Stretching and controlled motion of single-stranded DNA in locally heated solid-state nanopores

ACS Nano

Volumn 7, Issue 8, 2013, Pages 6816-6824

  Belkin, Maxim ^a   Maffeo, Christopher ^a   Wells, David B ^a   Aksimentiev, Aleksei ^a,b  

^a University of Illinois at Urbana Champaign   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

biosensors; DNA sequencing; molecular dynamics; molecular separation; nanopores; thermophoresis

Indexed keywords

ATOMISTIC MODELING; CONTROLLED MOTIONS; DNA SEQUENCING; ELECTROPHORETIC MOTION; MOLECULAR SEPARATION; SINGLE-STRANDED DNA; SOLID-STATE NANOPORE; THERMOPHORETIC FORCE;

BIOSENSORS; CONFORMATIONS; DNA SEQUENCES; ELECTROPHORETIC MOBILITY; GENE ENCODING; HEATING; MOLECULAR DYNAMICS; NANOPORES; THERMOPHORESIS;

DNA;

DNA; GOLD; METAL NANOPARTICLE; SINGLE STRANDED DNA;

CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; DRUG DESIGN; GENETIC PROCEDURES; HEAT; MECHANICAL STRESS; MOLECULAR DYNAMICS; MOTION; NANOPORE; NANOTECHNOLOGY; PROCEDURES; TEMPERATURE; ARTICLE; METHODOLOGY;

BIOSENSING TECHNIQUES; COMPUTER SIMULATION; DNA; DNA, SINGLE-STRANDED; DRUG DESIGN; GOLD; HOT TEMPERATURE; METAL NANOPARTICLES; MOLECULAR DYNAMICS SIMULATION; MOTION; NANOPORES; NANOTECHNOLOGY; NUCLEIC ACID CONFORMATION; STRESS, MECHANICAL; TEMPERATURE;

EID: 84883218258     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn403575n     Document Type: Article

References (68)

