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Avidin is a common basic protein, widely used for connecting DNA and modified surface in single-molecule techniques of biophysics, and it can also be used as a DNA vector in gene therapy. Avidin is highly positively charged and can condense DNA in solution. Understanding the physical mechanism of its condensing DNA is a key factor to promote avidin-DNA complex to be used for many purposes, such as a probe of biomacromlecules, signal enhancer or carrier of disease diagnosis.In the present study, we use atomic force microscope (AFM), dynamic light scattering (DLS), and single molecular magnetic tweezers (MT) to systematically investigate the interaction between DNA and avidin and the underlying mechanism of DNA condensation by avidin. The conformation of DNA-avidin complex is observed and measured by AFM and we find that the condensation includes two types: one is toroidal condensation of DNA induced by avidin, the other is the condensing structure by avidin compaction. Quantitative analysis shows that the size of avidin-DNA complex decreases monotonically with the concentration of avidin increasing. However, when the concentration of avidin reaches up to a critical value of 2 ngL-1, the size of complex begins to increase suddenly with avidin concentration increasing. The phenomenon is also confirmed by the corresponding DLS measurements. For example, when the concentration of avidin increases from 0 to 2 ngL-1, the size of condensed avidin-DNA complex reduces from 170 nm to about 125 nm. In the mean while, its electrophoretic mobility changes from -2.76 (10-4cm2V-1s-1) to -0.1 (10-4 cm2V-1s-1). The negative charge of DNA is mostly neutralized by avidin. From their force spectroscopy measured by MT, it is found that the extension of DNA varies almost linearly and a few stairlike jumps appear occasionally. For example, its characteristic trend is quite similar to the one by histones. The condensing force of DNA by avidin grows up with the concentration of avidin increasing. The statistics of force-extension curves by MT shows that the peak of unraveling steps of avidin-DNA complex is around 160 nm, which corresponds to the typical toroidal structure of DNA.In DNA condensation by avidin, electrostatic interaction plays a key role due to the neutralization of negatively charged phosphate groups of DNA by cationic avidin. From the comprehensive data by AFM, DLS and MT, we conclude that the process of DNA condensation induced by avidin consists of two mechnisms: the predominant DNA-avidin electrostatic attraction and the ancillary avidin aggregation.
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Keywords:
- DNA condensation /
- avidin /
- magnetic tweezers /
- atomic force microscope
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[21] Bigini P, Previdi S, Casarin E, Silvestri D, Violatto M B, Facchin S, Sitia L, Rosato A, Zuccolotto G, Realdon N, Fiordaliso F, Salmona M, Morpurgo M 2013 ACS Nano. 8 175
[22] Buda A, Facchin S, Dassie E, Casarin E, Jepson M A, Neumann H, Hatem G, Realdon S, D'Inc R, Sturniolo G C, Morpurgo M 2015 Int. J. Nanomed. 10 399
