Ionic liquid prolongs DNA translocation through graphene nanopores

被引:17
作者
Kulkarni, Mandar [1 ]
Mukherjee, Arnab [1 ]
机构
[1] Indian Inst Sci Educ & Res, Dept Chem, Pune 411008, Maharashtra, India
关键词
MOLECULAR-DYNAMICS; MECHANISM; TRANSPORT;
D O I
10.1039/c6ra07017e
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
The Lab-on-a-chip technology based on electrophoresis via nanopores is advancing at a fast pace to achieve low cost, fast, and reliable genomic sequencing. However, such a promising technique for genome sequencing is challenged by the uncontrolled faster DNA translocation speed and low signal to noise ratio. In this study, we have performed all-atom molecular dynamics simulations to investigate the effect of ionic liquid BMIM-Cl on dsDNA translocation through a nanopore grafted in a single layer of graphene. The presence of BMIM-Cl enhances DNA translocation time compared to the conventional KCl electrolyte solution. The study is capable of capturing the decelerating effect caused by ionic liquids. However, such a system has reduced ionic currents due to the low mobility of BMIM-Cl. The open pore current study demonstrated a pronounced effect of access resistance in such systems.
引用
收藏
页码:46019 / 46029
页数:11
相关论文
共 56 条
[1]   Slowing single-stranded DNA translocation through a solid-state nanopore by decreasing the nanopore diameter [J].
Akahori, Rena ;
Haga, Takanobu ;
Hatano, Toshiyuki ;
Yanagi, Itaru ;
Ohura, Takeshi ;
Hamamura, Hirotaka ;
Iwasaki, Tomio ;
Yokoi, Takahide ;
Anazawa, Takashi .
NANOTECHNOLOGY, 2014, 25 (27)
[2]   Imaging α-hemolysin with molecular dynamics:: Ionic conductance, osmotic permeability, and the electrostatic potential map [J].
Aksimentiev, A ;
Schulten, K .
BIOPHYSICAL JOURNAL, 2005, 88 (06) :3745-3761
[3]   Microscopic kinetics of DNA translocation through synthetic nanopores [J].
Aksimentiev, A ;
Heng, JB ;
Timp, G ;
Schulten, K .
BIOPHYSICAL JOURNAL, 2004, 87 (03) :2086-2097
[4]   MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH [J].
BERENDSEN, HJC ;
POSTMA, JPM ;
VANGUNSTEREN, WF ;
DINOLA, A ;
HAAK, JR .
JOURNAL OF CHEMICAL PHYSICS, 1984, 81 (08) :3684-3690
[5]   Association of ionic liquids in solution: a combined dielectric and conductivity study of [bmim][Cl] in water and in acetonitrile [J].
Bester-Rogac, Marija ;
Stoppa, Alexander ;
Hunger, Johannes ;
Hefter, Glenn ;
Buchner, Richard .
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2011, 13 (39) :17588-17598
[6]   Jamming - A new kind of phase transition? [J].
Biroli, Giulio .
NATURE PHYSICS, 2007, 3 (04) :222-223
[7]   Canonical sampling through velocity rescaling [J].
Bussi, Giovanni ;
Donadio, Davide ;
Parrinello, Michele .
JOURNAL OF CHEMICAL PHYSICS, 2007, 126 (01)
[8]   Ionic Current Inversion in Pressure-Driven Polymer Translocation through Nanopores [J].
Buyukdagli, Sahin ;
Blossey, Ralf ;
Ala-Nissila, T. .
PHYSICAL REVIEW LETTERS, 2015, 114 (08)
[9]  
Case J. T. B. D. A., 2015, AMBERTOOLS 15, V15
[10]   Groove Binding Mechanism of Ionic Liquids: A Key Factor in Long-Term Stability of DNA in Hydrated Ionic Liquids? [J].
Chandran, Aneesh ;
Ghoshdastidar, Debostuti ;
Senapati, Sanjib .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2012, 134 (50) :20330-20339