Nanopore detection of DNA molecules in magnesium chloride solutions
© Zhang et al.; licensee Springer. 2013
Received: 3 April 2013
Accepted: 7 May 2013
Published: 20 May 2013
High translocation speed of a DNA strand through a nanopore is a major bottleneck fornanopore detection of DNA molecules. Here, we choose MgCl2 electrolyte assalt solution to control DNA mobility. Experimental results demonstrate that theduration time for straight state translocation events in 1 M MgCl2solution is about 1.3 ms which is about three times longer than that for thesame DNA in 1 M KCl solution. This is because Mg2+ ions caneffectively reduce the surface charge density of the negative DNA strands and thenlead to the decrease of the DNA electrophoretic speed. It is also found that theMg2+ ions can induce the DNA molecules binding together and reduce theprobability of straight DNA translocation events. The nanopore with small diametercan break off the bound DNA strands and increase the occurrence probability ofstraight DNA translocation events.
KeywordsNanopore DNA sequencing Translocation speed
Nanopore sensor, which is derived from the Coulter counter , has been utilized for detection and analysis of various single chargedmolecules [2–9]. Now, it is a widespread concern as a potential candidate to achieve the‘$1,000 genome’ goal set by the US National Institutes of Health due to itshigh speed and low cost performance. In a typical nanopore-sensing experiment, ions andbiomolecules are driven by an external transmembrane electric field. Biomolecule passagethrough the nanopore can cause a characteristic temporary blockade in the trans-poreionic current. Information of the biomolecules such as length, composition, andinteractions with other biomolecules can be extracted from the blockade ionic current.In order to get the structural information of a DNA strand at the single base level, abottleneck to break through is to control the DNA translocation speed through ananopore. Intuitively, we can change the applied voltage, salt concentration, viscosity,and electrolyte temperature to reduce the translocation speed . The side effect of this method is the reduction of the signal amplitude,which leads to more difficulties in capturing the very weak ionic current change . Another method is to apply a salt gradient on the electrolyte solutionacross the pore, which can be used not only to prolong the translocation time but alsoto enhance the capture rate . Recently, some groups tried introducing positive charges into nanopores asmolecular ‘brakes’, which is proved to be an effective approach to increasethe attractive force between the negative DNA molecule and the positive nanopore innerwall, thus increasing the duration time more than 2 orders of magnitude . The shortcoming of this method is that the residual ionic current during theDNA translocation is insufficient for direct base identification. Aside from an electricfield applied along the nanopore axis direction, Tsutsui et al. added a transverseelectric field to slow down the translocation speed of DNA across the nanopore . It is reported that adding a transverse field of 10 mV/nm in a goldelectrode embedded silicon dioxide channel can make 400-fold decrease in the DNAtranslocation speed. Similarly, He et al. reported a method to control the DNAtranslocation speed by gate modulation of the nanopore wall surface charges. It is foundthat native surface-charge-induced counterions in the electro-osmotic layersubstantially enhance advection flow of fluid, which exerts stronger dragging forces ontranslocating DNA and thereby lowering the DNA translocation speed. Based on thisphenomenon, they regulate DNA translocation by modulating the effective wall surfacecharge density through lateral gate voltages. The DNA translocation speed can be reducedat a rate of about 55 μm/s per 1 mV/nm through this method [15, 16]. Yen et al.  and Ai et al.  reported that applying positive gate voltage could also induce DNA-nanoporeelectrostatic interaction, which can regulate the DNA translocation speed. Lately, afunctionalized soft nanopore composed of a solid-state nanopore and a functionalizedsoft layer was demonstrated that can not only increase DNA capture rate by counterionconcentration polarization occurring at the nanopore mouth but can also decrease DNAtranslocation speed in the nanopore through electro-osmotic flow . Stolovitzky's group designed a nanopore with a metal-dielectric sandwichstructure capable of controlling the DNA translocation process with a single-baseaccuracy by tuning the trapping electric fields inside the nanopore [20–22]. This design is verified by molecular dynamics (MD) simulations, but there isno device reported so far due to its difficulty in fabrication. Applying an externalforce in the opposite direction of the electric field force on DNA could control a DNAstrand through a nanopore at a very slow speed. It can be achieved using optical tweezer  or magnetic tweezer  technologies. However, it is hard to extend these methods to sequence DNA inparallel , such as employing thousands of nanopores on a chip concurrently .
