A multi-field approach to DNA condensation

doi:10.1088/1674-1056/24/12/128702

Abstract

DNA condensation is an important process in many fields including life sciences, polymer physics, and applied technology. In the nucleus, DNA is condensed into chromosomes. In polymer physics, DNA is treated as a semi-flexible molecule and a polyelectrolyte. Many agents, including multi-valent cations, surfactants, and neutral poor solvents, can cause DNA condensation, also referred to as coil-globule transition. Moreover, DNA condensation has been used for extraction and gene delivery in applied technology. Many physical theories have been presented to elucidate the mechanism underlying DNA condensation, including the counterion correlation theory, the electrostatic zipper theory, and the hydration force theory. Recently several single-molecule studies have focused on DNA condensation, shedding new light on old concepts. In this document, the multi-field concepts and theories related to DNA condensation are introduced and clarified as well as the advances and considerations of single-molecule DNA condensation experiments are introduced.

Keywords: DNA condensation coil-globule transition polyelectrolyte Manning theory counterion correlation hydration force single-molecule magnetic tweezers

Received: 22 January 2015
Revised: 24 March 2015
Accepted manuscript online:

PACS:	87.14.gk	(DNA)
	87.15.hp	(Conformational changes)
	82.37.Rs	(Single molecule manipulation of proteins and other biological molecules)
	82.35.Rs	(Polyelectrolytes)

Fund:

Project supported by the National Natural Science Foundation of China (Grant Nos. 21204065 and 20934004) and the Natural Science Foundation of Zhejiang Province, China (Grant No. Y4110357).

Corresponding Authors: Ran Shi-Yong
E-mail: syran@wzu.edu.cn

Cite this article:

Ran Shi-Yong (冉诗勇), Jia Jun-Li (贾俊丽) A multi-field approach to DNA condensation 2015 Chin. Phys. B 24 128702

