Please wait a minute...
Chin. Phys. B, 2021, Vol. 30(10): 106806    DOI: 10.1088/1674-1056/abf109
CONDENSED MATTER: STRUCTURAL, MECHANICAL, AND THERMAL PROPERTIES Prev   Next  

Oxidation degree dependent adsorption of ssDNA onto graphene-based surface

Huishu Ma(马慧姝)1,2, Jige Chen(陈济舸)1,4, Haiping Fang(方海平)3,4, and Xiaoling Lei(雷晓玲)3,†
1 Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China;
2 University of Chinese Academy of Sciences, Beijing 100049, China;
3 Department of Physics, East China University of Science and Technology, Shanghai 200237, China;
4 Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
Abstract  DNA/GO composite plays a significant role in the research field of biotechnology and nanotechnology, and attracts a great deal of interest. However, it is still unclear how the oxidation degree of the graphene-based surface affects the adsorption process of single-strand DNA (ssDNA). In this paper, based on the molecular dynamics simulations, we find that ssDNA molecule is absorbed on the GO surface in the most stable state with the oxidation degree around 15%. The microscopic mechanism is attributed to the van Der Walls and the electrostatic interactions between the ssDNA molecule and the graphene-based surface, which is accompanied with the π-π stacking and hydrogen bond formation. The number of π-π stacking between ssDNA and GO reaches the maximum value when the oxidation degree is around 15% among all the GO surfaces. Our simulation results also reveal the coexistence of stretched and curved configurations as well as the adsorption orientation of ssDNA on the GO surface. Furthermore, it is found that the absorbed ssDNA molecules are more likely to move on the graphene-based surface of low oxidation degree, especially on pristine graphene. Our work provides the physics picture of ssDNA's physisorption dynamics onto graphene-based surface and it is helpful in designing DNA/GO nanomaterials.
Keywords:  single-strand DNA (ssDNA)      molecular dynamics simulation      oxidation degrees      graphene-based surfaces  
Received:  07 January 2021      Revised:  04 March 2021      Accepted manuscript online:  23 March 2021
PACS:  68.43.Mn (Adsorption kinetics ?)  
  68.47.Gh (Oxide surfaces)  
  87.14.gk (DNA)  
  34.35.+a (Interactions of atoms and molecules with surfaces)  
Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 11305237 and 11974366), the Fundamental Research Funds for the Central Universities, China, the Natural Science Foundation of Shanghai, China (Grant No. 19ZR1463200), and the Key Research Program of Chinese Academy of Sciences (Grant No. QYZDJ-SSW-SLH053).
Corresponding Authors:  Xiaoling Lei     E-mail:  leixiaoling@ecust.edu.cn

Cite this article: 

Huishu Ma(马慧姝), Jige Chen(陈济舸), Haiping Fang(方海平), and Xiaoling Lei(雷晓玲) Oxidation degree dependent adsorption of ssDNA onto graphene-based surface 2021 Chin. Phys. B 30 106806

