Ethylene glycol solution-induced DNA conformational transitions

doi:10.1088/1674-1056/27/11/113102

中国物理B ›› 2018, Vol. 27 ›› Issue (11): 113102-113102.doi: 10.1088/1674-1056/27/11/113102

• SPECIAL TOPIC—Recent advances in thermoelectric materials and devices • 上一篇下一篇

Ethylene glycol solution-induced DNA conformational transitions

Nan Zhang(张楠), Ming-Ru Li(李明儒), Feng-Shou Zhang(张丰收)

1 Key Laboratory of Beam Technology of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China;
2 Beijing Radiation Center, Beijing 100875, China;
3 Center of Theoretical Nuclear Physics, National Laboratory of Heavy Ion Accelerator of Lanzhou, Lanzhou 730000, China

收稿日期:2018-07-10 修回日期:2018-08-26 出版日期:2018-11-05 发布日期:2018-11-05
通讯作者: Feng-Shou Zhang E-mail:fszhang@bnu.edu.cn
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11635003, 11025524, and 11161130520), the National Basic Research Program of China (Grant No. 2010CB832903), and the European Commissions 7th Framework Programme (FP7-PEOPLE-2010-IRSES) (Grant No. 269131).

Ethylene glycol solution-induced DNA conformational transitions

Nan Zhang(张楠)¹, Ming-Ru Li(李明儒)², Feng-Shou Zhang(张丰收)^1,2,3

1 Key Laboratory of Beam Technology of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China;
2 Beijing Radiation Center, Beijing 100875, China;
3 Center of Theoretical Nuclear Physics, National Laboratory of Heavy Ion Accelerator of Lanzhou, Lanzhou 730000, China

Received:2018-07-10 Revised:2018-08-26 Online:2018-11-05 Published:2018-11-05
Contact: Feng-Shou Zhang E-mail:fszhang@bnu.edu.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11635003, 11025524, and 11161130520), the National Basic Research Program of China (Grant No. 2010CB832903), and the European Commissions 7th Framework Programme (FP7-PEOPLE-2010-IRSES) (Grant No. 269131).

摘要/Abstract

摘要：

We study the properties of the ethylene glycol solutions and the conformational transitions of DNA segment in the ethylene glycol solutions by molecular dynamics simulations based on GROMACS. The hydrogen network structures of water-water and ethylene glycol-water are reinforced by ethylene glycol molecules when the concentrations of the solutions increase from 0% to 80%. As illustrated by the results, conformation of the double-stranded DNA in ethylene glycol solutions, although more compact, is similar to the structure of DNA in the aqueous solutions. In contrast, the DNA structure is an A-B hybrid state in the ethanol/water mixed solution. A fraying of terminal base-pairs is observed for the terminal cytosine. The ethylene glycol molecules preferentially form a ring structure around the phosphate groups to influence DNA conformation by hydrogen interactions, while water molecules tend to reside in the grooves. The repulsion between the negatively charged phosphate groups is screened by ethylene glycol molecules, preventing the repulsion from unwinding and extending the helix and thus making the conformation of DNA more compact.

关键词: DNA conformational transitions, ethylene glycol, molecular dynamics simulations

Abstract:

Key words: DNA conformational transitions, ethylene glycol, molecular dynamics simulations

中图分类号: (Molecular dynamics and other numerical methods)

31.15.xv

36.20.Ey (Conformation (statistics and dynamics)) 36.20.Hb (Configuration (bonds, dimensions))

张楠, 李明儒, 张丰收. Ethylene glycol solution-induced DNA conformational transitions[J]. 中国物理B, 2018, 27(11): 113102-113102.

Nan Zhang(张楠), Ming-Ru Li(李明儒), Feng-Shou Zhang(张丰收). Ethylene glycol solution-induced DNA conformational transitions[J]. Chin. Phys. B, 2018, 27(11): 113102-113102.

