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  • Open Access

Experimental demonstration of kinetic proofreading inherited in ligation-based information replication

Hiroyuki Aoyanagi, Yasuhiro Magi, and Shoichi Toyabe*

  • Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan

  • *Contact author: toyabe@tohoku.ac.jp
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Phys. Rev. Research 7, 043264 – Published 8 December, 2025

DOI: https://doi.org/10.1103/pdhn-ncpl

Abstract

We experimentally demonstrate that information replication by templated ligation of DNA strands inherits a kinetic proofreading mechanism and achieves significant error suppression through cascade replication. A simple simulation model derived from the experimental results shows that templated ligation has a significant advantage over replication by polymerization for error suppression of long strands. Specifically, longer chains show lower error rates, significantly distinct from the chain-growth polymerization where errors typically accumulate with chain length. This mechanism provides a plausible route for high-fidelity replication in prebiotic chemistry and illustrates how physical principles such as nonequilibrium kinetics and network architecture can drive reliable molecular information replication. The approach also offers strategies for error suppression in biotechnology.

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References (39)

  1. P. Schuster and M. Eigen, The Hypercycle: A Principle of Natural Self-Organization (Springer, Berlin, 1979).
  2. E. Domingo, R. A. Flavell, and C. Weissmann, In vitro site-directed mutagenesis: Generation and properties of an infectious extracistronic mutant of bacteriophage Qβ, Gene 1, 3 (1976).
  3. E. Domingo, D. Sabo, T. Taniguchi, and C. Weissmann, Nucleotide sequence heterogeneity of an RNA phage population, Cell 13, 735 (1978).
  4. D. R. Mills, R. L. Peterson, and S. Spiegelman, An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule, Proc. Natl. Acad. Sci. USA 58, 217 (1967).
  5. D. M. Whiley and T. P. Sloots, Sequence variation in primer targets affects the accuracy of viral quantitative PCR, J. Clin. Virol. 34, 104 (2005).
  6. A. A. Gibriel and O. Adel, Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications, Mutat. Res. Rev. Mutat. Res. 773, 66 (2017).
  7. D. Andrieux and P. Gaspard, Nonequilibrium generation of information in copolymerization processes, Proc. Natl. Acad. Sci. USA 105, 9516 (2008).
  8. P. Sartori and S. Pigolotti, Thermodynamics of error correction, Phys. Rev. X 5, 041039 (2015).
  9. T. E. Ouldridge and P. Rein ten Wolde, Fundamental costs in the production and destruction of persistent polymer copies, Phys. Rev. Lett. 118, 158103 (2017).
  10. J. Y. Matsubara, T. Nobuto, and K. Kaneko, Avoidance of error catastrophe via proofreading innate to template-directed polymerization, Phys. Rev. Res. 5, 013170 (2023).
  11. H. Aoyanagi, S. Pigolotti, S. Ono, and S. Toyabe, Error-suppression mechanism of PCR by blocker strands, Biophys. J. 122, 1334 (2023).
  12. T. Takahashi, H. Aoyanagi, S. Pigolotti, and S. Toyabe, Blocking uncertain mispriming errors of PCR, Biophys. J. 123, 3558 (2024).
  13. F. Barany, Genetic disease detection and DNA amplification using cloned thermostable ligase, Proc. Natl. Acad. Sci. USA 88, 189 (1991).
  14. P. W. Anderson, Suggested model for prebiotic evolution: The use of chaos, Proc. Nat. Acad. Sci. USA 80, 3386 (1983).
  15. S. Toyabe and D. Braun, Cooperative ligation breaks sequence symmetry and stabilizes early molecular replication, Phys. Rev. X 9, 011056 (2019).
  16. P. W. Kudella, A. V. Tkachenko, A. Salditt, S. Maslov, and D. Braun, Structured sequences emerge from random pool when replicated by templated ligation, Proc. Natl. Acad. Sci. USA 118, e2018830118 (2021).
  17. J. H. Rosenberger, T. Göppel, P. W. Kudella, D. Braun, U. Gerland, and B. Altaner, Self-assembly of informational polymers by templated ligation, Phys. Rev. X 11, 031055 (2021).