[1] Watson J D and Crick F H 1953 Nature 171 737
[2] Pray L 2008 Nature Education 1
[3] Liu Z, Liu B, Ding J and Liu J 2014 Anal. Bioanal. Chem. 406 6885
[4] Hu K, Lan D, Li X and Zhang S 2008 Anal. Chem. 80 9124
[5] Robinson D B, Persson H H J, Zeng H, Li G, Pourmand N, Sun S and Wang S X 2005 Langmuir 21 3096
[6] Song B, Cuniberti G, Sanvito S and Fang H 2012 Appl. Phys. Lett. 100 063101
[7] Morales-Narváez E and Merkoçi A 2019 Adv. Mater. 31 1805043
[8] Yang K, Feng L, Shi X and Liu Z 2013 Chem. Soc. Rev. 42 530
[9] Tang L, Wang Y and Li J 2015 Chem. Soc. Rev. 44 6954
[10] Kim J, Cote L J, Kim F, Yuan W, Shull K R and Huang J 2010 J. Am. Chem. Soc. 132 8180
[11] Lu N, Wang L, Lv M, Tang Z and Fan C 2019 Nano Res. 12 247
[12] Lu C, Huang Z, Liu B, Liu Y, Ying Y and Liu J 2017 Angew. Chem. Int. Edit. 56 6208
[13] Liu B and Liu J 2017 J. Am. Chem. Soc. 139 9471
[14] Geim A K 2009 Science 324 1530
[15] Rao C, Subrahmanyam K, Ramakrishna Matte H, Maitra U, Moses K and Govindaraj A 2011 Int. J. Mod. Phys. B 25 4107
[16] Nair R R, Blake P, Grigorenko A N, Novoselov K S, Booth T J, Stauber T, Peres N M and Geim A K 2008 Science 320 1308
[17] Qin Zhang H Z, Xin Lu Cheng 2018 Chin. Phys. B 27 27301
[18] Zheng Q, Geng Y, Wang S, Li Z and Kim J K 2010 Carbon 48 4315
[19] Pumera M 2013 Electrochem. Commun. 36 14
[20] Kemp K C, Seema H, Saleh M, Le N H, Mahesh K, Chandra V and Kim K S 2013 Nanoscale 5 3149
[21] Lei H, Mi L, Zhou X, Chen J, Hu J, Guo S and Zhang Y 2011 Nanoscale 3 3888
[22] Tu Y S, Zhao L, Sun J J, Wu Y Y, Zhou X J, Chen L, Lei X L, Fang H P and Shi G S 2020 Chin. Phys. Lett. 37 066803
[23] Lei H, Mi L, Zhou X, Chen J, Hu J, Guo S and Zhang Y 2011 Nanoscale 3 3888
[24] Tiwari J N, Kemp K C, Nath K, Tiwari R N, Nam H G and Kim K S 2013 ACS Nano 7 9223
[25] Shankla M and Aksimentiev A 2014 Nat. Commun. 5 5171
[26] Balapanuru J, Yang J X, Xiao S, Bao Q, Jahan M, Polavarapu L, Wei J, Xu Q H and Loh K P 2010 Angew. Chem. Int. Edit. 49 6549
[27] Park J S, Na H K, Min D H and Kim D E 2013 Analyst 138 1745
[28] Huang P J J and Liu J 2012 Anal. Chem. 84 4192
[29] Varghese N, Mogera U, Govindaraj A, Das A, Maiti P K, Sood A K and Rao C 2009 Chem. Phys. Chem. 10 206
[30] Manohar S, Mantz A R, Bancroft K E, Hui C Y, Jagota A and Vezenov D V 2008 Nano Lett. 8 4365
[31] Jin L, Yang K, Yao K, Zhang S, Tao H, Lee S T, Liu Z and Peng R 2012 ACS Nano 6 4864
[32] Patil A J, Vickery J L, Scott T B and Mann S 2009 Adv. Mater. 21 3159
[33] Zhao X 2011 J. Phys. Chem. C 115 6181
[34] Ma H, Xu Z, Fang H and Lei X 2020 Phys. Chem. Chem. Phys. 22 11740
[35] Lei X, Ma H and Fang H 2020 Nanoscale 12 6699
[36] Heerema S J and Dekker C 2016 Nat. Nanotechn. 11 127
[37] Lerf A, He H, Forster M and Klinowski J 1998 J. Phys. Chem. B 102 4477
[38] Gao W, Alemany L B, Ci L and Ajayan P M 2009 Nat. Chem. 1 403
