不同体积分数二甲基亚砜对DNA变性的影响

doi:10.3976/j.issn.1002-4026.2022.03.016

Abstract

Abstract:

The effects of different volume fractions of dimethyl sulfoxide (DMSO) on plasmid and linear DNA denaturation were investigated using atomic force microscopy and dynamic light scattering. It was found that a low volume fraction of 1% DMSO solution can also induce local DNA denaturation, which can be directly observed by atomic force microscopy. Simultaneously, due to the limitations of plasmid DNA linking number and single-stranded DNA generation, atomic force microscopy and dynamic light scattering showed that DNA gradually forms a superhelix structure with an increase in the volume fraction of DMSO. The average particle size of pBR322 DNA, 5 000 base pair DNA, and λ-DNA decreased from about (474±10) nm, (554±11) nm, and (871±17) nm, respectively, in 0 DMSO solution to (257±8) nm, (282±18) nm, and (449±21) nm, respectively, in 10% DMSO solution.

Key words: :DNA, denaturation, DNA topology structure, organic denaturation reagent, particle size

CLC Number:

XU Min,WANG Yan-wei,YANG Guang-can. Effects of different volume fractions of dimethyl sulfoxide on DNA denaturation[J].Shandong Science, 2022, 35(3): 131-137.

Figures/Tables 9

Fig.1

Fig.2

Fig.3

Fig.4

Fig.5

Fig.6

Fig.7

Fig.8

Fig.9

References 24

[1]	TEMPESTINI A, CASSINA V, BROGIOLI D, et al. Magnetic tweezers measurements of the nanomechanical stability of DNA against denaturation at various conditions of pH and ionic strength[J]. Nucleic Acids Research, 2013, 41(3): 2009-2019. DOI: 10.1093/nar/gks1206. doi: 10.1093/nar/gks1206
[2]	STRIDER W, CAMIEN M N, WARNER R C. Renaturation of denatured, covalently closed circular DNA[J]. Journal of Biological Chemistry, 1981, 256(15): 7820-7829. DOI: 10.1016/S0021-9258(18)43352-2. doi: 10.1016/S0021-9258(18)43352-2
[3]	HAMMOUDA B, WORCESTER D. The denaturation transition of DNA in mixed solvents[J]. Biophysical Journal, 2006, 91(6): 2237-2242. DOI: 10.1529/biophysj.106.083691. doi: 10.1529/biophysj.106.083691
[4]	REHMAN S U, SARWAR T, HUSAIN M A, et al. Studying non-covalent drug-DNA interactions[J]. Archives of Biochemistry and Biophysics, 2015, 576: 49-60. DOI: 10.1016/j.abb.2015.03.024. doi: 10.1016/j.abb.2015.03.024
[5]	NAKANO S I, SUGIMOTO N. The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents[J]. Biophysical Reviews, 2016, 8(1): 11-23.DOI: 10.1007/s12551-015-0188-0. doi: 10.1007/s12551-015-0188-0
[6]	HAMMOUDA B. Insight into the denaturation transition of DNA[J]. International Journal of Biological Macromolecules, 2009, 45(5): 532-534. DOI: 10.1016/j.ijbiomac.2009.09.002. doi: 10.1016/j.ijbiomac.2009.09.002
[7]	YAN L F, IWASAKI H. Thermal denaturation of plasmid DNA observed by atomic force microscopy[J]. Japanese Journal of Applied Physics, 2002, 41(12): 7556-7559. DOI: 10.1143/jjap.41.7556. doi: 10.1143/jjap.41.7556
[8]	THEODORAKOPOULOS N, DAUXOIS T, PEYRARD M. Order of the phase transition in models of DNA thermal denaturation[J]. Physical Review Letters, 2000, 85(1): 6-9. DOI: 10.1103/PhysRevLett.85.6. doi: 10.1103/PhysRevLett.85.6
[9]	YU Z W, QUINN P J. Dimethyl sulphoxide: A review of its applications in cell biology[J]. Bioscience Reports, 1994, 14(6): 259-281. DOI: 10.1007/BF01199051. doi: 10.1007/BF01199051
[10]	WANG X F, LIM H J, SON A. Characterization of denaturation and renaturation of DNA for DNA hybridization[J]. Environmental Health and Toxicology, 2014, 29: e2014007. DOI: 10.5620/eht.2014.29.e2014007. doi: 10.5620/eht.2014.29.e2014007
[11]	WANG X F, SON A. Effects of pretreatment on the denaturation and fragmentation of genomic DNA for DNA hybridization[J]. Environmental Science Processes & Impacts, 2013, 15(12): 2204-2212. DOI: 10.1039/c3em00457k. doi: 10.1039/c3em00457k