1. Dekker, C. Solid-State Nanopores Nat. Nanotechnol. 2007, 2, 209-215
2. Bezrukov, S. M.; Vodyanoy, I.; Parsegian, V. A. Counting Polymers Moving through a Single Ion Channel Nature 1994, 370, 279-281
3. Kasianowicz, J. J.; Brandin, E.; Branton, D.; Deamer, D. W. Characterization of Individual Polynucleotide Molecules Using a Membrane Channel Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 13770-13773
4. Kasianowicz, J.; Robertson, J. W. F.; Chan, E. R.; Reiner, J. E.; Stanford, V. M. Nanoscopic Porous Sensors Annu. Rev. Anal. Chem. 2008, 1, 737-766
5. Howorka, S.; Siwy, Z. Nanopore Analytics: Sensing of Single Molecules Chem. Soc. Rev. 2009, 38, 2360-2384
6. Manrao, E. A.; Derrington, I. M.; Laszlo, A. H.; Langford, K. W.; Hopper, M. K.; Gillgren, N.; Pavlenok, M.; Niederweis, M.; Gundlach, J. H. Reading DNA at Single-Nucleotide Resolution with a Mutant MspA Nanopore and Phi29 DNA Polymerase Nat. Biotechnol. 2012, 30, 349-353
7. Keyser, U. F. Controlling Molecular Transport through Nanopores J. R. Soc., Interface 2011, 8, 1369-1378
8. Luan, B.; Stolovitzky, G.; Martyna, G. Slowing and Controlling the Translocation of DNA in a Solid-State Nanopore Nanoscale 2012, 4, 1068-1077
9. Keyser, U.; Koeleman, B.; Dorp, S.; Krapf, D.; Smeets, R.; Lemay, S.; Dekker, N.; Dekker, C. Direct Force Measurements on DNA in a Solid-State Nanopore Nat. Phys. 2006, 2, 473-477
10. Peng, H.; Ling, X. S. Reverse DNA Translocation through a Solid-State Nanopore by Magnetic Tweezers Nanotechnology 2009, 20, 185101
11. Melnikov, D. V.; Leburton, J.-P.; Gracheva, M. E. Slowing Down and Stretching DNA with an Electrically Tunable Nanopore in a p-n Semiconductor Membrane Nanotechnology 2012, 23, 255501
12. Polonsky, S.; Rossnagel, S.; Stolovitzky, G. Nanopore in Metal-Dielectric Sandwich for DNA Position Control Appl. Phys. Lett. 2007, 91, 153103
13. Luan, B.; Peng, H.; 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, 238103
14. 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
15. Mirsaidov, U.; Comer, J.; Dimitrov, V.; Aksimentiev, A.; Timp, G. Slowing the Translocation of Double-Stranded DNA Using a Nanopore Smaller than the Double Helix Nanotechnology 2010, 21, 395501
16. Fologea, D.; Uplinger, J.; Thomas, B.; McNabb, D. S.; Li, J. Slowing DNA Translocation in a Solid-State Nanopore Nano Lett. 2005, 5, 1734-1737
17. Kowalczyk, S. W.; Wells, D. B.; Aksimentiev, A.; Dekker, C. Slowing Down DNA Translocation through a Nanopore in Lithium Chloride Nano Lett. 2012, 12, 1038-1044
18. Meller, A.; Nivon, L.; Branton, D. Voltage-Driven DNA Translocations through a Nanopore Phys. Rev. Lett. 2001, 86, 3435-3438
19. Wanunu, M.; Morrison, W.; Rabin, Y.; Grosberg, A. Y.; Meller, A. Electrostatic Focusing of Unlabelled DNA Into Nanoscale Pores Using a Salt Gradient Nat. Nanotechnol. 2010, 5, 160-165
20. Jung, Y.; Bayley, H.; Movileanu, L. Temperature-Responsive Protein Pores J. Am. Chem. Soc. 2006, 128, 15332-15340
21. Reber, N.; Kuchel, A.; Spohr, R.; Wolf, A.; Yoshida, M. Transport Properties of Thermo-Responsive Ion Track Membranes J. Membr. Sci. 2001, 193, 49-58
22. Schepelina, O.; Zharov, I. PNIPAAM-Modified Nanoporous Colloidal Films with Positive and Negative Temperature Gating Langmuir 2007, 23, 12704-12709
23. Yameen, B.; Ali, M.; Neumann, R.; Ensinger, W.; Knoll, W.; Azzaroni, O. Ionic Transport through Single Solid-State Nanopores Controlled with Thermally Nanoactuated Macromolecular Gates Small 2009, 5, 1287-1291
