Abstract
To understand the macroscopic mechanical behaviors of responsive DNA hydrogels integrated with DNA motors, we constructed a state map for the translocation process of a single FtsKC on a single DNA chain at the molecular level and then investigated the movement of single or multiple FtsKC motors on DNA chains with varied branch topologies. Our studies indicate that multiple FtsKC motors can have coordinated motion, which is mainly due to the force-responsive behavior of individual FtsKC motors. 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.
摘要
为理解整合了DNA马达的响应性DNA水凝胶的宏观力学行为, 文章在分子水平上构建了单个FtsKC在单个DNA链上的易位过程状态图, 并进一步研究了具有不同分支拓扑的DNA链上单个或多个FtsKC马达的运动. 研究表明, 多个FtsKC马达可以协调运动, 这主要是由于单个FtsKC马达的力响应行为. 文章进一步指出FtsKC马达结合特定分支拓扑的DNA链作为水凝胶中的应变传感器的潜在应用.
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C. A. Hong, J. C. Park, H. Na, H. Jeon, and Y. S. Nam, Short DNA-catalyzed formation of quantum dot-DNA hydrogel for enzyme-free femtomolar specific DNA assay, Biosens. Bioelectron. 182, 113110 (2021).
Q. Zhang, X. Liu, L. Duan, and G. Gao, A DNA-inspired hydrogel mechanoreceptor with skin-like mechanical behavior, J. Mater. Chem. A 9, 1835 (2021).
H. S. Kim, N. Abbas, and S. Shin, A rapid diagnosis of SARS-CoV-2 using DNA hydrogel formation on microfluidic pores, Biosens. Bioelectron. 177, 113005 (2021).
F. Mo, K. Jiang, D. Zhao, Y. Wang, J. Song, and W. Tan, DNA hydrogel-based gene editing and drug delivery systems, Adv. Drug Deliver. Rev. 168, 79 (2021).
S. Khajouei, H. Ravan, and A. Ebrahimi, Developing a colorimetric nucleic acid-responsive DNA hydrogel using DNA proximity circuit and catalytic hairpin assembly, Anal. Chim. Acta 1137, 1 (2020).
Y. Bi, X. Du, P. He, C. Wang, C. Liu, and W. Guo, Smart bilayer polyacrylamide/DNA hybrid hydrogel film actuators exhibiting programmable responsive and reversible macroscopic shape deformations, Small 16, 1906998 (2020).
M. L. Zhao, W. J. Zeng, Y. Q. Chai, R. Yuan, and Y. Zhuo, An affinity-enhanced DNA intercalator with intense ECL embedded in DNA hydrogel for biosensing applications, Anal. Chem. 92, 11044 (2020).
N. Xu, N. Ma, X. Yang, G. Ling, J. Yu, and P. Zhang, Preparation of intelligent DNA hydrogel and its applications in biosensing, Eur. Polym. J. 137, 109951 (2020).
X. Gao, X. Li, X. Sun, J. Zhang, Y. Zhao, X. Liu, and F. Li, DNA tetrahedra-cross-linked hydrogel functionalized paper for onsite analysis of DNA methyltransferase activity using a personal glucose meter, Anal. Chem. 92, 4592 (2020).
J. Y. Wang, Q. Y. Guo, Z. Y. Yao, N. Yin, S. Y. Ren, Y. Li, S. Li, Y. Peng, J. L. Bai, B. A. Ning, J. Liang, and Z. X. Gao, A low-field nuclear magnetic resonance DNA-hydrogel nanoprobe for bisphenol A determination in drinking water, Microchim. Acta 187, 333 (2020).
G. Urtel, A. Estevez-Torres, and J. C. Galas, DNA-based long-lived reaction-diffusion patterning in a host hydrogel, Soft Matter 15, 9343 (2019).
Y. Ke, Y. Liu, J. Zhang, and H. Yan, A study of DNA tube formation mechanisms using 4-, 8-, and 12-helix DNA nanostructures, J. Am. Chem. Soc. 128, 4414 (2015).
Y. Lin, X. Wang, Y. Sun, Y. Dai, W. Sun, X. Zhu, H. Liu, R. Han, D. Gao, and C. Luo, A chemiluminescent biosensor for ultrasensitive detection of adenosine based on target-responsive DNA hydrogel with Au@HKUST-1 encapsulation, Sens. Actuat. B-Chem. 289, 56 (2019).
F. Li, J. Tang, J. Geng, D. Luo, and D. Yang, Polymeric DNA hydrogel: design, synthesis and applications, Prog. Polym. Sci. 98, 101163 (2019).
H. Song, Y. Zhang, P. Cheng, X. Chen, Y. Luo, and W. Xu, A rapidly self-assembling soft-brush DNA hydrogel based on RCA products, Chem. Commun. 55, 5375 (2019).
Z. Xing, A. Caciagli, T. Cao, I. Stoev, M. Zupkauskas, T. O’Neill, T. Wenzel, R. Lamboll, D. Liu, and E. Eiser, Microrheology of DNA hydrogels, Proc. Natl. Acad. Sci. 115, 8137 (2018).
X. Zhou, C. Li, Y. Shao, C. Chen, Z. Yang, and D. Liu, Reversibly tuning the mechanical properties of a DNA hydrogel by a DNA nanomotor, Chem. Commun. 52, 10668 (2016).
J. B. Lee, S. Peng, D. Yang, Y. H. Roh, H. Funabashi, N. Park, E. J. Rice, L. Chen, R. Long, M. Wu, and D. Luo, A mechanical metamaterial made from a DNA hydrogel, Nat. Nanotech. 7, 816 (2012).
