Catch-bond behavior of DNA condensate under tension

doi:10.1088/1674-1056/24/12/128704

中国物理B ›› 2015, Vol. 24 ›› Issue (12): 128704-128704.doi: 10.1088/1674-1056/24/12/128704

• SPECIAL TOPIC—8th IUPAP International Conference on Biological Physics • 上一篇下一篇

Catch-bond behavior of DNA condensate under tension

李伟^a, Wong Wei-Juan^b, Lim Ci-Ji^b, 车海鹏^a, 李明^a, 严洁^b, 王鹏业^a

a Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China;
b Department of Physics, National University of Singapore, Singapore 117542, and Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore

收稿日期:2015-04-09 修回日期:2015-07-13 出版日期:2015-12-05 发布日期:2015-12-05
通讯作者: Li Wei, Yan Jie, Wang Peng-Ye E-mail:weili007@iphy.ac.cn;phyyj@nus.edu.sg;pywang@iphy.ac.cn
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11104341, 11474346, 11274374, and 61275192), the National Key Basic Research Program of China (Grant No. 2013CB837200), and the Mechanobiology Institute at National University of Singapore. These authors are contributed equally to this work.

Catch-bond behavior of DNA condensate under tension

Li Wei (李伟)^a, Wong Wei-Juan^b, Lim Ci-Ji^b, Ju Hai-Peng (车海鹏)^a, Li Ming (李明)^a, Yan Jie (严洁)^b, Wang Peng-Ye (王鹏业)^a

a Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China;
b Department of Physics, National University of Singapore, Singapore 117542, and Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore

Received:2015-04-09 Revised:2015-07-13 Online:2015-12-05 Published:2015-12-05
Contact: Li Wei, Yan Jie, Wang Peng-Ye E-mail:weili007@iphy.ac.cn;phyyj@nus.edu.sg;pywang@iphy.ac.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11104341, 11474346, 11274374, and 61275192), the National Key Basic Research Program of China (Grant No. 2013CB837200), and the Mechanobiology Institute at National University of Singapore. These authors are contributed equally to this work.

摘要/Abstract

摘要： Toroid formation is an important mechanism underlying DNA condensation, which has been investigated extensively by single-molecule experiments in vitro. Here, the de-condensation dynamics of DNA condensates were studied using magnetic tweezers combined with Brownian dynamics simulations. The experimental results revealed a surprising non-monotonic dependence of the unfolding rate on the force applied under strong adhesion conditions, resembling the catch-bond behavior reported in the field of ligand-receptor interactions. Simulation results showed that the different unfolding pathways of DNA condensate under large forces derive from the force-dependent deformation of the DNA toroid, which explains the catch-bond behavior of DNA condensate in the magnetic tweezers experiments. These results challenge the universality of the regular toroidal DNA unwrapping mechanism and provide the most complete description to date of multivalent cation-dependent DNA unwrapping under tension.

关键词: DNA toroid, magnetic tweezers, catch bond

Abstract: Toroid formation is an important mechanism underlying DNA condensation, which has been investigated extensively by single-molecule experiments in vitro. Here, the de-condensation dynamics of DNA condensates were studied using magnetic tweezers combined with Brownian dynamics simulations. The experimental results revealed a surprising non-monotonic dependence of the unfolding rate on the force applied under strong adhesion conditions, resembling the catch-bond behavior reported in the field of ligand-receptor interactions. Simulation results showed that the different unfolding pathways of DNA condensate under large forces derive from the force-dependent deformation of the DNA toroid, which explains the catch-bond behavior of DNA condensate in the magnetic tweezers experiments. These results challenge the universality of the regular toroidal DNA unwrapping mechanism and provide the most complete description to date of multivalent cation-dependent DNA unwrapping under tension.

Key words: DNA toroid, magnetic tweezers, catch bond

中图分类号: (Dynamics of biomolecules)

87.15.H-

82.37.Rs (Single molecule manipulation of proteins and other biological molecules) 87.15.La (Mechanical properties) 87.16.Sr (Chromosomes, histones)

李伟, Wong Wei-Juan, Lim Ci-Ji, 车海鹏, 李明, 严洁, 王鹏业. Catch-bond behavior of DNA condensate under tension[J]. 中国物理B, 2015, 24(12): 128704-128704.

Li Wei (李伟), Wong Wei-Juan, Lim Ci-Ji, Ju Hai-Peng (车海鹏), Li Ming (李明), Yan Jie (严洁), Wang Peng-Ye (王鹏业). Catch-bond behavior of DNA condensate under tension[J]. Chin. Phys. B, 2015, 24(12): 128704-128704.

参考文献 22

[1]	Luger K, Mader A W, Richmond R K, Sargent D F and Richmond T J 1997 Nature 389 251
[2]	Ishihama A 2012 Proc. Jpn. Acad. Ser. B Phys. Biol. Sci. 88 485
[3]	Lim C J, Lee S Y, Teramoto J, Ishihama A and Yan J 2013 Nucleic Acids Res. 41 746
[4]	Wilson M E and Miller L K 1986 Virology 151 315
[5]	Liu Y, Wu J, Chen H, Hew C L and Yan J 2010 Virology 408 197
[6]	Besteman K, Hage S, Dekker N H and Lemay S G 2007 Phys. Rev. Lett. 98 058103
[7]	Parsegian V A, Rand R P and Rau D C 2000 Proc. Natl. Acad. Sci. USA 97 3987
[8]	Hud N V and Vilfan I D 2005 Annu. Rev. Biophys. Biomol. Struct. 34 295
[9]	Keyser U F, van Dorp S and Lemay S G 2010 Chem. Soc. Rev. 39 939
[10]	Yoshikawa Y, Yoshikawa K and Kanbe T 1999 Langmuir 15 4085.
[11]	Baumann C G, Bloomfield V A, Smith S B, Bustamante C, Wang M D and Block S M 2000 Biophys. J. 78 1965
[12]	Fu W B, Wang X L, Zhang X H, Ran S Y, Yan J and Li M 2006 J. Am. Chem. Soc. 128 15040
[13]	Todd B A and Rau D C 2008 Nucleic Acids Res. 36 501
[14]	Ranjith P, Yan J and Marko J F 2007 Proc. Natl. Acad. Sci. USA 104 13649
[15]	Li W, Wang P Y, Yan J and Li M 2012 Phys. Rev. Lett. 109 218102
[16]	Li W, Hou X M, Wang P Y, Xi X G and Li M 2013 J. Am. Chem. Soc. 135 6423
[17]	Ju H P, Zhang H Y, Li W and Wang P Y 2014 Sci. China-Phys. Mech. Astron. 57 2114
[18]	Marshall B T, Long M, Pier J W, Ygo T, McEver R P and Zhu C 2003 Nature 423 6936
[19]	Forero M, Thomas W E, Bland C, Nilson L M, Sokurenko E V and Vogel V 2004 Nano Lett. 4 1593
[20]	Evans E, Leung A, Heinrich V and Zhu C 2004 Proc. Natl. Acad, Sci. USA 101 11281
[21]	Liphardt J, Onoa B, Smith S B, Tinoco I Jr and Bustamante C 2001 Science 292 733
[22]	Zhang X, Chen H, Le S, Rouzinac I, Doyle P S and Yan J 2013 Proc. Natl. Acad, Sci. USA 110 3865

Catch-bond behavior of DNA condensate under tension

Catch-bond behavior of DNA condensate under tension

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