A nanomachine made from DNA can measure the pH inside a cell.Punchstock

A tiny machine made from DNA can measure the acidity of living cells from the inside.

Yamuna Krishnan at the Tata Institute of Fundamental Research in Bangalore, India, and her colleagues designed three short pieces of DNA that spontaneously assemble into the nanoscale device when they are in close proximity. Two of the strands stick to the main strand through base-pairing between complementary nucleotides, leaving an overhang at either end of the main strand.

Krishnan's team introduced regions with extra cytosine bases into the DNA of these overhangs. Cytosine normally pairs up with guanine in DNA. But when these bases sit in an acidic environment, they bind to protons and stick to each other. That means that the two overhanging arms of the nanomachine link up and the whole construct changes shape — from being straight and open, to a triangle.

Shape-shifting sensor

To obtain a reading of this shape change, Krishnan introduced fluorescent tags called fluorophores to either end of the open structure. When the DNA machine is open, in a neutral environment, these tags glow green. But when the machine folds up, the fluorophores on the ends interact to give a red colour. The colours in between represent different ratios of each of these states, giving an accurate readout of the pH from 7 (neutral) to 5 (acidic).

"Just a ratio between donor to acceptor fluorophores is enough to tell you the pH of the solution that your assembly is sitting in," says Krishnan.

But DNA machines that can measure pH changes are not remarkable in themselves, says Krishnan. "What has been missing so far is actually showing functionality," she says; that is, showing that the machine works in a living system rather than in a test tube.

The device switches from an open state (left) to a closed, triangular shape (right) in acidic conditions.Nature

Krishnan's team then attached their nanomachine to a protein called transferrin so as to get it inside the fruitfly cells they used in their study. When transferrin reaches the cell membrane it is engulfed through endocytosis — a process used by the cell to import nutrients and other materials — and moves through the cell inside a membrane-bound bubble called an endosome, taking the DNA sensor with it.

The endosome moves through the cell and breaks open to deliver its cargo in response to a change in pH, which the team was able to track with their device. The work is published in Nature Nanotechnology¹.

Cancer signpost?

Krishnan envisages using sensors such as hers to study viruses, which can invade a cell by endocytosis. Part of that mechanism involves the virus altering the acidity of the endosome. "Little is understood about the causes and effects of this change in acidity," Krishnan says.

Disruption to endocytosis can cause disease. And pH changes occur inside cancerous cells, Krishnan points out.

"I'm not saying that pH is the reason why something happens, but it's a very good molecular correlate of biochemical events that have happened on the surface of the endosome that results in the change of pH," says Krishan. "There are lots of applications in biology to sense subtle changes in pH."

Getting the DNA sensor into the cell and showing that it works is an important proof of concept, says Taekjip Ha of the Center for the Physics of Living Cells at the University of Illinois at Urbana-Champaign.

"Delivery of macromolecular probes into the cytoplasm is the holy grail in the cellular-imaging-technology community, and is extremely difficult," he says. The problem is that molecular probes are often too big to do their job or to get out of the endosome once they're in the cell.

He doesn't see researchers rushing to use this system over existing organic-dye-based sensors. But he thinks that in future such a pH-sensing machine could form part of a bigger DNA-based cellular nanomachine, with other functions built in. 

• References

  1. Modi, S. et al. Nature Nanotech. doi:10.1038/nnano.2009.83 (2009).