24. Guo, W.; Xia, H.; Xia, F.; Hou, X.; Cao, L.; Wang, L.; Xue, J.; Zhang, G.; Song, Y.; Zhu, D. et al. Current Rectification in Temperature-Responsive Single Nanopores ChemPhysChem 2010, 11, 859-864
25. Nasir, S.; Ali, M.; Ensinger, W. Thermally Controlled Permeation of Ionic Molecules through Synthetic Nanopores Functionalized with Amine-Terminated Polymer Brushes Nanotechnology 2012, 23, 225502
26. Viasnoff, V.; Bockelmann, U.; Meller, A.; Isambert, H.; Laufer, L.; Tsori, Y. Localized Joule Heating Produced by Ion Current Focusing through Micron-Size Holes Appl. Phys. Lett. 2010, 96, 163701
27. Keyser, U. F.; Krapf, D.; Koeleman, B. N.; Smeets, R. M. M.; Dekker, N. H.; Dekker, C. Nanopore Tomography of a Laser Focus Nano Lett. 2005, 5, 2253-2256
28. Jonsson, M. P.; Dekker, C. Plasmonic Nanopore for Electrical Profiling of Optical Intensity Landscapes Nano Lett. 2013, 13, 1029-1033
29. Reiner, J. E.; Robertson, J. W. F.; Burden, D. L.; Burden, L. K.; Balijepalli, A.; Kasianowicz, J. J. Temperature Sculpting in Yoctoliter Volumes J. Am. Chem. Soc. 2013, 135, 3087-3094
30. Mast, C. B.; Braun, D. Thermal Trap for DNA Replication Phys. Rev. Lett. 2010, 104, 188102
31. Duhr, S.; Braun, D. Optothermal Molecule Trapping by Opposing Fluid Flow with Thermophoretic Drift Phys. Rev. Lett. 2006, 97, 038103
32. Jerabek-Willemsen, M.; Wienken, C. J.; Braun, D.; Baaske, P.; Duhr, S. Molecular Interaction Studies Using Microscale Thermophoresis Assay Drug Dev. Technol. 2011, 9, 342-353
33. He, Y.; Tsutsui, M.; Scheicher, R. H.; Bai, F.; Taniguchi, M.; Kawai, T. Thermophoretic Manipulation of DNA Translocation through Nanopores ACS Nano 2013, 7, 538-546
34. Healy, K.; Schiedt, B.; Morrison, A. P. Solid-State Nanopore Technologies for Nanopore-Based DNA Analysis Nanomedicine 2007, 2, 875-897
35. Miles, B. N.; Ivanov, A. P.; Wilson, K. A.; Dogan, F.; Japrung, D.; Edel, J. B. Single Molecule Sensing with Solid-State Nanopores: Novel Materials, Methods, and Applications Chem. Soc. Rev. 2013, 42, 15-28
36. Venkatesan, B. M.; Shah, A. B.; Zuo, J.-M.; Bashir, R. DNA Sensing Using Nanocrystalline Surface-Enhanced Al2O3 Nanopore Sensors Adv. Funct. Mater. 2010, 20, 1266-1275
37. Tjahjono, I. K.; Bayazitoglu, Y. Near-Infrared Light Heating of a Slab by Embedded Nanoparticles Int. J. Heat Mass Transfer 2008, 51, 1505-1515
38. Harata, A.; Shen, Q.; Sawada, T. Photothermal Applications of Lasers: Study of Fast and Ultrafast Photothermal Phenomena at Metal-Liquid Interfaces Annu. Rev. Phys. Chem. 1999, 50, 193-219
39. Hanson, G. W.; Patch, S. K. Optimum Electromagnetic Heating of Nanoparticle Thermal Contrast Agents at RF Frequencies J. Appl. Phys. 2009, 106
40. Roder, P. B.; Pauzauskie, P. J.; Davis, E. J. Nanowire Heating by Optical Electromagnetic Irradiation Langmuir 2012, 28, 16177-16185
41. Baffou, G.; Rigneault, H. Femtosecond-Pulsed Optical Heating of Gold Nanoparticles. Phys. Rev. B 2011, 84.
42. Hu, M.; Petrova, H.; Hartland, G. V. Investigation of the Properties of Gold Nanoparticles in Aqueous Solution at Extremely High Lattice Temperatures Chem. Phys. Lett. 2004, 391, 220-225
43. Plech, A.; Kotaidis, V.; Grésillon, S.; Dahmen, C.; von Plessen, G. Laser-Induced Heating and Melting of Gold Nanoparticles Studied by Time-Resolved X-ray Scattering Phys. Rev. B 2004, 70, 195423
44. Kotaidis, V.; Dahmen, C.; von Plessen, G.; Springer, F.; Plech, A. Excitation of Nanoscale Vapor Bubbles at the Surface of Gold Nanoparticles in Water J. Chem. Phys. 2006, 124, 184702
45. Pryor, R. Multiphysics Modeling Using COMSOL 4: A First Principles Approach; Mercury Learning Series; Mercury Learning & Information: Dulles, VA, 2012.