[39] Pacilé D, Meyer J, Rodríguez A F, Papagno M, Gomez-Navarro C, Sundaram R, Burghard M, Kern K, Carbone C and Kaiser U 2011 Carbon 49 966
[40] Gómez-Navarro C, Meyer J C, Sundaram R S, Chuvilin A, Kurasch S, Burghard M, Kern K and Kaiser U 2010 Nano Lett. 10 1144
[41] Erickson K, Erni R, Lee Z, Alem N, Gannett W and Zettl A 2010 Adv. Mater. 22 4467
[42] Saxena S, Tyson T A and Negusse E 2010 J. Phys. Chem. Lett. 1 3433
[43] Novoselov K S, Geim A K, Morozov S V, Jiang D, Zhang Y, Dubonos S V, Grigorieva I V and Firsov A A 2004 Science 306 666
[44] Kronberg B, Stenius P and Igeborn G 1984 J. Coll. Inter. Sci. 102 418
[45] Kim H S, Farmer B L and Yingling Y G 2017 Adv. Mater. Inte. 4 1601168
[46] Yan H, Tao X, Yang Z, Li K, Yang H, Li A and Cheng R 2014 J. Hazard. Mater. 268 191
[47] Tan P, Bi Q, Hu Y, Fang Z, Chen Y and Cheng J 2017 Appl. Sur. Sci. 423 1141
[48] Tu Y, Lv M, Xiu P, Huynh T, Zhang M, Castelli M, Liu Z, Huang Q, Fan C and Fang H 2013 Nat. Nanotech. 8 594
[49] Kim H S, Farmer B L and Yingling Y G 2017 Adv. Mater. Inter. 4 1601168
[50] Yang J, Shi G, Tu Y and Fang H 2014 Angew. Chem. Int. Edit. 53 10190
[51] Hess B, Kutzner C, Van Der Spoel D and Lindahl E 2008 J. Chem. Theory Comput. 4 435
[52] Duan Y, Wu C, Chowdhury S, Lee M C, Xiong G, Zhang W, Yang R, Cieplak P, Luo R and Lee T 2003 J. Comput. Chem. 24 1999
[53] Ponomarev S Y, Thayer K M and Beveridge D L 2004 Proc. Nat. Acad. Sci. USA 101 14771
[54] Ricci C G, de Andrade A S, Mottin M and Netz P A 2010 J. Phys. Chem. B 114 9882
[55] Chen J, Chen L, Wang Y and Chen S 2014 J. Phys. D 47 505401
[56] Wu Y Y, Bao L, Zhang X and Tan Z J 2015 J. Chem. Phys. 142 125103
[57] Xu Z, Lei X, Tu Y, Tan Z J, Song B and Fang H 2017 Chem. Eur. J. 23 13100
[58] Zuo G, Zhou X, Huang Q, Fang H and Zhou R 2011 J. Phys. Chem. C 115 23323
[59] Titov A V, Král P and Pearson R 2009 ACS Nano. 4 229
[60] Patra N, Wang B and Král P 2009 Nano Lett. 9 3766
[61] Jorgensen W L, Chandrasekhar J, Madura J D, Impey R W and Klein M L 1983 J. Chem. Phys. 79 926
[62] Darden T, York D and Pedersen L 1993 J. Chem. Phys. 98 10089
[63] Zeng S, Chen L, Wang Y and Chen J 2015 J. Phys. D 48 275402
[64] Ranganathan S V, Halvorsen K, Myers C A, Robertson N M, Yigit M V and Chen A A 2016 Langmuir 32 6028
[1] Effect of spatial heterogeneity on level of rejuvenation in Ni80P20 metallic glass
Tzu-Chia Chen, Mahyuddin KM Nasution, Abdullah Hasan Jabbar, Sarah Jawad Shoja, Waluyo Adi Siswanto, Sigiet Haryo Pranoto, Dmitry Bokov, Rustem Magizov, Yasser Fakri Mustafa, A. Surendar, Rustem Zalilov, Alexandr Sviderskiy, Alla Vorobeva, Dmitry Vorobyev, and Ahmed Alkhayyat. Chin. Phys. B, 2022, 31(9): 096401.
[2] Strengthening and softening in gradient nanotwinned FCC metallic multilayers
Yuanyuan Tian(田圆圆), Gangjie Luo(罗港杰), Qihong Fang(方棋洪), Jia Li(李甲), and Jing Peng(彭静). Chin. Phys. B, 2022, 31(6): 066204.