参考文献 69

[1]	Chaplin M 2006 Nat. Rev. Mol. Cell Bio. 7 861 doi: 10.1038/nrm2021
[2]	Huang Z Q, Yang R Y, Jiang W Z and Zhang Q L 2016 Chin. Phys. Lett. 33 013101 doi: 10.1088/0256-307X/33/1/013101
[3]	Abolfath R M, van Duin A C T and Brabec T 2011 J. Phys. Chem. A 115 11045 doi: 10.1021/jp204894m
[4]	Wang X, Li M, Ye F F and Zhou X 2017 Acta Phys. Sin. 66 150201(inChinese)
[5]	Cyphers S, Ruff E F, Behr J M, Chodera J D and Levinson N M 2017 Nat. Chem. Biol. 13 402 doi: 10.1038/nchembio.2296
[6]	Ulrich K, Galvosas P, Kärger J and Grinberg F 2009 Phys. Rev. Lett. 102 037801 doi: 10.1103/PhysRevLett.102.037801
[7]	Fernández A 2014 J. Chem. Phys. 140 221102 doi: 10.1063/1.4882895
[8]	Lynden-Bell R M and Debenedetti P G 2005 J. Phys. Chem. B 109 6527
[9]	Ball P 2005 Nature 436 1084 doi: 10.1038/4361084a
[10]	Gu B, Zhang F S, Wang Z P and Zhou H Y 2008 Phys. Rev. Lett. 100 088104 doi: 10.1103/PhysRevLett.100.088104
[11]	Errington J R and Debenedetti P G 2001 Nature 409 318 doi: 10.1038/35053024
[12]	Chakraborty D and Wales D J 2017 Phys. Chem. Chem. Phys. 19 878 doi: 10.1039/C6CP06309H
[13]	Samanta S, Mukherjee S, Chakrabarti J and Bhattacharyya D 2009 J. Chem. Phys. 130 115103 doi: 10.1063/1.3078797
[14]	Banavali N K and Roux B 2005 J. Am. Chem. Soc. 127 6866 doi: 10.1021/ja050482k
[15]	Lange A W and Herbert J M 2009 J. Am. Chem. Soc. 131 3913 doi: 10.1021/ja808998q
[16]	Shen X, Atamas N A and Zhang F S 2012 Phys. Rev. E 85 051913 doi: 10.1103/PhysRevE.85.051913
[17]	Maaloum M, Beker A F and Muller P 2011 Phys. Rev. E 83 031903 doi: 10.1103/PhysRevE.83.031903
[18]	Wang Y W and Yang G C 2017 Chin. Phys. B 26 128706 doi: 10.1088/1674-1056/26/12/128706
[19]	Lindahl T 2016 Nat. Rev. Mol. Cell Bio. 17 335
[20]	Eliasson R, Hammarsten E and Lindahl T 1962 Biotechnol. Bioeng. 4 53 doi: 10.1002/bit.260040107
[21]	Anagnostopoulos C and Spizizen J 1961 J. Bacteriol. 81 741
[22]	Pogozelski W K and Tullius T D 1998 Chem. Rev. 98 1089 doi: 10.1021/cr960437i
[23]	Tullius T D and Greenbaum J A 2005 Curr. Opin. Chem. Biol. 9 127 doi: 10.1016/j.cbpa.2005.02.009
[24]	Aydogan B, Bolch W E, Swarts S G, Turner J E and David T 2008 Radiat. Res. 169 223 doi: 10.1667/RR0293.1
[25]	Friedland W, Jacob P, Paretzke H G, Merzagora M and Ottolenghi A1999 Radiat. Environ. Biophys. 38 39
[26]	Abolfath R M, Biswas P K, Rajnarayanam R, Brabec T, Kodym R andPapiez L 2012 J. Phys. Chem. A 116 3940 doi: 10.1021/jp300258n
[27]	Merzel F, Fontaine-Vive F, Johnson M R and Kearley G J 2007 Phys. Rev. E 76 031917 doi: 10.1103/PhysRevE.76.031917
[28]	Smirnov D A, Morley M, Shin E, Spielman R S and Cheung V G 2009 Nature 459 587 doi: 10.1038/nature07940
[29]	Rak J, Chomicz L, Wiczk J, Westphal K, Zdrowowicz M, Wityk P,Zyndul M, Makurat S and Golon Ł 2015 J. Phys. Chem. B 119 8227 doi: 10.1021/acs.jpcb.5b03948
[30]	Hamelberg D, McFail-Isom L, Williams L D and Wilson W D 2000 J. Am. Chem. Soc. 122 10513 doi: 10.1021/ja000707l
[31]	Korolev N, Lyubartsev A P, Laaksonen A and Nordenskiold L 2003 Nucleic Acids Res. 31 5971 doi: 10.1093/nar/gkg802
[32]	Noy A, Pérez A, Laughton C A and Orozco M 2007 Nucleic Acids Res. 35 3330 doi: 10.1093/nar/gkl1135
[33]	Pastor N 2005 Biophys. J. 88 3262 doi: 10.1529/biophysj.104.058339
[34]	Freddolino P L, Arkhipov A S, Larson S B, McPherson A and Schultem K 2006 Structure 14 437 doi: 10.1016/j.str.2005.11.014
[35]	Shen H, Cheng W and Zhang F S 2015 RSC Adv. 5 9627 doi: 10.1039/C4RA14739A
[36]	Martínez L, Andrade R, Birgin E G and Martínez J M 2009 J. Comput. Chem. 30 2157 doi: 10.1002/jcc.21224
[37]	Schweitzer B I, Mikita T, Kellogg G W, Gardner K H and Beardsley GP 1994 Biochemistry 33 11460 doi: 10.1021/bi00204a008
