Skip to main content
SpringerLink
Log in

Coordinated motion of molecular motors on DNA chains with branch topology

  • Research Paper
  • Published:
Acta Mechanica Sinica Aims and scope Submit manuscript

Abstract

Toward understanding the macroscopic mechanical behaviors of responsive deoxyribonucleic acid (DNA) hydrogels integrated with DNA motors, here we construct the state map for the translocation process of a single C-terminal translocase domain (FtsKC) on a single DNA chain at the molecular level and then investigate the movement of single or multiple FtsKC motors on DNA chains with varied branch topology. Our studies indicate that multiple FtsKC motors can have coordinated motion, which is mainly due to the force responsive behavior of individual FtsKC motor. We further suggest the potential application of motors of FtsKC, together with DNA chains of specific branch topology, to serve as strain sensors in hydrogels.

Graphic 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

Similar content being viewed by others

References

  1. Hong, C.A., Park, J.C., Na, H., et al.: Short DNA-catalyzed formation of quantum dot-DNA hydrogel for enzyme-free femtomolar specific DNA assay. Biosens Bioelectron 182, 113110 (2021)

    Article  Google Scholar 

  2. Zhang, Q., Liu, X., Duan, L.G., et al.: A DNA-inspired hydrogel mechanoreceptor with skin-like mechanical behavior. J Mater Chem A 9, 1835–1844 (2021)

    Article  Google Scholar 

  3. Kim, H.S., Abbas, N., Shin, S.: A rapid diagnosis of SARS-CoV-2 using DNA hydrogel formation on microfluidic pores. Biosens Bioelectron 177, 113005 (2021)

    Article  Google Scholar 

  4. Mo, F., Jiang, K., Zhao, D., et al.: DNA hydrogel-based gene editing and drug delivery systems. Adv. Drug. Deliv. Rev. 168, 79–98 (2021)

    Article  Google Scholar 

  5. Khajouei, S., Ravan, H., Ebrahimi, A.: Developing a colorimetric nucleic acid-responsive DNA hydrogel using DNA proximity circuit and catalytic hairpin assembly. Anal. Chim. Acta. 1137, 1–10 (2020)

    Article  Google Scholar 

  6. Bi, Y., Du, X., He, P.C., et al.: Smart bilayer polyacrylamide/DNA hybrid hydrogel film actuators exhibiting programmable responsive and reversible macroscopic shape deformations. Small 16, 1906998 (2020)

    Article  Google Scholar 

  7. Zhao, M.L., Zeng, W.J., Chai, Y.Q., et al.: An affinity-enhanced DNA intercalator with intense ECL embedded in DNA hydrogel for biosensing applications. Anal. Chem. 92, 11044–11052 (2020)

    Article  Google Scholar 

  8. Xu, N., Ma, N., Yang, X., et al.: Preparation of intelligent DNA hydrogel and its applications in biosensing. Eur Poly J 137, 109951 (2020)

    Article  Google Scholar 

  9. Gao, X., Li, X., Sun, X., et al.: DNA tetrahedra-cross-linked hydrogel functionalized paper for onsite analysis of DNA methyltransferase activity using a personal glucose meter. Anal. Chem. 92, 4592–4599 (2020)

    Article  Google Scholar 

  10. Wang, J.Y., Guo, Q.Y., Yao, Z.Y., et al.: A low-field nuclear magnetic resonance DNA-hydrogel nanoprobe for bisphenol A determination in drinking water. Mikrochim. Acta 187, 333 (2020)

    Article  Google Scholar 

  11. Urtel, G., Estevez-Torres, A., Galas, J.C.: DNA-based long-lived reaction-diffusion patterning in a host hydrogel. Soft Matter 15, 9343–9351 (2019)

    Article  Google Scholar 

  12. Ke, Y., Liu, Y., Zhang, J., et al.: A study of DNA tube formation mechanisms using 4-, 8-, and 12-helix DNA nanostructures. J. Am. Chem. Soc. 128, 4414–4421 (2015)