[3] Investigation of the structural and dynamic basis of kinesin dissociation from microtubule by atomistic molecular dynamics simulations
Jian-Gang Wang(王建港), Xiao-Xuan Shi(史晓璇), Yu-Ru Liu(刘玉如), Peng-Ye Wang(王鹏业),Hong Chen(陈洪), and Ping Xie(谢平). Chin. Phys. B, 2022, 31(5): 058702.
[4] Evaluation on performance of MM/PBSA in nucleic acid-protein systems
Yuan-Qiang Chen(陈远强), Yan-Jing Sheng(盛艳静), Hong-Ming Ding(丁泓铭), and Yu-Qiang Ma(马余强). Chin. Phys. B, 2022, 31(4): 048701.
[5] Molecular dynamics simulations of A-DNA in bivalent metal ions salt solution
Jingjing Xue(薛晶晶), Xinpeng Li(李新朋), Rongri Tan(谈荣日), and Wenjun Zong(宗文军). Chin. Phys. B, 2022, 31(4): 048702.
[6] Evolution of defects and deformation mechanisms in different tensile directions of solidified lamellar Ti-Al alloy
Yutao Liu(刘玉涛), Tinghong Gao(高廷红), Yue Gao(高越), Lianxin Li(李连欣), Min Tan(谭敏), Quan Xie(谢泉), Qian Chen(陈茜), Zean Tian(田泽安), Yongchao Liang(梁永超), and Bei Wang(王蓓). Chin. Phys. B, 2022, 31(4): 046105.
[7] Molecular dynamics simulations on the wet/dry self-latching and electric fields triggered wet/dry transitions between nanosheets: A non-volatile memory nanostructure
Jianzhuo Zhu(朱键卓), Xinyu Zhang(张鑫宇), Xingyuan Li(李兴元), and Qiuming Peng(彭秋明). Chin. Phys. B, 2022, 31(2): 024703.
[8] Mechanism of microweld formation and breakage during Cu-Cu wire bonding investigated by molecular dynamics simulation
Beikang Gu(顾倍康), Shengnan Shen(申胜男), and Hui Li(李辉). Chin. Phys. B, 2022, 31(1): 016101.
[9] Non-monotonic temperature evolution of nonlocal structure-dynamics correlation in CuZr glass-forming liquids
W J Jiang(江文杰) and M Z Li(李茂枝). Chin. Phys. B, 2021, 30(7): 076102.
[10] Simulation and experiment of the cooling effect of trapped ion by pulsed laser
Chang-Da-Ren Fang(方长达人), Yao Huang(黄垚), Hua Guan(管桦), Yuan Qian(钱源), and Ke-Lin Gao(高克林). Chin. Phys. B, 2021, 30(7): 073701.
[11] Structure-based simulations complemented by conventional all-atom simulations to provide new insights into the folding dynamics of human telomeric G-quadruplex
Yun-Qiang Bian(边运强), Feng Song(宋峰), Zan-Xia Cao(曹赞霞), Jia-Feng Yu(于家峰), and Ji-Hua Wang(王吉华). Chin. Phys. B, 2021, 30(7): 078702.
[12] Coarse-grained simulations on interactions between spectrins and phase-separated lipid bilayers
Xuegui Lin(林雪桂), Xiaojie Chen(陈晓洁), and Qing Liang(梁清). Chin. Phys. B, 2021, 30(6): 068701.
[13] 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.
[14] Mechanical property and deformation mechanism of gold nanowire with non-uniform distribution of twinned boundaries: A molecular dynamics simulation study
Qi-Xin Xiao(肖启鑫), Zhao-Yang Hou(侯兆阳), Chang Li(李昌), and Yuan Niu(牛媛). Chin. Phys. B, 2021, 30(5): 056101.
[15] Multi-scale molecular dynamics simulations and applications on mechanosensitive proteins of integrins
Shouqin Lü(吕守芹), Qihan Ding(丁奇寒), Mingkun Zhang(张明焜), and Mian Long(龙勉). Chin. Phys. B, 2021, 30(3): 038701.
No Suggested Reading articles found!