Thermophoretic manipulation of DNA translocation through nanopores

ACS Nano

Volumn 7, Issue 1, 2013, Pages 538-546

  He, Yuhui ^a   Tsutsui, Makusu ^a   Scheicher, Ralph H ^b   Bai, Fan ^c   Taniguchi, Masateru ^a   Kawai, Tomoji ^a  

^a OSAKA UNIVERSITY   (Japan)

^b UPPSALA UNIVERSITY   (Sweden)

^c PEKING UNIVERSITY   (China)

Author keywords

DNA capture; DNA translocation; nanopore sequencing; thermophoresis

Indexed keywords

BASE-PAIRING; CAPTURE RATE; DNA TRANSLOCATION; DOUBLE STRANDED DNA; HIGH TEMPERATURE; LOW SPEED; NOVEL DESIGN; POLYMER CONFORMATION; SEQUENCING METHOD; TEMPERATURE DROPS; THEORETICAL EVALUATION; THERMAL-INSULATING; THERMOPHORETIC; ULTRA-FAST;

DNA; GENE ENCODING; POLYMERS; THERMOPHORESIS;

NANOPORES;

DNA; NANOMATERIAL;

ARTICLE; CHEMISTRY; ELECTROPHORESIS; HEAT; MATERIALS TESTING; METHODOLOGY; MICROMANIPULATION; PARTICLE SIZE; POROSITY; ULTRASTRUCTURE;

DNA; ELECTROPHORESIS; HOT TEMPERATURE; MATERIALS TESTING; MICROMANIPULATION; NANOSTRUCTURES; PARTICLE SIZE; POROSITY;

MLCS; MLOWN;

EID: 84872846190     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn304914j     Document Type: Article

References (45)