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[25] Wang Y W, Ran S Y, Yang G C 2014 Sci. Rep. 4 15040
[26] Fu W B, Wang X L, Zhang X H, Ran S Y, Yan J, Li M 2006 J. Am. Chem. Soc. 128 15040
[27] Liu Y Y, Dou S X, Wang P Y, Xie P, Wang W C 2005 Acta Phys. Sin. 54 622 (in Chinese) [刘玉颖, 窦硕星, 王鹏业, 谢平, 王渭池 2005 物理学报 54 622]
[28] Ran S Y, Wang X L, Fu W B, Lai Z H, Wang W C, Liu X Q, Mai Z H, Li M 2006 Chin. Phys. Lett. 23 504
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[1] Schiessel H 2003 J. Phys.: Condens. Matter 15 R699
[2] Kubčkov A, Kř'ižek T, Coufal P, Vazdar M, Wernersson E, Heyda J, Jungwirth P 2012 Phys. Rev. Lett. 108 186101
[3] Cortini R, Car B R, Victor J M, Barbi M 2015 J. Chem. Phys. 142 105102
[4] Yoo J, Aksimentiev A 2016 Nucleic Acids Res. 44 2036
[5] Bloomfield V A 1997 Biopolymers 44 269
[6] Mohanty U, Ninham B W, Oppenheim I 1996 Proc. Natl. Acad. Sci. U.S.A. 93 4342
[7] Akinchina A, Linse P 2002 Macromolecules 35 5183
[8] Manning G S 1978 Q. Rev. Biophys. 11 179
[9] Besteman K, Van E K, Lemay S 2007 Nat. Phys. 3 641
[10] Grosberg A Y, Nguyen T T, Shklovskii B I 2002 Rev. Mod. Phys. 74 329
[11] Besteman K, Hage S, Dekker N H, Lemay S G 2007 Phys. Rev. Lett. 98 058103
[12] Lin Y, Yang G C, Wang Y W 2013 Acta Phys. Sin. 62 118702 (in Chinese) [林瑜, 杨光参, 王艳伟 2013 物理学报 62 118702]
[13] Murayama Y, Wada H, Sano M 2007 Europhys. Lett. 79 58001
[14] Zhang X H, Xiao B, Hou X M, Xu C H, Wang P Y, Li M 2009 Acta Phys. Sin. 58 4301 (in Chinese) [张兴华, 肖彬, 侯锡苗, 徐春华, 王鹏业, 李明 2009 物理学报 58 4301]
[15] Hou X M, Zhang X H, Wei K J, Ji C, Dou S X, Wang W C, Li M, Wang P Y 2010 Physics 39 108 (in Chinese) [侯锡苗, 张兴华, 魏孔吉, 季超, 窦硕星, 王渭池, 李明, 王鹏业 2010 物理 39 108]
[16] Wang Y W, Ran S Y, Man B Y, Yang G C 2011 Soft Matte 7 4425
[17] Qiu S X, Wang Y W, Cao B Z, Guo Z L, Chen Y, Yang G C 2015 Soft Matter 11 4099
[18] Fraenkel-Conrat H, Snell N S, Ducay E D 1952 Arch. Biochem. Biophys. 39 80
[19] Pignatto M, Realdon N, Morpurgo M 2010 Bioconjugate Chem. 21 1254
[20] Morpurgo M, Facchin S, Pignatto M, Silvestri D, Casarin E, Realdon N 2012 Anal. Chem. 84 3433
[21] Bigini P, Previdi S, Casarin E, Silvestri D, Violatto M B, Facchin S, Sitia L, Rosato A, Zuccolotto G, Realdon N, Fiordaliso F, Salmona M, Morpurgo M 2013 ACS Nano. 8 175
[22] Buda A, Facchin S, Dassie E, Casarin E, Jepson M A, Neumann H, Hatem G, Realdon S, D'Inc R, Sturniolo G C, Morpurgo M 2015 Int. J. Nanomed. 10 399
[23] Morpurgo M, Radu A, Bayer E A, Wilchek M 2004 J. Mol. Recognit. 17 558
[24] Pastr D, Hamon L, Sorel I, Cam L E, Curmi P A, Pitrement O 2010 Langmuir 26 2618
[25] Wang Y W, Ran S Y, Yang G C 2014 Sci. Rep. 4 15040
[26] Fu W B, Wang X L, Zhang X H, Ran S Y, Yan J, Li M 2006 J. Am. Chem. Soc. 128 15040
[27] Liu Y Y, Dou S X, Wang P Y, Xie P, Wang W C 2005 Acta Phys. Sin. 54 622 (in Chinese) [刘玉颖, 窦硕星, 王鹏业, 谢平, 王渭池 2005 物理学报 54 622]
[28] Ran S Y, Wang X L, Fu W B, Lai Z H, Wang W C, Liu X Q, Mai Z H, Li M 2006 Chin. Phys. Lett. 23 504
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