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Genomic DNA i-motifs as fast sensors responsive to near-physiological pH microchanges

Researchers from Federal Research and Clinical Center of Physical-Chemical medicine and Institute of Bioorganic Chemistry RAS, in collaboration with Skolkovo University of Science and Technology and D.Mendeleev University of Chemical Technology of Russia developed simple and robust sensors for detecting microchanges in intracellular pH.

Turaev AV, Isaakova EA, Severov VV, Bogomazova AN, Zatsepin TS, Sardushkin MV, Aralov AV, Lagarkova MA, Pozmogova GE, Varizhuk AM

The sensors are based on unusual DNA structures - i-motifs, that are found in  cancer- and neudegeneration-related genes. The i-motifs appear to be genomic regulatory elements and might modulate transcription in response to pH stimuli. Given their intrinsic sensitivity to minor pH changes within the physiological range, such  DNA structures can be used as core elements of biocompatible sensors. Using stopped-flow techniques and FRET-melting assays, i-motifs with fast responses to pH alterations were selected. For the leading fast sensor, the labeling scheme was optimized and intracellular calibration was performed. Unlike known small-molecule pH indicators, the sensor was transferred efficiently to cell nuclei. Due to its favorable kinetic characteristics, the sensor is potentially applicable for monitoring proton dynamics in the nucleus or pH-jumps observed upon neuron activation. These results argue that genomic DNA sequences have prospects in the development of new efficient biocompatible molecular tools. The research was published in the journal Biosensors and Bioelectronics.

january 4, 2021