Giving DNA nanodevices a new role inside living systems

Over the past couple of decades, scientists have been toying with the versatility of Deoxyribonucleic acid (DNA) ? the material that carries the genetic code of organisms ? in constructing minuscule objects of various shapes in a field of research known as Structural DNA Nanotechnology.

Now, researchers at Bangalore?s National Centre for Biological Sciences (NCBS) have shown that these nano-structures can play a role inside a living organism as devices that perform specific tasks. Their findings potentially open the door to a variety of applications, such as bio-imaging, by using the nano-objects to carry sensors, or using them as compartments to study enzymes? activity. ?DNA has proven to be a remarkably powerful scaffold to build a variety of programmable synthetic nanomachines,? says Yamuna Krishnan, a senior assistant professor in the Chemical Biology Group at NCBS. ?However, such DNA nanodevices have only recently been considered to have potential applications in living systems.? Two recent experiments by Krishnan and fellow researchers Dhiraj Bhatia and Sunaina Surana, which involved introducing nano-devices into a roundworm, are among the first examples of a DNA device shown to be functional in an organism. The two papers, of which Bhatia and Surana were each the lead authors, were published in June.

While DNA is a carrier of genetic information, DNA nanotechnology uses the molecules more as a building material because it is chemically robust and can form a rich repertoire of unusual structures by self-assembly. A related area called DNA Origami, that involves folding long strands of DNA into different shapes like the Japanese art of folding paper, has also emerged in recent years after a techinque demonstrated in 2006 by computer scientist Paul WK Rothemund of California Institute of Technology.

DNA-based molecular devices can be vastly different in form and function. Some recent examples include a nano-box built by professor Jorgen Kjems? lab at Aarhus University in Denmark and a nano-vase from researcher Hao Yan?s lab at the Arizona State University, or shapes such as a railed bridge, a genie bottle and a square nut from the Shih Lab at the Dana-Farber Cancer Institute, a teaching affiliate of Harvard Medical School. The first device built by the NCBS researchers, called the I-switch, is simpler in design consisting of two rigid rods of DNA held together by a hinge. ?These rods carry on them certain portions of DNA that are sensitive to the acidity of the medium,? says Krishnan. ?At basic or neutral pH, the I-switch opens to form a linear rod, whereas at acidic pH, the nanodevice undergoes a conformational change, closing into a triangle.?

The team attached flourescent dyes on the I-switch to translate its actions into a pH sensing property. So, the device emitted a green light when it was straight and a red light in the triangular configuration. Inside the worm, the I-switch found its way into a specific set of cells called coelomocytes, which are scavenger cells that have certain proteins on their cell surface, which attract and engulf the device. The I-switch has a half life of eight hours inside these cells after which it is degraded by enzymes.

In a subsequent experiment, the team also demonstrated how a molecule delivered by a nano-capsule made of DNA was absorbed more efficiently because the device imparted its own uptake properties. The nano-capsule was built in the shape of an icosahedron, which is a polyhedron with 20 identical equilateral triangular faces.

The icosahedron contained a fluorescent biopolymer called FITC-Dextran within its cavity and the experiment showed that the fluorescent biopolymer in the DNA capsule were uptaken by cells of a live organism much more efficiently than a free biopolymer. ?We are trying to use nature?s own material to understand nature,? says Yamuna Krishnan, who reckons that bio-imaging could be a possible application for the DNA icosahedron. The device could even act as a nano-compartment to help study how enzymes might function inside an artificial confined environment, she says.

Drug delivery, however, may be a far-off possibility as of now, she adds. ?I think many in the scientific community consider DNA-based approaches promising. However, there are currently no examples in the market,? says Jeffrey Karp, co-director of the Center for Regenerative Therapeutics, Brigham, and Women’s Hospital, Harvard Medical School. ?The key for DNA devices, as with all clinically employed strategies, will be to show efficacy without major safety issues, and scale-up will likely be a critical issue.?

?If DNA nanodevices are to achieve their true potential in biology, there are a few outstanding problems that first need to be solved to integrate them to their biological surroundings,? says Yamuna Krishnan. ?I don?t know how far we?ll get, but that?s not going to stop us trying.?