As we know, counterions in solutions can bind to DNA molecules, which may provide a dragforce on the DNA and reduce the translocation speed. Dekker's group found that DNAtranslocation time in LiCl salt solution is longer than that in KCl or NaCl solutions.Through MD simulation, they elucidated that the root of this effect is attributed to thestronger Li+ ion binding DNA than that of K+ and Na+. The DNA electrophoretic mobility depends on its surface charge density andthe applied voltage. If we can adjust the DNA surface charge density, it is possible toactively control the DNA translocation through a nanopore. It has been found thatMg2+ could reduce electrophoretic mobility of DNA molecule more thanNa+ at the same concentration without worrying about changing the DNAmolecule charge to a positive value . It is also known that Mg2+ is regularly used in adhering the DNAto inorganic surfaces, which may also reduce the DNA mobility. Inspired by the processof reducing effective surface charge density of a DNA molecule and that increasing theattractive force between DNA molecule and nanopore inner surface can retard DNA moleculetranslocation, we employed bivalent salt solution such as MgCl2 to observethe DNA translocation event through nanopores. We hope the two kinds of phenomena occurat the same time, thus extending the translocation time further more.
Results and discussion
In Figure 3, some outliers we call as ‘trappedevents’ have been observed in 1 M MgCl2 experiments. Although theprobability is small, the duration time of these events is 22 ms, about 17 times ofthe other events in 1 M MgCl2 experiments. As we know,Si3N4 surface in aqueous solution at pH 8.0 is negativelycharged. The correlations between Mg2+ ions on both the negatively chargedDNA and the Si3N4 surface can generate a net attraction force andthen help stick the DNA into the nanopore, but the phenomenon only obviously occurredfor the 7-nm diameter nanopore experiments. This is because the gap between the DNA andthe inner surface of the nanopore is also increased with the increasing nanoporediameter. With the increase of the gap, the net attraction force is not strong enough tostick the DNA, which leads to the trapped events unremarkable in the 22-nm diameternanopore.
In summary, the duration time for DNA translocation through a nanopore can be extendedwith the use of MgCl2 electrolyte. The side effect is that Mg2+ions may induce more DNA strands binding together, which is harmful to do DNA sequencingin MgCl2 electrolyte. Reducing the nanopore diameter can effectively reducethe occurrence number of the folded DNA translocation events. So, we can say thattheMgCl2 solution is a good choice for nanopore DNA sequencing experimentsif nanopore diameter can be reduced further.
YZ is a PhD candidate of Mechanical Design and Theory at the School of MechanicalEngineering, Southeast University, Nanjing, P.R. China. He is interested in nanoporefabrication and nanopore biosensing. LL is an assistant professor of Mechanical Designand Theory at the School of Mechanical Engineering, Southeast University, Nanjing, P.R.China. His research interests are biomolecule sensing and biodegradable materialsdesign. JS is an assistant professor of Mechanical Design and Theory at the School ofMechanical Engineering, Southeast University, Nanjing, P.R. China. Her research interestis micro-nano fluidic device design. ZN is a professor of Mechanical Manufacture andAutomation at the School of Mechanical Engineering, Southeast University, Nanjing, P.R.China. His research interests are minimally invasive medical devices and microfluidicdiagnostic device design and manufacture. HY is a professor of Mechanical Manufactureand Automation at the School of Mechanical Engineering, Southeast University, Nanjing,P.R. China. His research interest is advanced manufacturing technology. YC is aprofessor of Mechanical Design and Theory at the School of Mechanical Engineering,Southeast University, Nanjing, P.R. China. His research interests cover heat transfer,tribology, micro-nano fluidics, and micro-nano biomedical instrument.
