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The application of DNA-mediated toehold strand

displacement in DNA memory rewrite and computation

Samuel Leung, Madalyn Graham, Madelynn Frappier, Brianna Abam, Li-Qun Gu

Department of Biomedical, Biological, and Chemical Engineering

University of Missouri Fall 2022

References

[1] Lee, S. Y. (2019, July 1). DNA data storage is closer than you think. Scientific American. Retrieved November 15, 2022, from https://www.scientificamerican.com/article/dna-data-storage-is-closer-than-you-think/

[2]Chauhan, D. T., & About The AuthorDr Tushar ChauhanDr Tushar Chauhan is a Scientist. (2019, September 6). DNA Digital Data Storage. Genetic Education. Retrieved November 15, 2022, from https://geneticeducation.co.in/dna-digital-data-storage/

[3] Engelen, Wouter & Janssen, Brian & Merkx, Maarten. (2016). DNA-based control of protein activity. Chem. Commun.. 52. 10.1039/C5CC09853J.

[4]Meiser, L. C., Nguyen, B. H., Chen, Y.-J., Nivala, J., Strauss, K., Ceze, L., & Grass, R. N. (2022). Synthetic DNA applications in Information Technology. Nature Communications, 13(1). https://doi.org/10.1038/s41467-021-27846-9

[5] Wood, L. (2022, April 25). Global DNA Digital Data Storage Market Forecast Report 2021-2028 - growing demand for long-term data storage & increasing applications of DNA data storage - researchandmarkets.com. Business Wire. Retrieved November 15, 2022, from https://www.businesswire.com/news/home/20220425005419/en/Global-DNA-Digital-Data-Storage-Market-Forecast-Report-2021-2028---Growing-Demand-for-Long-Term-Data-Storage-Increasing-Applications-of-DNA-Data-Storage---ResearchAndMarkets.com

[6] Aigrain, L. (2021, December 14). What is Oxford Nanopore Technology (ONT) sequencing? Your Genome. Retrieved December 2, 2022, from https://www.yourgenome.org/facts/what-is-oxford-nanopore-technology-ont-sequencing/

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Conclusion

DNA computing and memory rewrite using toehold strand displacement offers promising solutions to data storage issues. However, more research and experimentation is required in order to effectively use this technology. Due to unforeseen damage to the data collecting instrument, we were unable to conduct the necessary experiments to determine the viability of our designs. We did however gain knowledge in using nanopore technology, learned how to develop artificial membranes in the lab, and discovered the potential that DNA holds in memory capabilities.

Background

  • Data is being created on an exponential scale, with the total amount of electronic information totaling approximately 418 zettabytes per year [1]

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  • By storing all of this data, we will eventually run out of space and power.

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  • DNA offers an extensive amount of data density in comparison to modern storage methods.

Need and Task

  • Current problems with DNA storage and computing limit the possibilities and applications of this technology.
    • Expensive
    • Data saved on DNA should be erasable and rewritable
  • There is therefore an urgent need to develop an inexpensive method to be able to sequence the data and allow for a higher bandwidth DNA computing.
  • There are a limited amount of methods/processes in which DNA computing can be used to identify where data is within a given sequence.
  • Reasons for this are that the methods are generally unpractical, and they offer limited output (readout method) and throughput of the data. Nanopore, however, has been known to solve many of these issues.
  • This project aims to compute DNA though creating a system in which data can be identified within a sequence.

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The overall task:

  • Create a DNA long probe that DNA staples are able to hybridize to
  • The objective was to allow for both hard memory and diagnostic capabilities by using toehold mediated strand displacement via miRNA.

The method must be:

  • Error tolerant
  • Affordable
  • Able to read the DNA and identify when toeholds were displaced

Results and Discussion

During the testing phase of the project, the instrument used to collect the data was damaged caused by an electrostatic discharge. Due to this, testing of the engineered sequences was not done.

Methods

We identified functions that are essential to the design, allowing us to determine the means and possible alternative designs.

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Functions include:

  • miRNA sequence is less prone to self-hybridization
  • Engineered probe that allows for multiple data libraries
  • Design will have recognizably different current tracings after the toehold displaces the staple

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Means to achieve functions:

  • Choose miRNA that has a short sequence.
  • Choose various miRNAs from different cancer lines while another is to cut the miRNAs so that they attach to different parts of the DNA strand.
  • Perform wet experiments to determine current difference and to run simulation to determine current differences.

Acknowledgments

We would like to thank Dr. Li Qun Gu and Dr. Charles Darr for guiding us in our project. Special thanks to the undergraduate research office for providing an outlet for presentation of research. We would also like to acknowledge the Department of Biomedical, Biological, and Chemical Engineering - University of Missouri for funding the project. Without their support, this project would not be possible.

Figure 2: Toehold Displacement Diagram [3]

Figure 1: DNA Digital Storage [2]

Figure 3: miRNA/DNA sequences chosen

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Figure 4: (a) Final Sequence Design #1 (b) Final Sequence Design #2

Economic Analysis[5]

  • Total cost of materials added up to $300
  • DNA data storage market expected to grow from $57.81 million (2021) to $1,761.49 million by 2028
  • Estimated growth of CAGR is 61.29% during 2021 to 2028

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