Skip to main content
SpringerLink
Log in

Design and Simulation of an Autonomous Molecular Mechanism Using Spatially Localized DNA Computation

  • Original research article
  • Published:
Interdisciplinary Sciences: Computational Life Sciences Aims and scope Submit manuscript

Abstract

As a well-established technique, DNA synthesis offers interesting possibilities for designing multifunctional nanodevices. The micro-processing system of modern semiconductor circuits is dependent on strategies organized on silicon chips to achieve the speedy transmission of substances or information. Similarly, spatially localized structures allow for fixed DNA molecules in close proximity to each other during the synthesis of molecular circuits, thus providing a different strategy that of opening up a remarkable new area of inquiry for researchers. Herein, the Visual DSD (DNA strand displacement) modeling language was used to design and analyze the spatially organized DNA reaction network. The execution rules depend on the hybridization reaction caused by directional complementary nucleotide sequences. A series of DNA strand displacement calculations were organized on the locally coded travel track, and autonomous movement and addressing operations are gradually realized. The DNA nanodevice operates in this manner follows the embedded “molecular program”, which improves the reusability and scalability of the same sequence domain in different contexts. Through the communication between various building blocks, the DNA device-carrying the target molecule moves in a controlled manner along the programmed track. In this way, a variety of molecular functional group transport and specific partition storage can be realized. The simulation results of the visual DSD tool provide qualitative and quantitative proof for the operation of the system.

Graphical Abstract

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11
Fig. 12
Fig. 13

Similar content being viewed by others

Data availability

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

References

  1. Soloveichik D, Seelig G, Winfree E (2010) DNA as a universal substrate for chemical kinetics. Proc Natl Acad Sci U S A 107(12):5393–5398. https://doi.org/10.1073/pnas.0909380107. (Epub 2010 Mar 4. PMID: 20203007; PMCID: PMC2851759)

    Article  PubMed  PubMed Central  Google Scholar 

  2. Song X, Reif J (2019) Nucleic acid databases and molecular-scale computing. ACS Nano 13(6):6256–6268. https://doi.org/10.1021/acsnano.9b02562

    Article  CAS  PubMed  Google Scholar 

  3. Schaus TE, Woo S, Xuan F, Chen X, Yin P (2017) A DNA nanoscope via auto-cycling proximity recording. Commun 8:696. https://doi.org/10.1038/s41467-017-00542-3

    Article  CAS  Google Scholar 

  4. Gerasimova YV, Kolpashchikov DM (2016) Towards a DNA nanoprocessor: reusable tile-integrated DNA circuits. Angew Chem Int Ed 55(35):10244–10247. https://doi.org/10.1002/anie.201603265

    Article  CAS  Google Scholar 

  5. Chao J et al (2019) Solving mazes with single-molecule DNA navigators. Nat Mater 18(3):273–279. https://doi.org/10.1038/s41563-018-0205-3

    Article  CAS  PubMed  Google Scholar 

  6. Thubagere J, Li W, Johnson RF et al (2017) A cargo-sorting DNA robot. Science. https://doi.org/10.1126/science.aan6558

    Article  PubMed  Google Scholar 

  7. Lakin MR, Stefanovic D (2016) Supervised learning in adaptive DNA strand displacement networks. Acs Synth Biol 5(8):885–897. https://doi.org/10.1021/acssynbio.6b00009

    Article  CAS  PubMed  Google Scholar 

  8. Yurke B, Turberfifield AJ, Mills AP, Simmel FC, Neumann JL (2000) A DNA-fuelled molecular machine made of DNA. Nature 406(6796):605–608. https://doi.org/10.1038/35020524

    Article  CAS  PubMed  Google Scholar 

  9. Thubagere AJ, Thachuk C, Berleant J, Johnson RF, Ardelean DA, Cherry KM, Qian LL (2017) Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components. Nat Commun 8(1):103–113. https://doi.org/10.1038/ncomms14373

    Article  CAS  Google Scholar 

  10. Wang F, Lv H, Li Q, Li J, Zhang XL, Shi JY, Wang LH, Fan CH (2020) Implementing digital computing with DNA-based switching circuits. Nat Commun. https://doi.org/10.1038/s41467-019-13980-y

    Article  PubMed  PubMed Central  Google Scholar 

  11. Ordóñez-Guillén NE, Martínez-Pérez IM (2019) Catalytic DNA strand displacement cascades applied to logic programming. IEEE Acces 7:100428–100441. https://doi.org/10.1109/ACCESS.2019.2928273

    Article  Google Scholar 

  12. Qian L, Winfree E, Bruck J (2011) Neural network computation with DNA strand displacement cascades. Nature 475(7356):368–372. https://doi.org/10.1038/nature10262

    Article  CAS  PubMed  Google Scholar 

  13. Dai M, Jungmann R, Yin P (2016) Optical imaging of individual biomolecules in densely packed clusters. Nat Nanotechnol 11(9):798–807. https://doi.org/10.1038/nnano.2016.95

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Song TQ, Gopalkrishnan N et al (2018) Improving the performance of DNA strand displacement circuits by shadow cancellation. ACS Nano 12(11):11689–11697. https://doi.org/10.1021/acsnano.8b07394

    Article  CAS  PubMed  Google Scholar 

  15. Dunn KE, Trefzer MA, Johnson S, Tyrrell AM (2016) Investigating the dynamics of surface-immobilized DNA nanomachines. Sci Rep 6(1):631–633. https://doi.org/10.1038/srep29581