    Article  Google Scholar 

  13. Lin, Y., Wang, X., Sun, Y., et al.: A chemiluminescent biosensor for ultrasensitive detection of adenosine based on target-responsive DNA hydrogel with Au@HKUST-1 encapsulation. Sens. Actuators, B Chem. 289, 56–64 (2019)

    Article  Google Scholar 

  14. Li, F., Tang, J., Geng, J., et al.: Polymeric DNA hydrogel: design, synthesis and applications. Progress in Polymer Science 98, 101163 (2019)

    Article  Google Scholar 

  15. Song, H., Zhang, Y., Cheng, P., et al.: A rapidly self-assembling soft-brush DNA hydrogel based on RCA products. Chem. Commun. 55, 5375–5378 (2019)

    Article  Google Scholar 

  16. Xing, Z., Caciagli, A., Cao, T., et al.: Microrheology of DNA hydrogels. Proc. Natl. Acad. Sci. 15, 8137–8142 (2018)

    Article  Google Scholar 

  17. Zhou, X., Li, C., Shao, Y., et al.: Reversibly tuning the mechanical properties of a DNA hydrogel by a DNA nanomotor. Chem. Commun. 52, 10668–10671 (2016)

    Article  Google Scholar 

  18. Lee, J.B., Peng, S., Yang, D., et al.: A mechanical metamaterial made from a DNA hydrogel. Nat. Nanotechnol. 7, 816–820 (2012)

    Article  Google Scholar 

  19. Qi, H., Ghodousi, M., Du, Y., et al.: DNA-directed self-assembly of shape-controlled hydrogels. Nat. Commun. 4, 2275 (2013)

    Article  Google Scholar 

  20. Bertrand, O.J., Fygenson, D.K., Saleh, O.A.: Active, motor-driven mechanics in a DNA gel. Proc. Natl. Acad. Sci. 109, 17342–17347 (2012)

    Article  Google Scholar 

  21. Sherratt, D.J., Arciszewska, L.K., Crozat, E., et al.: The Escherichia coli DNA translocase FtsK. Biochem. Soc. Trans. 38, 395–398 (2010)

    Article  Google Scholar 

  22. Graham, J.E., Sherratt, D.J., Szczelkun, M.D.: Sequence-specific assembly of FtsK hexamers establishes directional translocation on DNA. Proc. Natl. Acad. Sci. 107, 20263–20268 (2010)

    Article  Google Scholar 

  23. Bigot, S., Saleh, O.A., Cornet, F., et al.: Oriented loading of FtsK on KOPS. Nat. Struct. Mol. Biol. 13, 1026–1028 (2006)

    Article  Google Scholar 

  24. Bigot, S., Saleh, O.A., Lesterlin, C., et al.: KOPS: DNA motifs that control E. coli chromosome segregation by orienting the FtsK translocase. EMBO J. 24, 3770–3780 (2005)

    Article  Google Scholar 

  25. Saleh, O.A., Perals, C., Barre, F.X., et al.: Fast, DNA-sequence independent translocation by FtsK in a single-molecule experiment. EMBO J. 23, 2430–2439 (2004)

    Article  Google Scholar 

  26. Ptacin, J.L., Nollmann, M., Bustamante, C., et al.: Identification of the FtsK sequence-recognition domain. Nat. Struct. Mol. Biol. 13, 1023–1025 (2006)

    Article  Google Scholar 

  27. Bigot, S., Sivanathan, V., Possoz, C., et al.: FtsK, a literate chromosome segregation machine. Mol. Microbiol. 64, 1434–1441 (2007)

    Article  Google Scholar 

  28. Chowdhury, D.: Stochastic mechano-chemical kinetics of molecular motors: a multidisciplinary enterprise from a physicist’s perspective. Phys. Rep. 529, 1–197 (2013)

    Article  Google Scholar 

  29. Crozat, E., Meglio, A., Allemand, J.F., et al.: Separating speed and ability to displace roadblocks during DNA translocation by FtsK. EMBO J. 29, 1423–1433 (2010)

