Papers
Topics
Authors
Recent
Gemini 2.5 Flash
Gemini 2.5 Flash
173 tokens/sec
GPT-4o
7 tokens/sec
Gemini 2.5 Pro Pro
46 tokens/sec
o3 Pro
4 tokens/sec
GPT-4.1 Pro
38 tokens/sec
DeepSeek R1 via Azure Pro
28 tokens/sec
2000 character limit reached

Representing Information on DNA using Patterns Induced by Enzymatic Labeling (2405.08475v1)

Published 14 May 2024 in cs.IT and math.IT

Abstract: Enzymatic DNA labeling is a powerful tool with applications in biochemistry, molecular biology, biotechnology, medical science, and genomic research. This paper contributes to the evolving field of DNA-based data storage by presenting a formal framework for modeling DNA labeling in strings, specifically tailored for data storage purposes. Our approach involves a known DNA molecule as a template for labeling, employing patterns induced by a set of designed labels to represent information. One hypothetical implementation can use CRISPR-Cas9 and gRNA reagents for labeling. Various aspects of the general labeling channel, including fixed-length labels, are explored, and upper bounds on the maximal size of the corresponding codes are given. The study includes the development of an efficient encoder-decoder pair that is proven optimal in terms of maximum code size under specific conditions.

Definition Search Book Streamline Icon: https://streamlinehq.com
References (23)
  1. A. Moter and U. B. Göbel, “Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms,” Journal of microbiological methods, vol. 41, no. 2, pp. 85–112, 2000.
  2. B. Chen, W. Zou, H. Xu, Y. Liang, and B. Huang, “Efficient labeling and imaging of protein-coding genes in living cells using CRISPR-tag,” Nature communications, vol. 9, no. 1, p. 5065, 2018.
  3. D. Gruszka, J. Jeffet, S. Margalit, Y. Michaeli, and Y. Ebenstein, “Single-molecule optical genome mapping in nanochannels: Multidisciplinarity at the nanoscale,” Essays in Biochemistry, vol. 65, no. 1, pp. 51–66, 2021.
  4. H. Ma, A. Naseri, P. Reyes-Gutierrez, S. A. Wolfe, S. Zhang, and T. Pederson, “Multicolor crispr labeling of chromosomal loci in human cells,” Proceedings of the National Academy of Sciences, vol. 112, no. 10, pp. 3002–3007, 2015.
  5. J. Deen, C. Vranken, V. Leen, R. K. Neely, K. P. Janssen, and J. Hofkens, “Methyltransferase-directed labeling of biomolecules and its applications,” Angewandte Chemie International Edition, vol. 56, no. 19, pp. 5182–5200, 2017.
  6. A. P. Young, D. J. Jackson, and R. C. Wyeth, “A technical review and guide to rna fluorescence in situ hybridization,” PeerJ, vol. 8, p. e8806, 2020.
  7. S. K. Tabatabaei, B. Wang, N. B. M. Athreya, B. Enghiad, A. G. Hernandez, C. J. Fields, J.-P. Leburton, D. Soloveichik, H. Zhao, and O. Milenkovic, “Dna punch cards for storing data on native dna sequences via enzymatic nicking,” Nature communications, vol. 11, no. 1, p. 1742, 2020.
  8. A. Sadremomtaz, R. F. Glass, J. E. Guerrero, D. R. LaJeunesse, E. A. Josephs, and R. Zadegan, “Digital data storage on DNA tape using CRISPR base editors,” Nature Communications, vol. 14, no. 1, p. 6472, 2023.
  9. M. Jinek, K. Chylinski, I. Fonfara, M. Hauer, J. A. Doudna, and E. Charpentier, “A programmable dual-rna–guided dna endonuclease in adaptive bacterial immunity,” science, vol. 337, no. 6096, pp. 816–821, 2012.
  10. L. Cong, F. A. Ran, D. Cox, S. Lin, R. Barretto, N. Habib, P. D. Hsu, X. Wu, W. Jiang, L. A. Marraffini et al., “Multiplex genome engineering using crispr/cas systems,” Science, vol. 339, no. 6121, pp. 819–823, 2013.
  11. I. Amit, O. Iancu, A. Levy-Jurgenson, G. Kurgan, M. S. McNeill, G. R. Rettig, D. Allen, D. Breier, N. Ben Haim, Y. Wang et al., “Crispector provides accurate estimation of genome editing translocation and off-target activity from comparative ngs data,” Nature Communications, vol. 12, no. 1, p. 3042, 2021.
  12. D. Hanania, D. Bar-Lev, Y. Nogin, Y. Shechtman, and E. Yaakobi, “On the capacity of dna labeling,” in 2023 IEEE International Symposium on Information Theory (ISIT), 2023, pp. 567–572.
  13. Y. Nogin, D. Bar-Lev, D. Hanania, T. Detinis Zur, Y. Ebenstein, E. Yaakobi, N. Weinberger, and Y. Shechtman, “Design of optimal labeling patterns for optical genome mapping via information theory,” Bioinformatics, vol. 39, no. 10, p. btad601, 09 2023.
  14. M. Levy-Sakin and Y. Ebenstein, “Beyond sequencing: Optical mapping of DNA in the age of nanotechnology and nanoscopy,” Current opinion in biotechnology, vol. 24, no. 4, pp. 690–698, 2013.
  15. V. Müller and F. Westerlund, “Optical DNA mapping in nanofluidic devices: Principles and applications,” Lab on a Chip, vol. 17, no. 4, pp. 579–590, 2017.
  16. B. H. Marcus, R. M. Roth, and P. H. Siegel, “An introduction to coding for constrained systems,” San Diego, CA, USA:Lecture Notes, 2001. [Online]. Available: http://www.math.ubc.ca/~marcus/Handbook/
  17. S. McLaughlin, J. Luo, and Q. Xie, “On the capacity of m-ary runlength-limited codes,” IEEE Transactions on Information Theory, vol. 41, no. 5, pp. 1508–1511, 1995.
  18. O. Elishco, R. Gabrys, E. Yaakobi, and M. Médard, “Repeat-free codes,” IEEE Transactions on Information Theory, vol. 67, no. 9, pp. 5749–5764, 2021.
  19. R. Adler, D. Coppersmith, and M. Hassner, “Algorithms for sliding block codes-an application of symbolic dynamics to information theory,” IEEE Transactions on Information Theory, vol. 29, no. 1, pp. 5–22, 1983.
  20. M. Levy and E. Yaakobi, “Mutually uncorrelated codes for dna storage,” IEEE Transactions on Information Theory, vol. 65, no. 6, pp. 3671–3691, 2018.
  21. V. I. Levenshtein, “Maximum number of words in codes without overlaps,” Problemy Peredachi Informatsii, vol. 6, no. 4, pp. 88–90, 1970.
  22. S. T. Yazdi, H. M. Kiah, R. Gabrys, and O. Milenkovic, “Mutually uncorrelated primers for dna-based data storage,” IEEE Transactions on Information Theory, vol. 64, no. 9, pp. 6283–6296, 2018.
  23. S. R. Blackburn, “Non-overlapping codes,” IEEE Transactions on Information Theory, vol. 61, no. 9, pp. 4890–4894, 2015.

Summary

We haven't generated a summary for this paper yet.

X Twitter Logo Streamline Icon: https://streamlinehq.com