  18. G. Laurent, T. Göppel, D. Lacoste, and U. Gerland, Emergence of homochirality via template-directed ligation in an RNA reactor, PRX Life 2, 013015 (2024).
  19. A. V. Tkachenko and S. Maslov, Spontaneous emergence of autocatalytic information-coding polymers, J. Chem. Phys. 143, 045102 (2015).
  20. J. Luo, D. E. Bergstrom, and F. Barany, Improving the fidelity of Thermus thermophilus DNA ligase, Nucleic Acids Res. 24, 3071 (1996).
  21. L. Zhou, D. K. O'Flaherty, and J. W. Szostak, Template-directed copying of RNA by non-enzymatic ligation, Angew. Chem., Int. Ed. 59, 15682 (2020).
  22. J. J. Hopfield, Kinetic proofreading: A new mechanism for reducing errors in biosynthetic processes requiring high specificity, Proc. Natl. Acad. Sci. USA 71, 4135 (1974).
  23. J. Ninio, Kinetic amplification of enzyme discrimination, Biochimie 57, 587 (1975).
  24. A. Murugan, D. A. Huse, and S. Leibler, Speed, dissipation, and error in kinetic proofreading, Proc. Natl. Acad. Sci. USA 109, 12034 (2012).
  25. R. Mukherjee, A. Sengar, J. Cabello-García, and T. E. Ouldridge, Kinetic proofreading can enhance specificity in a nonenzymatic DNA strand displacement network, J. Am. Chem. Soc. 146, 18916 (2024).
  26. See Supplemental Material at http://link.aps.org/supplemental/10.1103/pdhn-ncpl for supplementary methods and results.
  27. C. E. Pritchard and E. M. Southern, Effects of base mismatches on joining of short oligodeoxynucleotides by DNA ligases, Nucleic Acids Res. 25, 3403 (1997).
  28. A. Doricchi, C. M. Platnich, A. Gimpel, F. Horn, M. Earle, G. Lanzavecchia, A. L. Cortajarena, L. M. Liz-Marzán, N. Liu, R. Heckel, R. N. Grass, R. Krahne, U. F. Keyser, and D. Garoli, Emerging approaches to DNA data storage: Challenges and prospects, ACS Nano 16, 17552 (2022).
  29. W.-S. Wei, A. Trubiano, C. Sigl, S. Paquay, H. Dietz, M. F. Hagan, and S. Fraden, Hierarchical assembly is more robust than egalitarian assembly in synthetic capsids, Proc. Natl. Acad. Sci. USA 121, e2312775121 (2024).
  30. G. Bradski, The OpenCV library, Dr. Dobb's J. Software Tools 120, 122 (2000).
  31. P. Yaroshchyk and J. E. Eberhardt, Automatic correction of continuum background in laser-induced breakdown spectroscopy using a model-free algorithm, Spectrochim. Acta B 99, 138 (2014).
  32. G. J. Boggy and P. J. Woolf, A mechanistic model of PCR for accurate quantification of quantitative PCR data, PLoS One 5, e12355 (2010).
  33. R. Palais and C. T. Wittwer, Mathematical algorithms for high-resolution DNA melting analysis, in Methods in Enzymology, Computer Methods, Part A (Academic Press, Cambridge, 2009), Vol. 454, pp. 323–343.
  34. K. Tawa, D. Yao, and W. Knoll, Matching base-pair number dependence of the kinetics of DNA–DNA hybridization studied by surface plasmon fluorescence spectroscopy, Biosens. Bioelectron. 21, 322 (2005).
  35. J. X. Zhang, J. Z. Fang, W. Duan, L. R. Wu, A. W. Zhang, N. Dalchau, B. Yordanov, R. Petersen, A. Phillips, and D. Y. Zhang, Predicting DNA hybridization kinetics from sequence, Nat. Chem. 10, 91 (2018).
  36. J. A. Nelder and R. Mead, A simplex method for function minimization, Comput. J. 7, 308–313 (1965).
  37. V. K. Dixit and C. Rackauckas, Optimization.Jl: A unified optimization package, Zenodo (2023), https://zenodo.org/records/7738525.
  38. M. Weitz, J. Kim, K. Kapsner, E. Winfree, E. Franco, and F. C. Simmel, Diversity in the dynamical behavior of a compartmentalized programmable biochemical oscillator, Nat. Chem. 6, 295 (2014).
  39. B. Yurke and A. P. Mills, Using DNA to power nanostructures, Genet. Program. Evolvable Mach. 4, 111 (2003).

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Phys. Rev. Research 7, 043264– Published 8 December, 2025
  • Received 13 May 2025
  • Accepted 23 October 2025
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Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI.

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