The authors thank the financial support from the National Basic Research Program ofChina (2011CB707601 and 2011CB707605), the Natural Science Foundation of China(grantno.50925519), and the research funding for the Doctorate Program from ChinaEducational Ministry (20100092110051).
- Coulter WH: Means for counting for counting particles suspended in a fluid. US Patent Specification 2656508 20 October 1953 20 October 1953
- Nakane JJ, Akeson M, Marziali A: Nanopore sensors for nucleic acid analysis. J Phys-Condens Mat 2003, 15(32):R1365-R1393. 10.1088/0953-8984/15/32/203View Article
- Li JL, Gershow M, Stein D, Brandin E, Golovchenko JA: DNA molecules and configurations in a solid-state nanopore microscope. Nat Mater 2003, 2(9):611–615. 10.1038/nmat965View Article
- Chen P, Gu JJ, Brandin E, Kim YR, Wang Q, Branton D: Probing single DNA molecule transport using fabricated nanopores. Nano Lett 2004, 4(11):2293–2298. 10.1021/nl048654jView Article
- Storm AJ, Storm C, Chen JH, Zandbergen H, Joanny JF, Dekker C: Fast DNA translocation through a solid-state nanopore. Nano Lett 2005, 5(7):1193–1197. 10.1021/nl048030dView Article
- Healy K, Schiedt B, Morrison AP: Solid-state nanopore technologies for nanopore-based DNA analysis. Nanomedicine-UK 2007, 2(6):875–897. 10.2217/174358188.8.131.525View Article
- Dekker C: Solid-state nanopores. Nat Nanotechnol 2007, 2(4):209–215. 10.1038/nnano.2007.27View Article
- Aksimentiev A: Deciphering ionic current signatures of DNA transport through a nanopore. Nanoscale 2010, 2(4):468–483. 10.1039/b9nr00275hView Article
- Venkatesan BM, Bashir R: Nanopore sensors for nucleic acid analysis. Nat Nanotechnol 2011, 6(10):615–624. 10.1038/nnano.2011.129View Article
- Fologea D, Uplinger J, Thomas B, McNabb DS, Li JL: Slowing DNA translocation in a solid-state nanopore. Nano Lett 2005, 5(9):1734–1737. 10.1021/nl051063oView Article
- Wanunu M, Sutin J, McNally B, Chow A, Meller A: DNA translocation governed by interactions with solid-state nanopores. Biophys J 2008, 95(10):4716–4725. 10.1529/biophysj.108.140475View Article
- Wanunu M, Morrison W, Rabin Y, Grosberg AY, Meller A: Electrostatic focusing of unlabelled DNA into nanoscale pores using a saltgradient. Nat Nanotechnol 2010, 5(2):160–165. 10.1038/nnano.2009.379View Article
- Rincon-Restrepo M, Milthallova E, Bayley H, Maglia G: Controlled translocation of individual DNA molecules through protein nanoporeswith engineered molecular brakes. Nano Lett 2011, 11(2):746–750. 10.1021/nl1038874View Article
- Tsutsui M, He Y, Furuhashi M, Rahong S, Taniguchi M, Kawai T: Transverse electric field dragging of DNA in a nanochannel. Sci Rep 2012, 2: 394.
