Facilitating chemical and biochemical experiments with electronic microcontrollers and single-board computers

Abstract

Since the advent of modern science, researchers have had to rely on their technical skills or the support of specialized workshops to construct analytical instruments. The notion of the ‘fourth industrial revolution’ promotes construction of customized systems by individuals using widely available, inexpensive electronic modules. This protocol shows how chemists and biochemists can utilize a broad range of microcontroller boards (MCBs) and single-board computers (SBCs) to improve experimental designs and address scientific questions. We provide seven example procedures for laboratory routines that can be expedited by implementing this technology: (i) injection of microliter-volume liquid plugs into microscale capillaries for low-volume assays; (ii) transfer of liquid extract to a mass spectrometer; (iii) liquid–gas extraction of volatile organic compounds (called ‘fizzy extraction’), followed by mass spectrometric detection; (iv) monitoring of experimental conditions over the Internet cloud in real time; (v) transfer of analytes to a mass spectrometer via a liquid microjunction interface, data acquisition, and data deposition into the Internet cloud; (vi) feedback control of a biochemical reaction; and (vii) optimization of sample flow rate in direct-infusion mass spectrometry. The protocol constitutes a primer for chemists and biochemists who would like to take advantage of MCBs and SBCs in daily experimentation. It is assumed that the readers have not attended any courses related to electronics or programming. Using the instructions provided in this protocol and the cited material, readers should be able to assemble simple systems to facilitate various procedures performed in chemical and biochemical laboratories in 1–2 d.

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Fig. 1: Functions and applications of MCBs and SBCs in (bio)chemical research.
Fig. 2: Procedure 1: using Arduino MCB to control injection of microliter-volume liquid plugs into microscale capillaries for low-volume assays.
Fig. 3: Procedure 2: using Ardbox PLC (Arduino Leonardo) to control transfer of liquid extract from a liquid–liquid extraction system to an APCI-MS system in real time.
Fig. 4: Procedure 3: using chipKIT MCB to perform FE.
Fig. 5: Procedure 4: using Particle MCB to transmit experimental data to the cloud in real time.
Fig. 6: Procedure 5: using RPI SBC to control extract transfer from a liquid microextraction device to mass spectrometer to acquire data and to upload the acquired data to the cloud.
Fig. 7: Procedure 6: using BBB SBC to compensate for substrate depletion in a biochemical reaction (feedback control).
Fig. 8: Procedure 7: using IE SBC to optimize sample flow rate in direct-infusion MS.
Fig. 9: Photographs of the electronic systems described in Procedures 1–7.

Data availability

The data that support the findings of this study are available from the corresponding author upon reasonable request.

Code availability

The computer code used in this protocol is provided as Supplementary Data 17.

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Acknowledgements

We acknowledge the Ministry of Science and Technology (MOST), Taiwan (grant nos. 104-2628-M-007-006-MY4, 108-2113-M-007-017, and 108-3017-F-007-003); the National Chiao Tung University; the National Tsing Hua University (grant no. 108QI009E1); the Frontier Research Center on Fundamental and Applied Sciences of Matters; and the Featured Areas Research Center Program within the framework of the Higher Education Sprout Project established by the Ministry of Education (MOE), Taiwan.

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Authors

Contributions

G.R.D.P., T.-H.Y., C.-Y.H., C.-P.S., C.-M.C., P.-H.L., and H.-T.N. all took part in acquiring, analyzing, and interpreting the data and writing the manuscript. P.L.U. conceptualized the experimental work, secured the research infrastructure, and took part in interpreting the data and writing the manuscript.

Corresponding author

Correspondence to Pawel L. Urban.

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The authors declare no competing interests.

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Peer review information Nature Protocols thanks Leroy Cronin and the other, anonymous, reviewer(s) for their contribution to the peer review of this work

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Key references using this protocol

Yang, H.-H., Dutkiewicz, E. P. & Urban, P. L. Anal. Chim. Acta 1034, 85–91 (2018): https://doi.org/10.1016/j.aca.2018.06.072

Chang, C.-H. & Urban, P. L. Anal. Chem. 88, 8735–8740 (2016): https://pubs.acs.org/doi/10.1021/acs.analchem.6b02074

Prabhu, G. R. D., Witek, H. A. & Urban, P. L. Sens. Actuators B Chem. 282, 992–998 (2019): https://doi.org/10.1016/j.snb.2018.11.033

Supplementary information

41596_2019_272_MOESM10_ESM.mp4

Soldering wires and electronic components.

41596_2019_272_MOESM11_ESM.mp4

Procedure 1: securing tubing onto the holder and setting up the in-capillary assay experiment.

41596_2019_272_MOESM12_ESM.mp4

Procedure 2: setting up the CLLE experiment.

41596_2019_272_MOESM13_ESM.mp4

Procedure 3: setting up the sample chamber for fizzy extraction.

41596_2019_272_MOESM14_ESM.mp4

Procedure 4: setting up the chamber with sensors to monitor yeast growth.

41596_2019_272_MOESM15_ESM.mp4

Procedure 5: setting up the circuit, assembling LMJ-SSP.

Supplementary Information

Supplementary Figs. 1–22.

Reporting Summary

Supplementary Data 1

Scripts used in example Procedure 1

Supplementary Data 2

Scripts used in example Procedure 2

Supplementary Data 3

Scripts used in example Procedure 3

Supplementary Data 4

Scripts used in example Procedure 4

Supplementary Data 5

Scripts used in example Procedure 5

Supplementary Data 6

Scripts used in example Procedure 6

Supplementary Data 7

Scripts used in example Procedure 7

Supplementary Video 1

Soldering wires and electronic components.

Supplementary Video 2

Procedure 1: securing tubing onto the holder and setting up the in-capillary assay experiment.

Supplementary Video 3

Procedure 2: setting up the CLLE experiment.

Supplementary Video 4

Procedure 3: setting up the sample chamber for fizzy extraction.

Supplementary Video 5

Procedure 4: setting up the chamber with sensors to monitor yeast growth.

Supplementary Video 6

Procedure 5: setting up the circuit, assembling LMJ-SSP.

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Prabhu, G.R.D., Yang, T., Hsu, C. et al. Facilitating chemical and biochemical experiments with electronic microcontrollers and single-board computers. Nat Protoc 15, 925–990 (2020). https://doi.org/10.1038/s41596-019-0272-1

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