Frontier of soft matter experimental technique: single molecular manipulation

Qian Hui; Chen Hu; Yan Jie

doi:10.7498/aps.65.188706

Abstract

Biomolecules such as proteins and nucleic acids play critical roles in biological processes. Traditional molecular biological experimental techniques usually measure the properties of an ensemble of molecules. The detected signal originates from the average response of large number of molecules, which often conceals the detailed dynamic information about conformational transitions. In addition, many biomolecules, such as cytoskeleton proteins and molecular motors, are subjected to stretching forces or are able to generate force while playing their biological roles in vivo. It is difficult for traditional experimental methods to be used to study the mechanical response of biomolecules. Single molecule manipulation techniques developed in recent twenty years are capable of manipulating and measuring the property of single molecule. Especially, the force response of single molecule can be measured in high precision. The most popular single molecular manipulation techniques are atomic force microscope, optical tweezers, and magnetic tweezers. Here we introduce the principle, capability of force and extension measurement, spatial and temporal resolutions of these three techniques. Applications of single molecular manipulation techniques in the conformation transitions of DNA, protein, and their interactions, and mechanism of molecular motors will be briefly reviewed. This review will provide a useful reference to biologists to learn and use single molecular manipulation techniques to solve biological problems.

Keywords:

Authors and contacts

1.
Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China;
2.
Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore;
3.
Department of Physics, National University of Singapore, Singapore 117542, Singapore;
4.
Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore

Corresponding author: Chen Hu, chenhu@xmu.edu.cn;phyyj@nus.edu.cn ; Yan Jie, chenhu@xmu.edu.cn;phyyj@nus.edu.cn

Funds: Project supported by the National Natural Science Foundation of China (Grant Nos. 11474237, 11574310), the 111 Project, China (Grant No. B16029), the Fundamental Research Funds for the Central Universities, China (Grant No. 2013121005), and the National Research Foundation of Singapore through the NRF Investigatorship and the Mechanobiology Institute (to JY).