    Article  CAS  Google Scholar 

  16. Chatterjee G, Dalchau N, Muscat RA, Phillips A, Seelig G (2017) A spatially localized architecture for fast and modular DNA computing. Nat Nanotechnol 12(9):920–927. https://doi.org/10.1038/nnano.2017.127

    Article  CAS  PubMed  Google Scholar 

  17. Boemo MA, Lucas AE, Turberfield AJ, Cardelli L (2016) The formal language and design principles of autonomous DNA walker circuits. Acs Synth Biol 5(8):878–884. https://doi.org/10.1021/acssynbio.5b00275

    Article  CAS  PubMed  Google Scholar 

  18. Li SP, Jiang Q, Liu SL et al (2018) A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo. Nat Biotechnol 36(3):258–264. https://doi.org/10.1038/nbt.4071

    Article  CAS  PubMed  Google Scholar 

  19. Grossi G, Jepsen MDE, Kjems J, Andersen ES (2017) Control of enzyme reactions by a reconfigurable DNA nanovault. Nat Commun 8(1):65–87. https://doi.org/10.1038/s41467-017-01072-8

    Article  CAS  Google Scholar 

  20. Kroener F, Heerwig A, Kaiser W, Mertig M, Rant U (2017) Electrical actuation of a DNA origami Nanolever on an electrode. J Am Chem Soc 139(46):16510–16513. https://doi.org/10.1021/jacs.7b10862

    Article  CAS  PubMed  Google Scholar 

  21. Zhou LF, Marras AE, Huang CM, Castro CE, Su HJ (2018) Paper origami-inspired design and actuation of DNA nanomachines with complex motions. Small. https://doi.org/10.1002/smll.201802580

    Article  PubMed  PubMed Central  Google Scholar 

  22. Wang F, Zhang XL, Liu XG, Fan CH, Li Q (2019) Programming motions of DNA origami nanomachines. Small. https://doi.org/10.1002/smll.201900013

    Article  PubMed  PubMed Central  Google Scholar 

  23. Kopperger E, List J, Madhira S, Rothfischer F, Lamb DC, Simmel FC (2018) A self-assembled nanoscale robotic arm controlled by electric fields. Science 359(6373):296–300. https://doi.org/10.1126/science.aao4284

    Article  CAS  PubMed  Google Scholar 

  24. Hagiya M, Konagaya A, Kobayashi S, Saito H, Murata S (2014) Molecular robots with sensors and intelligence. Acc Chem Res 47(6):1681–1690. https://doi.org/10.1021/ar400318d

    Article  CAS  PubMed  Google Scholar 

  25. Aubert N, Mosca C, Fujii T, Hagiya M, Rondelez Y (2014) Computer-assisted design for scaling up systems based on DNA reaction networks. J R Soc Interface. https://doi.org/10.1098/rsif.2013.1167

    Article  PubMed  PubMed Central  Google Scholar 

  26. Lakin MR, Youssef S, Cardelli L, Phillips A (2012) Abstractions for DNA circuit design. J R Soc Interface 9(68):470–486. https://doi.org/10.1098/rsif.2011.0343

    Article  PubMed  Google Scholar 

  27. Petersen RL, Lakin MR, Phillips A (2016) A strand graph semantics for DNA-based computation. Theor Comput Sci 632:43–73. https://doi.org/10.1016/j.tcs.2015.07.041

    Article  PubMed  PubMed Central  Google Scholar 

  28. Lakin MR, Phillips A (2017) Automated, constraint-based analysis of tethered DNA nanostructures. In: 23rd International Conference on DNA computing and molecular programming, pp 1–16, https://doi.org/10.1007/978-3-319-66799-7_1

  29. Zhang DY, Turberfield AJ, Yurke B, Winfree E (2007) Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318(5853):1121–1125. https://doi.org/10.1126/science.1148532

    Article  CAS  PubMed  Google Scholar 

  30. Bath J, Green SJ, Turberfield AJ (2005) A free-running DNA motor powered by a nicking enzyme. Angew Chem 44(48):4358–4361. https://doi.org/10.1002/anie.200501262

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This research This work was supported by National Natural Science Foundation of China (no. 62073207), Natural Science Basic Research Plan in Shaanxi Province of China (no. 2020JM-298). The authors are very grateful to the anonymous reviewers for their valuable comments and suggestions for improving the quality of the paper.

Author information

Author notes

  1. Yue Wang and Luhui Wang have contributed equally to the work.

Authors and Affiliations

  1. School of Life Science, Shaanxi Normal University, Xi’an, 710119, Shaanxi, China

    Yue Wang, Luhui Wang, Wenxiao Hu, Mengyao Qian & Yafei Dong

  2. Department of Information Engineering, Taiyuan City Vocational and Technical College, Taiyuan, 030027, Shanxi, China

    Yue Wang

Authors
  1. Yue Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Luhui Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wenxiao Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mengyao Qian
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yafei Dong
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yafei Dong.

Ethics declarations

Conflict of interest

The authors declare that they have no competing interests.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 810 KB)

Supplementary file2 (PDF 562 KB)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, Y., Wang, L., Hu, W. et al. Design and Simulation of an Autonomous Molecular Mechanism Using Spatially Localized DNA Computation. Interdiscip Sci Comput Life Sci 15, 1–14 (2023). https://doi.org/10.1007/s12539-023-00551-5

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12539-023-00551-5

Keywords

Search

Navigation