Playing Lego With DNA

One of a kind Yamuna Krishnan is among the few people in India working on DNA nanostructures, Photo: Aniruddha Chawdhury/Mint

Yamuna Krishnan is fond of using everyday analogies and the odd aphorism. That, for a scientist whose playthings are microscopic, helical strands of DNA, is unusual.
Imagine a strand of DNA — she tells the audience at a talk she is giving — to be a long, old-fashioned wooden pointer. At this length, the rod is rigid. But if the pointer were to grow to 20 m in length, it would quite likely bend.
DNA bricks  A worm is injected with a fluorescent DNA nanodevice — the I-switch. (inset) Once inside, the switch is specifically taken up by a set of six cells called coelomocytes

DNA, at short lengths of 50 nanometres (a nanometre is a billionth of a metre), is similarly rigid. But longer strands can, “like the leaves of a coconut tree”, be woven into fanciful structures and shapes. That is what her laboratory at the National Centre for Biological Sciences in Bengaluru has been doing.
Krishnan, 38, a PhD in chemistry from Indian Institute of Science, Bengaluru, makes it sound simple, but DNA origami, as this field has playfully come to be known, is at the cutting edge of science. And the use of these DNA nanostructures to investigate biological processes and carry cargo within living systems is even more nascent. Hers is one of a handful of laboratories in the world that are working on it.
In this DNA Legoland, sequences of the molecule so tiny that 20,000 of them can fit on the tip of pencil, can be cut to exact lengths using restriction enzymes present in bacteria; they can be “super-glued” together in a manner that their ends are either ‘ragged’ or flush together. Literally any molecule can be coupled with these DNA sequences; and the locations in the sequence where this happens can also be determined exactly.
DNA rods can be joined together at junctions to create two-dimensional matrices, and these, in turn, can be piled up to form elaborate scaffolds. The objects created can be rigid, “like baskets”, or dynamic like “scissors, whose flexibility gives it function.”
So malleable is the material that scientists have created miniature “stars, triangles and boxes” using it, according to Krishnan. But these are to her what “Porsches and Ferraris” are to someone looking to get as easily as possible from one point to another — flights of fancy.
Schematic of an icosahedron made from DNA containing nanoscale cargo within its internal void

Instead of trying to create more elaborate structures, she is focussing on trying to find uses for them. These nanostructures, she realised a few years ago, would be ideal to set right what goes wrong on the nanoscale. “It does after all,” she says, “take a thief to catch a thief.”
The first structure her lab created was the I-switch — two strands of DNA joined by a flexible hinge at the centre, and with each open end connected to a fluorescent compound. The hinge of the I-switch opens and closes in response to changes in the level of acidity. In mildly acidic solutions, the switch stayed open and the fluorescent compounds emitted a green light, while at higher acidity, the hinge closed into a ‘V’ formation with the chemicals now emitting a red light.
The nanodevice functioned perfectly in the petri dish, detecting changes in acidity with far greater accuracy than other compounds. But would this work inside a living cell?
To test that, Krishnan’s team injected the I-switch into a worm. Not only did the device work as well inside the worm as it had outside, but miraculously, it went only to a particular type of cell inside the worm. It seemed it was possible for DNA-based nanodevices to be exactly targeted within a living organism.
Based on this, she hopes that it might be possible in the future to use the I-switch in humans. Tagged with compounds that attach themselves to particular cells in the body, the I-switch could be sent to individual organs. It could then minutely monitor changes in acidity, which are responsible for a large number of diseases.
Disease is complicated phenomena, one or more errors in a long sequence of events, a bit like a bus ride “from Kanyakumari to Mumbai” that passes through many towns en route. We can, says Krishnan, currently only determine that the bus arrived late in Mumbai. It isn’t possible to detect where en route it might have malfunctioned.
But with the I-switch, we would be able to tell where exactly in the body the normal sequence of reactions was disrupted.
This could have applications in tracking (or imaging) neurological and enzyme-related disorders, and embryonic development.
Krishnan’s next project was more ambitious. Using DNA junctions that had five open ends, she created an icosahedron, a solid shaped a bit like a ball, except with 20 triangular faces instead of a smooth curve. It took a week of reactions in the laboratory to do this.
The icosaherdon had two things going for it — it could be assembled in two halves, and it had a remarkably large cavity. It was, in other words, the perfect container to trap other nanoparticles. It took another three days of reactions for Krishnan’s team to encapsulate gold nanoparticles into a DNA icosahedron.
An electron micrograph of an actual DNA icosahedron containing encapsulated gold nanoparticles

Now the team repeated what they had done with the I-switch. A natural, fluorescent polymer (also an indicator of acidity) was encapsulated within the DNA icosahedron. The compound was once again injected into a worm, and in a repeat of the previous success, it went straight to the very same cells. Except that the implications this time around were far greater.
The I-switch could only monitor acidity, but the DNA icosahedron could contain any molecule. It could, therefore, be used for the targeted delivery of molecules that could monitor many other things.
In parallel, a group of researchers in the US had used a DNA-based solid structure to deliver molecules that suppress tumours in mice. The icosahedron could similarly be used for drug delivery.
These DNA-based structures have other advantages over synthetic chemical structures too — they are more easily accepted by living organisms, and they are, according to Krishnan, absolutely identical, “much more uniform than other compounds.”
Exciting as these discoveries have been, Krishnan and her team know that they have many hurdles to cross. The range of the I-switch needs to be augmented; the DNA icosahedron needs to be tested for targeted delivery to other cells; and most importantly, a “cheaper way of manufacturing DNA-based structures needs to be found.”
According to Dr K Vijayraghavan, head of the Central government’s Department of Biotechnology, even though novel DNA based structures have started finding “extraordinary applications”, there are very few people in India working in this uncharted field. “Yamuna Krishnan’s team has done a terrific job by jumping right in,” he says.
Going by her plans though, it seems like she has just about put her toe in the water. “In the next five years,” says Krishnan, “I want to uncover new biological processes using DNA nanodevices. Processes that we have been unable to understand because we haven’t had the tools to do that.”
“I’m going to find new biology to surprise biology.”