References

[1]	Lewin B 2004 Genes VIII (Upper Saddle River: Pearson Prentice Hall)
[2]	Moore S W, Roca-Cusachs P, Sheetz M P 2010 Dev. Cell 19 194
[3]	Fersht A R 1995 Curr. Opin. Struct. Biol. 5 79
[4]	SantaLucia J, Hicks D 2004 Annu. Rev. Biophys. Biomol. Struct. 33 415
[5]	Visscher K, Block S M 2000 Nat. Cell Biol. 2 718
[6]	Zhu C 2014 Ann. Biomed. Eng. 42 388
[7]	Bustamante C, Cheng W, Mejia Y X 2011 Cell 144 480
[8]	Xie X S, Choi P J, Li G W, Lee N K, Lia G 2008 Annu. Rev. Biophys. 37 417
[9]	Bockelmann U 2004 Curr. Opin. Struct. Biol. 14 368
[10]	Strick T R, Dessinges M N, Charvin G, Dekker N H, Allemand J F, Bensimon D, Croquette V 2003 Rep. Prog. Phys. 66 1
[11]	Wang M D 1999 Curr. Opin. Biotechnol. 10 81
[12]	Neuman K C, Nagy A 2008 Nat. Methods 5 491
[13]	Huang B, Bates M, Zhuang X 2009 Annu. Rev. Biochem. 78 993
[14]	Huang B, Babcock H, Zhuang X 2010 Cell 143 1047
[15]	Roy R, Hohng S, Ha T 2008 Nat. Methods 5 507
[16]	Weiss S 1999 Science 283 1676
[17]	Rief M, Gautel M, Oesterhelt F, Fernandez J M, Gaub H E 1997 Science 276 1109
[18]	Smith S B, Cui Y, Bustamante C 1996 Science 271 795
[19]	Strick T R, Allemand J F, Bensimon D, Bensimon A, Croquette V 1996 Science 271 1835
[20]	Cluzel P, Lebrun A, Heller C, Lavery R, Viovy J L, Chatenay D, Caron F 1996 Science 271 792
[21]	Sitters G, Kamsma D, Thalhammer G, Ritsch-Marte M, Peterman E J G, Wuite G J L 2015 Nat. Methods 12 47
[22]	Fisher T E, Marszalek P E, Fernandez J M 2000 Nat. Struct. Biol. 7 719
[23]	Javadi Y, Fernandez J M, Perez-Jimenez R 2013 Physiology 28 9
[24]	Liu F, Ouyang Z C 2006 Phys. Rev. E 74 051904
[25]	Thomas W E, Vogel V, Sokurenko E 2008 Annu. Rev. Biophys. 37 399
[26]	Zhang X, Ma L, Zhang Y 2013 Yale J. Biol. Med. 86 367
[27]	Moffitt J R, Chemla Y R, Smith S B, Bustamante C 2008 Annu. Rev. Biochem. 77 205
[28]	Gosse C, Croquette V 2002 Biophys. J. 82 3314
[29]	Chen H, Chandrasekar S, Sheetz M P, Stossel T P, Nakamura F, Yan J 2013 Sci. Rep. 3 1642
[30]	Chen H, Fu H, Zhu X, Cong P, Nakamura F, Yan J 2011 Biophys. J. 100 517
[31]	Chen H, Zhu X, Cong P, Sheetz M P, Nakamura F, Yan J 2011 Biophys. J. 101 1231
[32]	Lipfert J, Skinner G M, Keegstra J M, Hensgens T, Jager T, Dulin D, Kber M, Yu Z, Donkers S P, Chou F C, Das R, Dekker N H 2014 Proc. Natl. Acad. Sci. USA 111 15408
[33]	Lipfert J, Kerssemakers J W J, Jager T, Dekker N H 2010 Nat. Methods 7 977
[34]	Lipfert J, Wiggin M, Kerssemakers J W J, Pedaci F, Dekker N H 2011 Nat. Commun. 2 439
[35]	Chen H, Yuan G, Winardhi R S, Yao M, Popa I, Fernandez J M, Yan J 2015 J. Am. Chem. Soc. 137 3540
[36]	Marko J F, Siggia E D 1995 Macromolecules 28 8759
[37]	Bustamante C, Marko J F, Siggia E D, Smith S 1994 Science 265 1599
[38]	Smith S B, Finzi L, Bustamante C 1992 Science 258 1122
[39]	Yan J, Marko J F 2003 Phys. Rev. E 68 011905
[40]	Cao Y, Li H 2007 Nat. Mater. 6 109
[41]	Cao Y, Li H 2011 Langmuir 27 1440
[42]	Fernandez J M, Li H 2004 Science 303 1674
[43]	Broekmans O D, King G A, Stephens G J, Wuite J G L 2016 Phys. Rev. Lett. 116 258102
[44]	Zhang X, Chen H, Le S, Rouzina I, Doyle P S, Yan J 2013 Proc. Natl. Acad. Sci. USA 110 3865
[45]	Zhang X, Chen H, Fu H, Doyle P S, Yan J 2012 Proc. Natl. Acad. Sci. USA 109 8103
[46]	Brower-Toland B, Wang M D 2004 Methods Enzymol. 376 62
[47]	Skoko D, Yan J, Johnson R C, Marko J F 2005 Phys. Rev. Lett. 95 208101
[48]	Xiao B, Johnson R C, Marko J F 2010 Nucleic Acids Res. 38 6176
[49]	Liu Y, Chen H, Kenney L J, Yan J 2010 Genes Dev. 24 339
[50]	King G M, Carter A R, Churnside A B, Eberle L S, Perkins T T 2009 Nano Lett. 9 1451
[51]	Edwards D T, Faulk J K, Sanders A W, Bull M S, Walder R, LeBlanc M A, Sousa M C, Perkins T T 2015 Nano. Lett. 15 7091
[52]	Neupane K, Manuel A P, Woodside M T 2016 Nat. Phys. 12 700
[53]	Comstock M J, Ha T, Chemla Y R 2011 Nat. Methods 8 335
[54]	Lee M, Kim S H, Hong S C 2010 Proc. Natl. Acad. Sci. USA 107 4985