46. Aksimentiev, A. Deciphering Ionic Current Signatures of DNA Transport through a Nanopore Nanoscale 2010, 2, 468-483
47. Pelesko, J.; Bernstein, D. Modeling MEMS and NEMS; CRC Press LLC: Boca Raton, FL, 2002.
48. Merabia, S.; Shenogin, S.; Joly, L.; Keblinski, P.; Barrat, J.-L. Heat Transfer From Nanoparticles: A Corresponding State Analysis Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 15113-15118
49. Seol, Y.; Skinner, G. M.; Visscher, K. Stretching of Homopolymeric RNA Reveals Single-Strand Helices and Base-Stacking Phys. Rev. Lett. 2007, 98, 158103-158106
50. Ke, C.; Jiang, Y.; Rivera, M.; Clark, R. L.; Marszalek, P. E. Pulling Geometry Induced Errors in Single Molecule Force Spectroscopy Measurements Biophys. J. 2007, 92, 76-78
51. Lagerqvist, J.; Zwolak, M.; Ventra, M. D. Fast DNA Sequencing via Transverse Electronic Transport Nano Lett. 2006, 6, 779-782
52. Huang, S.; He, J.; Chang, S.; Zhang, P.; Liang, F.; Li, S.; Tuchband, M.; Fuhrmann, A.; Ros, R.; Lindsay, S. Identifying Single Bases in a DNA Oligomer with Electron Tunnelling Nat. Nanotechnol. 2010, 5, 868-873
53. Ohshiro, T.; Matsubara, K.; Tsutsui, M.; Furuhashi, M.; Taniguchi, M.; Kawai, T. Single-Molecule Electrical Random Resequencing of DNA and RNA. Sci. Rep. 2012, 2.
54. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. Scalable Molecular Dynamics with NAMD J. Comput. Chem. 2005, 26, 1781-1802
55. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S. et al. All-atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586-3616
56. Comer, J.; Dimitrov, V.; Zhao, Q.; Timp, G.; Aksimentiev, A. Microscopic Mechanics of Hairpin DNA Translocation through Synthetic Nanopores Biophys. J. 2009, 96, 593-608
57. 2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems J. Phys. Chem. Lett. 2012, 3, 45-50
58. Miyamoto, S.; Kollman, P. A. SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithm for Rigid Water Molecules J. Comput. Chem. 1992, 13, 952-962
59. Andersen, H. Rattle: A "Velocity" Version of the Shake Algorithm for Molecular Dynamics Calculations J. Comput. Phys. 1983, 52, 24-34
60. Batcho, P. F.; Case, D. A.; Schlick, T. Optimized Particle-Mesh Ewald/Multiple-Time Step Integration for Molecular Dynamics Simulations J. Chem. Phys. 2001, 115, 4003-4018
61. Skeel, R.; Hardy, D.; Phillips, J. Correcting Mesh-Based Force Calculations to Conserve Both Energy and Momentum in Molecular Dynamics Simulations J. Comput. Phys. 2007, 225, 1-5
62. Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics J. Mol. Graphics 1996, 14, 33-38
63. Wells, D. B.; Abramkina, V.; Aksimentiev, A. Exploring Transmembrane Transport through α-Hemolysin with Grid-Steered Molecular Dynamics J. Chem. Phys. 2007, 127, 125101
64. Brünger, A. T. X-PLOR, Version 3.1: A System for X-ray Crystallography and NMR. The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, 1992.
65. Martyna, G. J.; Tobias, D. J.; Klein, M. L. Constant Pressure Molecular Dynamics Algorithms J. Chem. Phys. 1994, 101, 4177-4189
66. Aksimentiev, A.; Heng, J. B.; Timp, G.; Schulten, K. Microscopic Kinetics of DNA Translocation through Synthetic Nanopores Biophys. J. 2004, 87, 2086-2097
67. Isralewitz, B.; Izrailev, S.; Schulten, K. Binding Pathway of Retinal to Bacterio-Opsin: A Prediction by Molecular Dynamics Simulations Biophys. J. 1997, 73, 2972-2979
68. Koopman, E.; Lowe, C. Advantages of a Lowe-Andersen Thermostat in Molecular Dynamics Simulations J. Chem. Phys. 2006, 124, 204103