[1]	Robert F W 2001 Molecular Biology: Mcgraw-Hill Companies
[2]	Bloomfield V A 1991 Biopolymers 31 1471
[3]	Lerman L 1971 Proc. Nat. Acad. Sci. 68 1886
[4]	Lasic D D 1997 Liposomes in gene delivery: CRC
[5]	Bloomfield V A 1997 Biopolymers 44 269
[6]	Bloomfield V A 1996 Curr. Opin. Struct. Biol. 6 334
[7]	Grosberg A Y, Nguyen T T and Shklovskii B I 2002 Rev. Mod. Phys. 74 329
[8]	Teif V B and Bohinc K 2011 Prog. Biophys. Mol. Bio. 105 208
[9]	Zhou T, Llizo A, Wang C, Xu G Y and Yang Y L 2013 Nanoscale 5 8288
[10]	Iwaki T, Saito T and Yoshikawa K 2007 Coll. Surf. B: Biointerfaces 56 126133
[11]	Jan L, Sebastian D, Rhiju D and Daniel H 2014 Ann. Rev. Biochem. 83 813
[12]	Kornyshev A A 2010 Phys. Chem. Chem. Phys. 12 12352
[13]	Devries R 2010 Biochimie 92 1715
[14]	Marko J F and Cocco S 2003 Physics World 3 37
[15]	Marko J F and Siggia E D 1995 Macromolecules 28 8759
[16]	Schiessel H 2003 J. Phys.: Condens. Matter 15 699
[17]	Pelta J, Livolant F and Sikorav J L 1996 J. Biochem. 271 5656
[18]	Nguyen T T, Rouzina I and Shklovskii B I 2000 J. Chem. Phys. 112 2562
[19]	Andrushchenko V, van de Sande H and Wieser H 2003 Biopolymers 69 529
[20]	Shklovskii B I 1999 Phys. Rev. E 60 5802
[21]	Hsiao P Y 2008 J. Phys. Chem. B 112 7347
[22]	Walter N G, Huang C Y, Manzo A J and Sobhy M A 2008 Nat. Meth. 5 475
[23]	Ran S Y, Sun B and Li M 2007 Physics 36 228 (in Chinese)
[24]	Deniz A A, Mukhopadhyay S and Lemke E A 2008 J. R. Soc. Interface 5 15
[25]	Zhang C and Vander Maarel J R C 2008 J. Phys. Chem. B 112 3552
[26]	Wang Y W, Ran S Y, Man B Y and Yang G C 2011 Soft Matter 7 4425
[27]	Mel'nikov S M, Khan M O, Lindman B and Jonsson B 1999 J. Am. Chem. Soc. 121 1130
[28]	Cheng C and Ran S Y 2014 Sci. World J. 2014 863049
[29]	Toma A C, Frutos M, Livolant F and Raspaud E 2009 Biomacromolecules 10 2129
[30]	Vilfan I D, Conwell C C, Sarkar T and Hud N V 2006 Biochemistry 45 8174
[31]	Ran S Y, Wang Y W, Yang G C and Zhang L X 2011 J. Phys. Chem. B 115 4568
[32]	Golan R, Pietrasanta L I, Hsieh W and Hansma H G 1999 Biochemistry 38 14069
[33]	Guo X, Cui B, Li Y and Ding J 2012 J. Polym. Sci. Polym. Chem. 50 17401745
[34]	Tan Z J, Chen S J 2006 Nucleic Acids Res. 34 6629
[35]	Tan Z J, Chen S J 2006 Biophys.J. 90 1175
[36]	Chai A H, Ran S Y, Zhang D, Jiang Y W, Yang G C and Zhang L X 2013 Chin. Phys. B 22 098701
[37]	Victor J M 1991 J. Chem. Phys. 95 600
[38]	Fixman M 1979 J. Chem. Phys. 70 4995
[39]	Lamm G and Pack G R 2010 Biopolymers 93 619
[40]	Manning G S 1979 Accounts Chem. Res. 12 443449
[41]	Manning G S 1978 Q. Rev. Biophys. 11 179
[42]	Manning G S 1969 J. Chem. Phys. 51 924
[43]	Rouzina I and Bloomfield V A 1996 J. Phys. Chem. 100 9977
[44]	Nguyen T and Shklovskii B I 2001 J. Chem. Phys. 114 5905
[45]	Leikin S, Parsegian V A, Rau D C and Rand R P 1993 Ann. Rev. Phys. Chem. 44 369
[46]	Kornyshev A and Leikin S 1989 Phys. Rev. A 40 6431
[47]	Kornyshev A and Leikin S 1999 Phys. Rev. Lett. 82 4138
[48]	Dobrynin A and Rubinstein M 2005 Prog. Poly. Sci. 30 10491118
[49]	Mcintosh D B, Ribeck N and Saleh O A 2009 Phys. Rev. E 80 041803
[50]	Yoshikawa K, Takahashi M, Vasilevskaya V V, Khokhlov A R 1996 Phys. Rev. Lett. 76 3029
[51]	Zhang R and Shklovskii B I 2005 Physica A 349 563
[52]	Mamasakhlisov Y S, Todd B A, Badasyan A V, Mkrtchyan A V, Morozov V F and Parsegian V A 2009 Phys. Rev. E 80 031915
[53]	Kulic I M and Schiessel H 2004 Phys. Rev. Lett. 92 4
[54]	Ubbink J and Odijk T 1995 Biophys. J. 68 54
[55]	Miller I, Keentok M, Pereira G and Williams D 2005 Phys. Rev. E 71 031802
[56]	Levin Y 2002 Rep. Prog. Phys. 65 1577
[57]	Rau D C, Lee B and Parsegian V A 1984 Proc. Nat. Acad. Sci. 81 2621
[58]	Israelachvili J and Wennerström H 1996 Nature 379 219
[59]	Parsegian V A and Zemb T 2011 Curr. Opin. Colloid Interface Sci. 16 618624
[60]	Yoshikawa K, Takahashi M, Vasilevskaya V V and Khokhlov A R 1996 Phys. Rev. Lett. 76 3029
[61]	Ueda M and Yoshikawa K 1996 Phys. Rev. Lett. 77 2133
[62]	Lifshitz I M, Grosberg A Y and Khokhlov A R 1978 Rev. Mod. Phys. 50 683
[63]	Baumann C G, Smith S B, Bloomfield V A and Bustamante C 1997 Proc. Nat. Acad. Sci. 94 6185
[64]	Ran S Y 2012 Acta Phys. Sin. 61 170503 (in Chinese)
[65]	Hays J B, Magar M E and Zimm B H 1969 Biopolymers 8 531
[66]	Stefan M I and Nov'ere N L 2013 PLos Comput. Biology 9 e1003106
[67]	Ran S Y, Wang X L, Fu W B, Wang W C and Li M 2008 Chin. Sci. Bull. 53 836
[68]	Besteman K, Van Eijk K and Lemay S G 2007 Nat. Phys. 3 641
[69]	Todd B A and Rau D C 2008 Nucleic Acids Res. 36 501
[70]	Todd B A, Adrian P V, Shirahata A, Thomas T J and Rau D C 2008 Biophys. J. 94 4775
[71]	Cheng C, Jia J L and Ran S Y 2015 Soft Matter 11 3927