Cited By

[1]	Lewin B 2004 Genes VIII (Upper Saddle River: Pearson Prentice Hall)
[2]	Moore S W, Roca-Cusachs P, Sheetz M P 2010 Dev. Cell 19 194
[3]	Fersht A R 1995 Curr. Opin. Struct. Biol. 5 79
[4]	SantaLucia J, Hicks D 2004 Annu. Rev. Biophys. Biomol. Struct. 33 415
[5]	Visscher K, Block S M 2000 Nat. Cell Biol. 2 718
[6]	Zhu C 2014 Ann. Biomed. Eng. 42 388
[7]	Bustamante C, Cheng W, Mejia Y X 2011 Cell 144 480
[8]	Xie X S, Choi P J, Li G W, Lee N K, Lia G 2008 Annu. Rev. Biophys. 37 417
[9]	Bockelmann U 2004 Curr. Opin. Struct. Biol. 14 368
[10]	Strick T R, Dessinges M N, Charvin G, Dekker N H, Allemand J F, Bensimon D, Croquette V 2003 Rep. Prog. Phys. 66 1
[11]	Wang M D 1999 Curr. Opin. Biotechnol. 10 81
[12]	Neuman K C, Nagy A 2008 Nat. Methods 5 491
[13]	Huang B, Bates M, Zhuang X 2009 Annu. Rev. Biochem. 78 993
[14]	Huang B, Babcock H, Zhuang X 2010 Cell 143 1047
[15]	Roy R, Hohng S, Ha T 2008 Nat. Methods 5 507
[16]	Weiss S 1999 Science 283 1676
[17]	Rief M, Gautel M, Oesterhelt F, Fernandez J M, Gaub H E 1997 Science 276 1109
[18]	Smith S B, Cui Y, Bustamante C 1996 Science 271 795
[19]	Strick T R, Allemand J F, Bensimon D, Bensimon A, Croquette V 1996 Science 271 1835
[20]	Cluzel P, Lebrun A, Heller C, Lavery R, Viovy J L, Chatenay D, Caron F 1996 Science 271 792
[21]	Sitters G, Kamsma D, Thalhammer G, Ritsch-Marte M, Peterman E J G, Wuite G J L 2015 Nat. Methods 12 47
[22]	Fisher T E, Marszalek P E, Fernandez J M 2000 Nat. Struct. Biol. 7 719
[23]	Javadi Y, Fernandez J M, Perez-Jimenez R 2013 Physiology 28 9
[24]	Liu F, Ouyang Z C 2006 Phys. Rev. E 74 051904
[25]	Thomas W E, Vogel V, Sokurenko E 2008 Annu. Rev. Biophys. 37 399
[26]	Zhang X, Ma L, Zhang Y 2013 Yale J. Biol. Med. 86 367
[27]	Moffitt J R, Chemla Y R, Smith S B, Bustamante C 2008 Annu. Rev. Biochem. 77 205
[28]	Gosse C, Croquette V 2002 Biophys. J. 82 3314
[29]	Chen H, Chandrasekar S, Sheetz M P, Stossel T P, Nakamura F, Yan J 2013 Sci. Rep. 3 1642
[30]	Chen H, Fu H, Zhu X, Cong P, Nakamura F, Yan J 2011 Biophys. J. 100 517
[31]	Chen H, Zhu X, Cong P, Sheetz M P, Nakamura F, Yan J 2011 Biophys. J. 101 1231
[32]	Lipfert J, Skinner G M, Keegstra J M, Hensgens T, Jager T, Dulin D, Kber M, Yu Z, Donkers S P, Chou F C, Das R, Dekker N H 2014 Proc. Natl. Acad. Sci. USA 111 15408
[33]	Lipfert J, Kerssemakers J W J, Jager T, Dekker N H 2010 Nat. Methods 7 977
[34]	Lipfert J, Wiggin M, Kerssemakers J W J, Pedaci F, Dekker N H 2011 Nat. Commun. 2 439
[35]	Chen H, Yuan G, Winardhi R S, Yao M, Popa I, Fernandez J M, Yan J 2015 J. Am. Chem. Soc. 137 3540
[36]	Marko J F, Siggia E D 1995 Macromolecules 28 8759
[37]	Bustamante C, Marko J F, Siggia E D, Smith S 1994 Science 265 1599
[38]	Smith S B, Finzi L, Bustamante C 1992 Science 258 1122
[39]	Yan J, Marko J F 2003 Phys. Rev. E 68 011905
[40]	Cao Y, Li H 2007 Nat. Mater. 6 109
[41]	Cao Y, Li H 2011 Langmuir 27 1440
[42]	Fernandez J M, Li H 2004 Science 303 1674
[43]	Broekmans O D, King G A, Stephens G J, Wuite J G L 2016 Phys. Rev. Lett. 116 258102
[44]	Zhang X, Chen H, Le S, Rouzina I, Doyle P S, Yan J 2013 Proc. Natl. Acad. Sci. USA 110 3865
[45]	Zhang X, Chen H, Fu H, Doyle P S, Yan J 2012 Proc. Natl. Acad. Sci. USA 109 8103
[46]	Brower-Toland B, Wang M D 2004 Methods Enzymol. 376 62
[47]	Skoko D, Yan J, Johnson R C, Marko J F 2005 Phys. Rev. Lett. 95 208101
[48]	Xiao B, Johnson R C, Marko J F 2010 Nucleic Acids Res. 38 6176
[49]	Liu Y, Chen H, Kenney L J, Yan J 2010 Genes Dev. 24 339
[50]	King G M, Carter A R, Churnside A B, Eberle L S, Perkins T T 2009 Nano Lett. 9 1451
[51]	Edwards D T, Faulk J K, Sanders A W, Bull M S, Walder R, LeBlanc M A, Sousa M C, Perkins T T 2015 Nano. Lett. 15 7091
[52]	Neupane K, Manuel A P, Woodside M T 2016 Nat. Phys. 12 700
[53]	Comstock M J, Ha T, Chemla Y R 2011 Nat. Methods 8 335
[54]	Lee M, Kim S H, Hong S C 2010 Proc. Natl. Acad. Sci. USA 107 4985

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Vol. 65, Issue 18 - 2016-09-20

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