Team:Purdue/Model

Modelling

Extraction of RNA from Saliva via a Chitosan Capillary

Chitosan—a polysaccharide found in the exoskeletons of insects and crustaceans—is a bioadhesive polymer that attaches to negatively-charged molecules at specific pH values. At an acidic pH, chitosan is positively charged and readily adheres to any negatively-charged molecules. At a basic pH, chitosan is negatively charged and consequently lets go of any negatively-charged molecules. This electrostatic property has been used in various applications of synthetic biology, including the development of drug delivery systems and the design of medical devices.

The cArgo diagnostic test utilizes the bioadhesive properties of chitosan to capture the RNA present within the saliva sample being tested for COVID-19. Specifically, a lysed saliva sample will flow through a chitosan-treated silica-dioxide capillary where any RNA molecules will be separated from the remainder of the sample as a result of changes in pH. This process is illustrated in the provided diagram.

At a pH of 5.5, RNA molecules within the sample will adhere to the positively-charged chitosan while impurities leave the capillary with the wash buffer. At a pH of 8.5, RNA molecules will separate from the negatively-charged chitosan and leave the capillary within an elution buffer. This final solution of RNA and elution buffer will then continue through the remainder of the diagnostic device.

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Documentation of Our Model

The PDF below contains the derivation of the model along with supplemental figures and equations

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Benefits of the Model

This model will allow us to find the optimal length for efficient RNA extraction that will also be suitable for the dimensions of our microfluidic chip. As outlined in our project description, our current chip design has dimensions in the order of magnitude of 50 mm x 50 mm, considerably smaller and thus unable to fit the 8 cm capillaries referenced previously in the literature. Therefore, we developed this model to determine how much the capillaries’ dimensions could be reduced without compromising the amount of RNA eluted. Our future goal is to characterize our RPA-Argonaute system to establish a limit of detection and then use this model to determine the minimum capillary length required to extract sufficient RNA for subsequent detection.

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References

Zhu, X., Zhao, J., Hu, A., Pan, J., Deng, G., Hua, C., Zhu, C., Liu, Y., Yang, K., & Zhu, L. (2020). A Novel Microfluidic Device Integrated with Chitosan-Modified Capillaries for Rapid ZIKV Detection. Micromachines, 11(2), 186.https://doi.org/10.3390/mi11020186

Hagan, K. A., Meier, W. L., Ferrance, J. P., & Landers, J. P. (2009). Chitosan-Coated Silica as a Solid Phase for RNA Purification in a Microfluidic Device. Analytical Chemistry, 81(13), 5249-5256. doi: 10.1021/ac900820z

Johns Hopkins University. (n.d.). Derivation of the Langmuir isotherm. Retrieved from https://pages.jh.edu/~chem/fairbr/OLDS/derive.html