[12]	KASHINO G, LIU Y, SUZUKI M, et al. An alternative mechanism for radioprotection by dimethyl sulfoxide; possible facilitation of DNA double-strand break repair[J]. Journal of Radiation Research, 2010, 51(6): 733-740. DOI: 10.1269/jrr.09106. doi: 10.1269/jrr.09106
[13]	NODA M, MA Y, YOSHIKAWA Y, et al. A single-molecule assessment of the protective effect of DMSO against DNA double-strand breaks induced by photo-and γ-ray-irradiation, and freezing[J]. Scientific Reports, 2017, 7: 8557. DOI: 10.1038/s41598-017-08894-y. doi: 10.1038/s41598-017-08894-y
[14]	JIA Z Q, ZHU H, LI Y B, et al. Potent inhibition of peroxynitrite-induced DNA strand breakage and hydroxyl radical formation by dimethyl sulfoxide at very low concentrations[J]. Experimental Biology and Medicine (Maywood, N J), 2010, 235(5): 614-622. DOI: 10.1258/ebm.2010.009368. doi: 10.1258/ebm.2010.009368
[15]	TUNÇER S, GURBANOV R, SHERAJ I, et al. Low dose dimethyl sulfoxide driven gross molecular changes have the potential to interfere with various cellular processes[J]. Scientific Reports, 2018, 8: 14828. DOI: 10.1038/s41598-018-33234-z. doi: 10.1038/s41598-018-33234-z
[16]	QIU S X, WANG Y W, CAO B Z, et al. The suppression and promotion of DNA charge inversion by mixing counterions[J]. Soft Matter, 2015, 11(20): 4099-4105. DOI: 10.1039/c5sm00326a. doi: 10.1039/c5sm00326a
[17]	GAO T Y, ZHANG W, WANG Y W, et al. DNA compaction and charge neutralization regulated by divalent ions in very low pH solution[J]. Polymers, 2019, 11(2): 337. DOI: 10.3390/polym11020337. doi: 10.3390/polym11020337
[18]	LIU Y F, RAN S Y. Divalent metal ions and intermolecular interactions facilitate DNA network formation[J]. Colloids and Surfaces B: Biointerfaces, 2020, 194: 111117. DOI: 10.1016/j.colsurfb.2020.111117. doi: 10.1016/j.colsurfb.2020.111117
[19]	MA F Q, WANG Y W, YANG G C. The modulation of chitosan-DNA interaction by concentration and pH in solution[J]. Polymers, 2019, 11(4): 646. DOI: 10.3390/polym11040646. doi: 10.3390/polym11040646
[20]	郭子龙, 王艳伟, 杨光参. 铁离子引起的DNA电荷逆转和凝聚[J]. 山东科学, 2016, 29(4): 93-98. DOI: 10.3976/j.issn.1002-4026.2016.04.018. doi: 10.3976/j.issn.1002-4026.2016.04.018
[21]	李聪聪, 杨光参, 王艳伟. 不同价态的阴离子在DNA凝聚效应中的抑制作用[J]. 山东科学, 2020, 33(5): 119-126.
[22]	CHEN B T, WANG Y W, YANG G C. The promotion and suppression of DNA charge neutralization by the cosolute ectoine[J]. RSC Advances, 2019, 9(70): 41050-41057. DOI: 10.1039/c9ra09355a. doi: 10.1039/c9ra09355a
[23]	BAUER W R, LUND R A, WHITE J H. Twist and writhe of a DNA loop containing intrinsic bends[J]. PNAS, 1993, 90(3): 833-837. DOI: 10.1073/pnas.90.3.833. doi: 10.1073/pnas.90.3.833
[24]	CRICK F H. Linking numbers and nucleosomes[J]. PNAS, 1976, 73(8): 2639-2643.DOI: 10.1073/pnas.73.8.2639. doi: 10.1073/pnas.73.8.2639

Metrics

Comments

Recommended 0

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0), which permits third parties to freely share (i.e., copy and redistribute the material in any medium or format) and adapt (i.e., remix, transform, or build upon the material) the articles published in this journal, provided that appropriate credit is given, a link to the license is provided, and any changes made are indicated. The material may not be used for commercial purposes. For details of the CC BY-NC 4.0 license, please visit: https://creativecommons.org/licenses/by-nc/4.0

Effects of different volume fractions of dimethyl sulfoxide on DNA denaturation

RichHTML

PDF (PC)

Like

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 9

References 24

Related Articles 1

Metrics

Comments

Recommended 0