    Article  Google Scholar 

  30. Graham, J.E., Sivanathan, V., Sherratt, D.J., et al.: FtsK translocation on DNA stops at XerCD-dif. Nucleic Acids Res. 38, 72–81 (2010)

    Article  Google Scholar 

  31. Pease, P.J., Levy, O., Cost, G.J., et al.: Sequence-directed DNA translocation by purified FtsK. Science 307, 586–590 (2005)

    Article  Google Scholar 

  32. Kunwar, A., Mogilner, A.: Robust transport by multiple motors with nonlinear force–velocity relations and stochastic load sharing. Phys. Biol. 7, 016012 (2010)

    Article  Google Scholar 

  33. Gross, P., Laurens, N., Oddershede, L.B., et al.: Quantifying how DNA stretches, melts and changes twist under tension. Nat. Phys. 7, 731–736 (2011)

    Article  Google Scholar 

  34. Kuimova, M.K.: Mapping viscosity in cells using molecular rotors. Phys. Chem. Chem. Phys. 14, 12671–12686 (2012)

    Article  Google Scholar 

  35. Fieller, E.C., Hartley, H.O., Pearson, E.S.: Tests for rank correlation coefficient. I. Biometrika 44, 470–481 (1957)

    Article  MathSciNet  MATH  Google Scholar 

  36. Marko, J.F.: Stretching must twist DNA. Europhys. Lett. 38, 183–188 (1997)

    Article  MathSciNet  Google Scholar 

  37. Duke, T.A.: Molecular model of muscle contraction. Proc. Natl. Acad. Sci. USA 96, 2770–2775 (1999)

    Article  Google Scholar 

  38. Lee, J.Y., Finkelstein, I.J., Arciszewska, L.K., et al.: Single-molecule imaging of FtsK translocation reveals mechanistic features of protein-protein collisions on DNA. Mol. Cell 54, 832–843 (2014)

    Article  Google Scholar 

  39. McLeish, T.C.B.: Tube theory of entangled polymer dynamics. Adv. Phys. 51, 1379–1527 (2002)

    Article  Google Scholar 

  40. Weerakoon, S., Fernando, T.G.I.: A variant of Newton’s method with accelerated third-order convergence. Appl. Math. Lett. 13, 87–93 (2000)

    Article  MathSciNet  MATH  Google Scholar 

  41. Chen, B.: Self-regulation of motor force through chemomechanical coupling in skeletal muscle contraction. J. Appl. Mech. 80, 051013 (2013)

    Article  Google Scholar 

  42. Chen, B., Dong, C.: Modeling deoxyribose nucleic acid as an elastic rod inlaid with fibrils. J. Appl. Mech. 81, 071005 (2014)

    Article  Google Scholar 

  43. Dong, C., Chen, B.: Coupling of bond breaking with state transition leads to high apparent detachment rates of a single Myosin. J. Appl. Mech. 83, 051011 (2016)

    Article  Google Scholar 

  44. Chen, X., Chen, B.: Simplified analysis for the association of a constrained receptor to an oscillating ligand. J. Appl. Mech. 83, 091006 (2016)

    Article  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Natural Science Foundation of China (Grant 11872334).

Author information

Authors and Affiliations

  1. Department of Engineering Mechanics, Zhejiang University, Hangzhou, 310027, China

    Di Lu & Bin Chen

  2. Key Laboratory of Soft Machines and Smart Devices of Zhejiang Province, Hangzhou, 310027, China

    Bin Chen

Authors
  1. Di Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Bin Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Bin Chen.

Additional information

Executive Editor: Xiqiao Feng

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lu, D., Chen, B. Coordinated motion of molecular motors on DNA chains with branch topology. Acta Mech. Sin. 37, 1580–1588 (2021). https://doi.org/10.1007/s10409-021-01131-w

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10409-021-01131-w

Keywords

Search

Navigation