A DNA machine to measure cell acidity

In a recently published paper in the prestigious international journal Nature Nanotechnology entitled A DNA nanomachine that maps spatial and temporal pH changes inside living cells, Yamuna Krishnan and her team of students at the Chemical Biology Group, National Centre for Biological Sciences (NCBS), Bangalore have described the successful operation of an artificially designed DNA nanomachine inside living cells that functions as a pH sensor. The researchers add, “pH is very important to living cells because most living cells only survive in a very specific range of pH and the smallest variation out of that range could cause the cell to die.”

Yamuna adds, “If we could correlate changes in acidity and therefore pH, in a cell to a disease; this machine could play a role in sensing the pH change. Viruses enter cells through the endocytic pathway and modulate the acidity of the cell. This device could combat virus entry by indicating the presence of viruses in the cell.”

DNA nanomachine

“We named our DNA nanomachine the I-switch,” says Yamuna Krishnan and adds that the I-switch has sensitivity between pH 5.5 and 6.8, which is ideal for monitoring changes in intracellular pH. The I – switch would in fact be a tiny machine made from DNA that can measure the acidity of living cells from the inside. Using the latest biotechnology and nanotechnology tools the scientists have reported the design and working principle of the I-switch; in vitro characterisation of the I-switch, its pH calibration and tracking pH changes for a given protein.

According to Yamuna, “the device is externally triggered by protons and functions as a pH sensor based on fluorescence resonance energy transfer (FRET) inside living cells”. The DNA assembly developed by her team is a robust pH-triggered nanoswitch with reasonably fast response times, sustained efficiency over several cycles, and a working cycle that does not generate toxic byproducts (the byproducts of a complete cycle for the I-switch are salt and water). As of now, the switch only gives a temporal resolution of five minutes with response times of one to two minutes. However, this can be solved with new and improved designs, something her group is already working on and she adds that faster DNA switches will be able to measure pH changes on shorter timescales, as well as over different ranges of pH sensitivity.

Opening up new vistas

From the test tube to a living system, Yamuna Krishnan’s work on DNA nanomachines in the form of synthetic DNA assemblies is opening up new vistas in the field of structural DNA nanotechnology. Getting the DNA sensor into the cell and showing that it works is an important proof of concept and the work being carried out by the scientists at NCBS will eventually have potential practical applications in several fields, including cancer biology.

“This first generation of DNA nanoswitches, although promising, must overcome some limitations before they can be as widely used as current pH sensors. Faster DNA switches that can measure pH changes on shorter timescales, as well as over different ranges of pH sensitivity, need to be engineered. Most importantly, to address compartment mixing issues, methods to specifically target such DNA nanostructures to different cellular organelles would be a crucial development,” says Yamuna.

Cellular Stress is now considered the hallmark of every disease from cancer, diabetes and obesity to neurodegenerative disorders and early identification of such stresses by nanotechnology may help us to prevent these disorders. Hence the artificially designed DNA nano pH sensor by Yamuna and her group opens up a wide range of possibilities for DNA based cellular devices for sensing, diagnostics and targeted therapies in living systems.