469701 DNA-Based Sensor Particles Enable Distributed Light and Temperature Measurement in Difficult to Access Areas

Monday, November 14, 2016: 3:45 PM
Divisadero (Parc 55 San Francisco)
Gediminas Mikutis, Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland, Carlos A. Mora, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland, Michela Puddu, ieLab, ETH Zürich, Zürich, Switzerland, Daniela Paunescu, ETH Zürich, Robert N. Grass, Institute for Chemical- and Bioengineering, ETH Zurich, Zurich, Switzerland and Wendelin J. Stark, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland

With continuous technology miniaturization it is becoming increasingly important to measure properties and characterize systems on a micro- and nanoscale. The demand to assess previously inaccessible setups, such as underground reservoirs or single cells, has spurred the development of nanosensors – devices that transduce a chemical, physical or biological signal from a nanoparticle to the macroscopic world. Currently used nanosensors produce either an optical, mechanical, electrical or magnetic signal in response to a property that is measured. Such information is not stored over time inside the sensor and has to be read out immediately. If a measurement is done inside an organism, underground, or in closed setups, on-line signal transfer can be challenging or even impossible.

In this contribution, we present submicron size particles capable of measuring physical properties in remote areas and storing the recorded information until a readout. One attractive way to chemically store information is inscribing it into a DNA sequence, which can later be read out. [1, 2] However, for a physical property (e.g. light or temperature) to be saved in nucleic acids, the chemical structure of DNA has to be changed as a result of a physical stress that a sensor has been exposed to. We developed a sensing platform based on encapsulating two distinct species of nucleic acids inside silica particles (~150 nm) and using their stability differences to measure physical properties.

To quantify temperature, we used nucleic acids with different degradation kinetics (DNA and RNA) and related the difference in their decay (measured by quantitative polymerase chain reaction (qPCR)) to temperatures that a sensor has been exposed to. Such nanothermometer allowed measuring temperatures between 55° and 80° C. The scale could be further tuned by tailoring the nucleic acid sequences towards more specific applications. [3] To measure the amount of light irradiation, ultraviolet-sensitive protecting groups (caging groups) were installed on a sensing DNA molecule. As soon as light reaches a particle containing caged DNA, the protecting groups are gradually released and the amount of uncaged DNA is quantified using qPCR and related to the cumulative irradiation. As a proof of concept, we measured light exposure in paramecia, a single-cellular organism. With a detection limit of individual cells, we could distinguish between cells that have been exposed to different duration of sunlight (between 0 and 2 hours). [4]

An important attribute of the DNA-based chemical sensors is the information storage capacity: in addition to the cumulative temperature or light information, nucleic acids serve as an identity unit, enabling tracing its origin. Therefore, such DNA-based tracer/sensor particles can be applied to track the flows and measure properties in environmental monitoring, material quality control, reservoir characterization, or other complex settings.

[1] Grass, R. N., Heckel, R., Puddu, M., Paunescu, D. and Stark, W. J. (2015), Robust Chemical Preservation of Digital Information on DNA in Silica with Error-Correcting Codes. Angew. Chem. Int. Ed., 54: 2552–2555.

[2] Paunescu, D., Fuhrer, R. and Grass, R. N. (2013), Protection and Deprotection of DNA—High-Temperature Stability of Nucleic Acid Barcodes for Polymer Labeling . Angew. Chem. Int. Ed., 52: 4269–4272.

[3] Puddu, M., Mikutis, G., Stark, W. J. and Grass, R. N. (2016), Submicrometer-Sized Thermometer Particles Exploiting Selective Nucleic Acid Stability. Small, 12: 452–456.

[4] Mikutis, G., Mora, C. A., Puddu, M., Paunescu, D., Grass, R. N. and Stark, W. J. (2016), DNA-Based Sensor Particles Enable Measuring Light Intensity in Single Cells. Adv. Mater., 28: 2765–2770.

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