[38]	Dans P D, Danilāne L, Ivani I, Dršata T, Lankaš F, Hospital A, Walther J, Pujagut R I, Battistini F, Gelpí J L, Lavery R and Orozco M 2016 Nucleic Acids Res. 44 4052 doi: 10.1093/nar/gkw264
[39]	Pérez A, Luque F J and Orozco M 2007 J. Am. Chem. Soc. 129 14739 doi: 10.1021/ja0753546
[40]	Dršata T, Pérez A, Orozco M, Morozov A V, Šponer J and Lankaš F 2013 J. Chem Theory Comput. 9 707 doi: 10.1021/ct300671y
[41]	Mark P and Nilsson L 2002 J. Phys. Chem. B 106 9440 doi: 10.1021/jp025965e
[42]	Ivani I, Dans P D, Noy A, Pérez A, Faustino I, Hospital A, Walther J, Andrio P, Goñi R, Balaceanu A, Portella G, Battistini F, Gelpí J L,González C, Vendruscolo M, Laughton C A, Harris S A, Case D A and Orozco M 2016 Nat. Methods 13 55 doi: 10.1038/nmeth.3658
[43]	Darden T, York D and Pedersen L 1998 J. Chem. Phys. 98 10089
[44]	Allen M P and Tildesley D J 1989 Computer Simulation of Liquids (Oxford University Press)
[45]	Hess B, Bekker H, Berendsen H J C and Fraaije J G E M 1997 J. Comput. Chem. 18 1463 doi: 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
[46]	Berendsen H J C, Grigera J R and Straatsma T P 1987 J. Phys. Chem. 91 6269 doi: 10.1021/j100308a038
[47]	Zhang F S and Lynden-Bell R M 2005 Phy. Rev. E 71 021502 doi: 10.1103/PhysRevE.71.021502
[48]	Lindahl E, Hess B and van der Spoel D 2001 J. Mol. Model. 7 306 doi: 10.1007/s008940100045
[49]	Tsierkezos N G and Molinou I E 1998 J. Chem. Eng. Data 43 989 doi: 10.1021/je9800914
[50]	Nose S and Klein M L 1983 Mol. Phys. 50 1055 doi: 10.1080/00268978300102851
[51]	Berendsen H J C, Postma J P M, van Gunsteren W F, DiNola A andHaak J R 1984 J. Chem. Phys. 81 3684 doi: 10.1063/1.448118
[52]	Lavery R, Moakher M, Maddocks J H, Petkeviciute D and ZakrzewskaK 2009 Nucleic Acids Res. 37 5917 doi: 10.1093/nar/gkp608
[53]	Lavery R and Sklenar H 1989 J. Biomol. Struct. Dyn. 6 655 doi: 10.1080/07391102.1989.10507728
[54]	Kumar R, Schmidt J R and Skinner J L 2007 J. Chem. Phys. 126 204107 doi: 10.1063/1.2742385
[55]	Herskovits T T 1962 Arch. Biochem. Biophys. 97 474 doi: 10.1016/0003-9861(62)90110-8
[56]	Zgarbová M, Otyepka M, Šponer J, Lankaš F and Jurečka P 2014 J. Chem. Theory Comput. 10 3177 doi: 10.1021/ct500120v
[57]	Leroy J L, Kochoyan M, Huynh-Dinh T and Guéron M 1988 J. Mol. Biol. 200 223 doi: 10.1016/0022-2836(88)90236-7
[58]	Andreatta D, Sen S, Lustres J L P, Kovalenko S A, Ernsting N P, Murphy C J, Coleman R S and Berg M A 2006 J. Am. Chem. Soc. 128 6885 doi: 10.1021/ja0582105
[59]	McConnell K J and Beveridge D L 2000 J. Mol. Biol. 304 803 doi: 10.1006/jmbi.2000.4167
[60]	Dickerson R E, Drew H R, Conner B N, Wing R M, Fratini A V andKopka M L 1982 Science 216 475 doi: 10.1126/science.7071593
[61]	Allahyarov E, Gompper G and Lowen H 2013 Phys. Rev. E 69 041904
[62]	Saenger W, Hunter W N and Kennard O 1986 Nature 324 385 doi: 10.1038/324385a0
[63]	Hartmann B, Piazzola D and Lavery R 1993 Nucleic Acids Res. 21 561 doi: 10.1093/nar/21.3.561
[64]	Schwieters C D and Clore G M 2007 Biochemistry 46 1152 doi: 10.1021/bi061943x
[65]	Djuranovic D and Hartmann B 2004 Biopolymers 73 356 doi: 10.1002/bip.10528
[66]	Heddi B, Oguey C, Lavelle C, Foloppe N and Hartmann B 2010 Nucleic Acids Res. 38 1034 doi: 10.1093/nar/gkp962
[67]	Wecker K, Bonnet M C and Meurs E F 2002 Nucleic Acids Res. 30 4452 doi: 10.1093/nar/gkf559
[68]	Madhumalar A and Bansal M 2005 J. Biomol. Struct. Dyn. 23 13 doi: 10.1080/07391102.2005.10507043
[69]	Dans P D, Faustino I, Battistini F, Zakrzewska K, Lavery R and OrozcoM 2014 Nucleic Acids Res. 42 11304 doi: 10.1093/nar/gku809

Ethylene glycol solution-induced DNA conformational transitions

Ethylene glycol solution-induced DNA conformational transitions

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