[1]	Current spin polarization of a platform molecule with compression effect Zhi Yang(羊志), Feng Sun(孙峰), Deng-Hui Chen(陈登辉), Zi-Qun Wang(王子群), Chuan-Kui Wang(王传奎), Zong-Liang Li(李宗良), and Shuai Qiu(邱帅). Chin. Phys. B, 2022, 31(7): 077202.
[2]	Enhancing the thermoelectric performance through the mutual interaction between conjugated polyelectrolytes and single-walled carbon nanotubes Shuxun Wan(万树勋), Zhongming Chen(陈忠明), Liping Hao(郝丽苹), Shichao Wang(王世超), Benzhang Li(李本章), Xiao Li(黎潇), Chengjun Pan(潘成军), and Lei Wang(王雷). Chin. Phys. B, 2022, 31(2): 028104.
[3]	Single-molecular methodologies for the physical biology of protein machines Shuang Wang(王爽), Ying Lu(陆颖), and Ming Li(李明). Chin. Phys. B, 2022, 31(12): 128702.
[4]	Equilibrium folding and unfolding dynamics to reveal detailed free energy landscape of src SH3 protein by magnetic tweezers Huanhuan Su(苏环环), Hao Sun(孙皓), Haiyan Hong(洪海燕), Zilong Guo(郭子龙), Ping Yu(余平), and Hu Chen(陈虎). Chin. Phys. B, 2021, 30(7): 078201.
[5]	Bias-controlled spin memory and spin injector scheme in the tunneling junction with a single-molecule magnet Zheng-Zhong Zhang(张正中) and Hao Liu(刘昊). Chin. Phys. B, 2021, 30(6): 067501.
[6]	Morphologies of a spherical bimodal polyelectrolyte brush induced by polydispersity and solvent selectivity Qing-Hai Hao(郝清海) and Jie Cheng(成洁). Chin. Phys. B, 2021, 30(6): 068201.
[7]	Theoretical design of single-molecule NOR and XNOR logic gates by using transition metal dibenzotetraaza[14]annulenes Zi-Qun Wang(王子群), Fei Tang(唐菲), Mi-Mi Dong(董密密), Ming-Lang Wang(王明郎), Gui-Chao Hu(胡贵超), Jian-Cai Leng(冷建材), Chuan-Kui Wang(王传奎), Guang-Ping Zhang(张广平). Chin. Phys. B, 2020, 29(6): 067202.
[8]	Interaction between human telomeric G-quadruplexes characterized by single molecule magnetic tweezers Yi-Zhou Wang(王一舟), Xi-Miao Hou(侯锡苗), Hai-Peng Ju(车海鹏), Xue Xiao(肖雪), Xu-Guang Xi(奚绪光), Shuo-Xing Dou(窦硕星), Peng-Ye Wang(王鹏业), Wei Li(李伟). Chin. Phys. B, 2018, 27(6): 068701.
[9]	Bio-macromolecular dynamic structures and functions, illustrated with DNA, antibody, and lipoprotein Lu Gou(缑璐), Taoli Jin(金桃丽), Shuyu Chen(陈淑玉), Na Li(李娜), Dongxiao Hao(郝东晓), Shengli Zhang(张胜利), Lei Zhang(张磊). Chin. Phys. B, 2018, 27(2): 028708.
[10]	Molecular dynamics simulation of the response of bi-disperse polyelectrolyte brushes to external electric fields Fen Zhang(张芬), Huan-Da Ding(丁欢达), Chao Duan(段超), Shuang-Liang Zhao(赵双良), Chao-Hui Tong(童朝晖). Chin. Phys. B, 2017, 26(8): 088204.
[11]	Catch-bond behavior of DNA condensate under tension 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). Chin. Phys. B, 2015, 24(12): 128704.
[12]	A new manganese-based single-molecule magnet with a record-high antiferromagnetic phase transition temperature Cui Yan (崔岩), Li Yan-Rong (李艳荣), Li Rui-Yuan (李瑞元), Wang Yun-Ping (王云平). Chin. Phys. B, 2014, 23(6): 067504.
[13]	Mechano-chemical selections of two competitive unfolding pathways of a single DNA i-motif Xu Yue (徐悦), Chen Hu (陈虎), Qu Yu-Jie (璩玉杰), Artem K. Efremov, Li Ming (黎明), Ouyang Zhong-Can(欧阳钟灿) , Liu Dong-Sheng(刘冬生), Yan Jie (严洁). Chin. Phys. B, 2014, 23(6): 068702.
[14]	Self-consistent field theory of adsorption of flexible polyelectrolytes onto an oppositely charged sphere Tong Zhao-Yang (童朝阳), Zhu Yue-Jin (诸跃进), Tong Chao-Hui (童朝晖). Chin. Phys. B, 2014, 23(3): 038202.
[15]	Processes of DNA condensation induced by multivalent cations：Approximate annealing experiments and molecular dynamics simulations Chai Ai-Hua (柴爱华), Ran Shi-Yong (冉诗勇), Zhang Dong (张冬), Jiang Yang-Wei (蒋杨伟), Yang Guang-Can (杨光参), Zhang Lin-Xi (章林溪). Chin. Phys. B, 2013, 22(9): 098701.

No Suggested Reading articles found!

Viewed

Full text

Abstract

Cited

Metrics
Related Articles

A multi-field approach to DNA condensation

Cite this article:

Online attention