheme, the marker protein started glowing with renewed strength, indicating that new DNA molecules were formed, as the first strands separated from their graphene substrate. According to the researchers, this property could pave the way to creating new classes of biosensors.

Graphene-DNA nanostructures will be used in hospitals for detecting conditions such as cancer, toxins in decaying and altered food and also to scan packages suspected of carrying biological weapons for any traces of pathogens.

DNA machines

Oxford Centre for Soft and Biological Matter reports that the elegant selectivity of Watson-Crick base-pairing makes DNA an extremely useful tool for the construction of nanoscale objects and machines. Stable structures and mechanical cycles can be programmed into a system of single strands by careful choice of the sequences of bases.

DNA nanostructure scaffold

Researchers at Arizona State University have developed various shapes and sizes of DNA nanostructure which can carry molecules to trigger an immune response in the body. They have already developed DNA nanostructures which could function as scaffolding material and created synthetic vaccine complexes resembling natural virus without the disease component. Synthetic vaccine complexes were then attached to DNA nanostructures of pyramid shape and branch-like structures. This holds great potential for the development of targeted therapeutics.

DNA crystals

New York University chemists have created three-dimensional DNA structures which have a range of potential industrial and pharmaceutical applications, such as the creation of nanoelectronic components and the organization of drug receptor targets to enable illumination of their 3D structures.

The researchers created DNA crystals by making synthetic sequences of DNA that have the ability to self-assemble into a series of 3D triangle-like motifs. The creation of the crystals was dependent on putting "sticky ends"—small cohesive sequences on each end of the motif—that attach to other molecules and place them in a set order and orientation. The make-up of these sticky ends allows the motifs to attach to each other in a programmed fashion. By using genetic engineering technique multiple helices were linked together through single-stranded sticky ends lattice-like structures were formed that extends in six different directions, thereby yielding a 3D crystal.