H. Qi, M. Ghodousi, Y. Du, C. Grun, H. Bae, P. Yin, and A. Khademhosseini, DNA-directed self-assembly of shape-controlled hydrogels, Nat. Commun. 4, 2275 (2013).
O. J. N. Bertrand, D. K. Fygenson, and O. A. Saleh, Active, motor-driven mechanics in a DNA gel, Proc. Natl. Acad. Sci. 109, 17342 (2012).
D. J. Sherratt, L. K. Arciszewska, E. Crozat, J. E. Graham, and I. Grainge, The Escherichia coli DNA translocase FtsK, Biochem. Soc. Trans. 38, 395 (2010).
J. E. Graham, D. J. Sherratt, and M. D. Szczelkun, Sequence-specific assembly of FtsK hexamers establishes directional translocation on DNA, Proc. Natl. Acad. Sci. 107, 20263 (2010).
S. Bigot, O. A. Saleh, F. Cornet, J. F. Allemand, and F. X. Barre, Oriented loading of FtsK on KOPS, Nat. Struct. Mol. Biol. 13, 1026 (2006).
S. Bigot, O. A. Saleh, C. Lesterlin, C. Pages, M. El Karoui, C. Dennis, M. Grigoriev, J. F. Allemand, F. X. Barre, and F. Cornet, KOPS: DNA motifs that control E. coli chromosome segregation by orienting the FtsK translocase, EMBO J 24, 3770 (2005).
O. A. Saleh, C. Pérals, F. X. Barre, and J. F. Allemand, Fast, DNA-sequence independent translocation by FtsK in a single-molecule experiment, EMBO J 23, 2430 (2004).
J. L. Ptacin, M. Nöllmann, C. Bustamante, and N. R. Cozzarelli, Identification of the FtsK sequence-recognition domain, Nat Struct Mol Biol 13, 1023 (2006).
S. Bigot, V. Sivanathan, C. Possoz, F. X. Barre, and F. Cornet, FtsK, a literate chromosome segregation machine, Mol. Microbiol. 64, 1434 (2007).
D. Chowdhury, Stochastic mechano-chemical kinetics of molecular motors: a multidisciplinary enterprise from a physicist’s perspective, Phys. Rep. 529, 1 (2013).
E. Crozat, A. Meglio, J. F. Allemand, C. E. Chivers, M. Howarth, C. Vénien-Bryan, I. Grainge, and D. J. Sherratt, Separating speed and ability to displace roadblocks during DNA translocation by FtsK, EMBO J 29, 1423 (2010).
J. E. Graham, V. Sivanathan, D. J. Sherratt, and L. K. Arciszewska, FtsK translocation on DNA stops at XerCD-dif, Nucleic Acids Res. 38, 72 (2010).
P. J. Pease, O. Levy, G. J. Cost, J. Gore, J. L. Ptacin, D. Sherratt, C. Bustamante, and N. R. Cozzarelli, Sequence-directed DNA translocation by purified FtsK, Science 307, 586 (2005).
A. Kunwar, and A. Mogilner, Robust transport by multiple motors with nonlinear force-velocity relations and stochastic load sharing, Phys. Biol. 7, 016012 (2010).
P. Gross, N. Laurens, L. B. Oddershede, U. Bockelmann, E. J. G. Peterman, and G. J. L. Wuite, Quantifying how DNA stretches, melts and changes twist under tension, Nat. Phys. 7, 731 (2011).
M. K. Kuimova, Mapping viscosity in cells using molecular rotors, Phys. Chem. Chem. Phys. 14, 12671 (2012).
E. C. Fieller, H. O. Hartley, and E. S. Pearson, Tests for rank correlation coefficients. I, Biometrika 44, 470 (1957).
J. F. Marko, Stretching must twist DNA, Europhys. Lett. 38, 183 (1997).
T. A. J. Duke, Molecular model of muscle contraction, Proc. Natl. Acad. Sci. 96, 2770 (1999).
J. Y. Lee, I. J. Finkelstein, L. K. Arciszewska, D. J. Sherratt, and E. C. Greene, Single-molecule imaging of FtsK translocation reveals mechanistic features of protein-protein collisions on DNA, Mol. Cell 54, 832 (2014).
T. C. B. McLeish, Tube theory of entangled polymer dynamics, Adv. Phys. 51, 1379 (2002).
S. Weerakoon, and T. G. I. Fernando, A variant of Newton’s method with accelerated third-order convergence, Appl. Math. Lett. 13, 87 (2000).
B. Chen, Self-regulation of motor force through chemomechanical coupling in skeletal muscle contraction, J. Appl. Mech. 80, 051013 (2013).
B. Chen, and C. Dong, Modeling Deoxyribose Nucleic Acid as an elastic rod inlaid with fibrils, J. Appl. Mech. 81, 071005 (2014).
C. Dong, and B. Chen, Coupling of bond breaking with state transition leads to high apparent detachment rates of a single Myosin, J. Appl. Mech. 83, 051011 (2016).
X. Chen, and B. Chen, Simplified analysis for the association of a constrained receptor to an oscillating ligand, J. Appl. Mech. 83, 091006 (2016).
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This work was supported by the National Natural Science Foundation of China (Grant No. 11872334).
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Lu, D., Chen, B. Coordinated motion of molecular motors on DNA chains with branch topology. Acta Mech. Sin. 38, 621225 (2022). https://doi.org/10.1007/s10409-021-09045-x
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DOI: https://doi.org/10.1007/s10409-021-09045-x