- He YH, Tsutsui M, Fan C, Taniguchi M, Kawai T: Gate manipulation of DNA capture into nanopores. ACS Nano 2011, 5(10):8391–8397. 10.1021/nn203186cView Article
- He YH, Tsutsui M, Fan C, Taniguchi M, Kawai T: Controlling DNA translocation through gate modulation of nanopore wall surfacecharges. ACS Nano 2011, 5(7):5509–5518. 10.1021/nn201883bView Article
- Yen PC, Wang CH, Hwang GJ, Chou YC: Gate effects on DNA translocation through silicon dioxide nanopore. Rev Sci Instrum 2012, 83(3):034301. 10.1063/1.3692746View Article
- Ai Y, Liu J, Zhang BK, Qian S: Field effect regulation of DNA translocation through a nanopore. Anal Chem 2010, 82(19):8217–8225. 10.1021/ac101628eView Article
- Yeh LH, Zhang MK, Qian SZ, Hsu JP: Regulating DNA translocation through functionalized soft nanopores. Nanoscale 2012, 4(8):2685–2693. 10.1039/c2nr30102dView Article
- Polonsky S, Rossnagel S, Stolovitzky G: Nanopore in metal-dielectric sandwich for DNA position control. Appl Phys Lett 2007, 91(15):153103. 10.1063/1.2798247View Article
- Luan BQ, Peng HB, Polonsky S, Rossnagel S, Stolovitzky G, Martyna G: Base-by-base ratcheting of single stranded DNA through a solid-state nanopore. Phys Rev Lett 2010, 104(23):238103.View Article
- Luan BQ, Martyna G, Stolovitzky G: Characterizing and controlling the motion of ssDNA in a solid-state nanopore. Biophys J 2011, 101(9):2214–2222. 10.1016/j.bpj.2011.08.038View Article
- Keyser UF, Koeleman BN, Van Dorp S, Krapf D, Smeets RMM, Lemay SG, Dekker NH, Dekker C: Direct force measurements on DNA in a solid-state nanopore. Nat Phys 2006, 2(7):473–477. 10.1038/nphys344View Article
- Peng HB, Ling XSS: Reverse DNA translocation through a solid-state nanopore by magnetic tweezers. Nanotechnology 2009, 20(18):185101. 10.1088/0957-4484/20/18/185101View Article
- Luan BQ, Stolovitzky G, Martyna G: Slowing and controlling the translocation of DNA in a solid-state nanopore. Nanoscale 2012, 4(4):1068–1077. 10.1039/c1nr11201eView Article
- Kim MJ, Wanunu M, Bell DC, Meller A: Rapid fabrication of uniformly sized nanopores and nanopore arrays for parallelDNA analysis. Adv Mater 2006, 18(23):3149–3153. 10.1002/adma.200601191View Article
- Kowalczyk SW, Wells DB, Aksimentiev A, Dekker C: Slowing down DNA translocation through a nanopore in lithium chloride. Nano Lett 2012, 12(2):1038–1044. 10.1021/nl204273hView Article
- Luan BQ, Aksimentiev A: Electric and electrophoretic inversion of the DNA charge in multivalentelectrolytes. Soft Matter 2010, 6(2):243–246. 10.1039/b917973aView Article
- Tabard-Cossa V, Trivedi D, Wiggin M, Jetha NN, Marziali A: Noise analysis and reduction in solid-state nanopores. Nanotechnology 2007, 18(30):305505. 10.1088/0957-4484/18/30/305505View Article
- Wanunu M, Dadosh T, Ray V, Jin JM, McReynolds L, Drndić M: Rapid electronic detection of probe-specific microRNAs using thin nanoporesensors. Nat Nanotechnol 2010, 5(11):807–814. 10.1038/nnano.2010.202View Article
- Kowalczyk SW, Grosberg AY, Rabin Y, Dekker C: Modeling the conductance and DNA blockade of solid-state nanopores. Nanotechnology 2011, 22(31):315101. 10.1088/0957-4484/22/31/315101View Article
- Dean JA, Lange NA: Lange's Handbook of Chemistry. 15th edition. New York: McGraw-Hill; 1999.
- Storm AJ, Chen JH, Zandbergen HW, Dekker C: Translocation of double-strand DNA through a silicon oxide nanopore. Phys Rev E 2005, 71(5):051903.View Article
- Luan B, Aksimentiev A: DNA attraction in monovalent and divalent electrolytes. J Am Chem Soc 2008, 130(47):15754–15755. 10.1021/ja804802uView Article
- Besteman K, Van Eijk K, Lemay SG: Charge inversion accompanies DNA condensation by multivalent ions. Nat Phys 2007, 3(9):641–644. 10.1038/nphys697View Article
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative CommonsAttribution License (http://creativecommons.org/licenses/by/2.0), whichpermits unrestricted use, distribution, and reproduction in any medium, provided theoriginal work is properly cited.