1. 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
2. Akeson, M.; Branton, D.; Kasianowicz, J. J.; Brandin, E.; Deamer, D. W. Microsecond Time-Scale Discrimination Among Polycytidylic Acid, Polyadenylic Acid, and Polyuridylic Acid as Homopolymers or as Segments Within Single RNA Molecules Biophys. J. 1999, 77, 3227-3233
3. Meller, A.; Nivon, L.; Brandin, E.; Golovchenko, J.; Branton, D. Rapid Nanopore Discrimination between Single Polynucleotide Molecules Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 1079-1084
4. Zwolak, M.; Di Ventra, M. Colloquium: Physical Approaches to DNA Sequencing and Detection Rev. Mod. Phys. 2008, 80, 141-165
5. Branton, D.; Deamer, D. W.; Marziali, A.; Bayley, H.; Benner, S. A.; Butler, T.; Di Ventra, M.; Garaj, S.; Hibbs, A.; Huang, X. The Potential and Challenges of Nanopore Sequencing Nat. Biotechnol. 2008, 26, 1146-1153
6. Venkatesan, B. M.; Bashir, R. Nanopore Sensors for Nucleic Acid Analysis Nat. Nanotechnol. 2011, 6, 615-624
7. Zwolak, M.; Di Ventra, M. Electronic Signature of DNA Nucleotides via Transverse Transport Nano Lett. 2005, 5, 421-424
8. Lagerqvist, J.; Zwolak, M.; Di Ventra, M.; Fast, D. N. A. Sequencing via Transverse Electronic Transport Nano Lett. 2006, 6, 779-782
9. Postma, H. W. C. Rapid Sequencing of Individual DNA Molecules in Graphene Nanogaps Nano Lett. 2010, 10, 420-425
10. Tsutsui, M.; Taniguchi, M.; Yokota, K.; Kawai, T. Identifying Single Nucleotides by Tunnelling Current Nat. Nanotechnol. 2010, 5, 286-290
11. Heng, J. B.; Aksimentiev, A.; Ho, C.; Marks, P.; Grinkova, Y. V.; Sligar, S.; Schulten, K.; Timp, G. Stretching DNA Using the Electric Field in a Synthetic Nanopore Nano Lett. 2005, 5, 1883-1888
12. Cherf, G. M.; Lieberman, K. R.; Rashid, H.; Lam, C. E.; Karplus, K.; Akeson, M. Automated Forward and Reverse Ratcheting of DNA in a Nanopore at 5 Å Precision Nat. Biotechnol. 2012, 30, 344-348
13. 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
14. Fologea, D.; Gershow, M.; Ledden, B.; McNabb, D. S.; Golovchenko, J. A.; Li, J. L. Detecting Single Stranded DNA with a Solid State Nanopore Nano Lett. 2005, 5, 1905-1909
15. Maglia, G.; Henricus, M.; Wyss, R.; Li, Q.; Cheley, S.; Bayley, H. DNA Strands from Denatured Duplexes are Translocated through Engineered Protein Nanopores at Alkaline pH Nano Lett. 2009, 9, 3831-3836
16. Keyser, U. F.; Koeleman, B. N.; van Dorp, S.; Krapf, D.; Smeets, R. M. M.; Lemay, S. G.; Dekker, N. H.; Dekker, C. Direct Force Measurements on DNA in a Solid-State Nanopore Nat. Phys. 2006, 2, 473-477
17. Keyser, U. F.; van der Does, J.; Dekker, C.; Dekker, N. H. Optical Tweezers for Force Measurements on DNA in Nanopores Rev. Sci. Instrum. 2006, 77, 105105
18. Peng, H.; Ling, X. S. Reverse DNA Translocation through a Solid-State Nanopore by Magnetic Tweezers Nanotechnology 2009, 20, 185101
19. 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
20. Keyser, U. Controlling Molecular Transport through Nanopores J. R. Soc. Interface 2011, 8, 1369-1378
21. Thamdrup, L. H.; Larsen, N. B.; Kristensen, A. Light-Induced Local Heating for Thermophoretic Manipulation of DNA in Polymer Micro- and Nanochannels Nano Lett. 2010, 10, 826-832
22. Garaj, S.; Hubbard, W.; Reina, A.; Kong, J.; Branton, D.; Golovchenko, J. A. Graphene as a Subnanometre trans -Electrode Membrane Nature 2010, 467, 190-193
23. Tsutsui, M.; Hongo, S.; He, Y.; Taniguchi, M.; Gemma, N.; Kawai, T. Single-Nanoparticle Detection Using a Low-Aspect-Ratio Pore ACS Nano 2012, 6, 3499-3505
24. Hall, J. E. Access Resistance of a Small Circular Pore J. Gen. Physiol. 1975, 66, 531-532
25. Wanunu, M.; Morrison, W.; Rabin, Y.; Grosberg, A. Y.; Meller, A. Electrostatic Focusing of Unlabeled DNA into Nanoscale Pores using a Salt Gradient Nat. Nanotechnol. 2010, 5, 160-165
26. Muthukumar, M. Theory of Capture Rate in Polymer Translocation J. Chem. Phys. 2010, 132, 195101
27. Duhr, S.; Braun, D. Why Molecules Move along a Temperature Gradient Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 19678-19682
28. Reineck, P.; Wienken, C. J.; Braun, D. Thermophoresis of Single Stranded DNA Electrophoresis 2010, 31, 279-286
29. Keyser, U.; van Dorpb, S.; Lemay, S. G. Tether Forces in DNA Electrophoresis Chem. Soc. Rev. 2010, 39, 939-947
30. Tinland, B.; Pluen, A.; Sturm, J.; Weill, G. Persistence Length of Single-Stranded DNA Macromolecules 1997, 30, 5763-5765
31. Geggier, S.; Kotlyar, A.; Vologodskii, A. Temperature Dependence of DNA Persistence Length Nucleic Acids Res. 2011, 39, 1419-1426
32. He, Y.; Tsutsui, M.; Fan, C.; Taniguchi, M.; Kawai, T. Controlling DNA Translocation through Gate Modulation of Nanopore Wall Surface Charges ACS Nano 2011, 5, 5509-5518
33. Wurger, A. Thermophoresis in Colloidal Suspensions Driven by Marangoni Forces Phys. Rev. Lett. 2007, 98, 138301
34. Weinert, F. M.; Braun, D. Observation of Slip Flow in Thermophoresis Phys. Rev. Lett. 2008, 101, 168301
35. Di Leonardo, R.; Ianni, F.; Ruocco, G. Colloidal Attraction Induced by a Temperature Gradient Langmuir 2009, 25, 4247-4250
36. Storm, A. J.; Storm, C.; Chen, J.; Zandbergen, H.; Joanny, J.-F.; Dekker, C.; Fast, D. N. A. Translocation through a Solid-State Nanopore Nano Lett. 2005, 5, 1193-1197
37. van Dorp, S.; Keyser, U. F.; Dekker, N. H.; Dekker, C.; Lemay, S. G. Origin of the Electrophoretic Force on DNA in Solid-State Nanopores Nat. Phys. 2009, 5, 347-351
38. Ghosal, S. Effect of Salt Concentration on the Electrophoretic Speed of a Polyelectrolyte through a Nanopore Phys. Rev. Lett. 2007, 98, 238104
39. Wurger, A. Thermal Non-Equilibrium Transport in Colloids Rep. Prog. Phys. 2010, 73, 126601
40. Vigolo, D.; Buzzaccaro, S.; Piazza, R. Thermophoresis and Thermoelectricity in Surfactant Solutions Langmuir 2010, 26, 7792-7801
41. Chiritescu, C.; Cahill, D.; Nguyen, N.; Johnson, D.; Bodapati, A.; Keblinski, P.; Zschack, P. Ultralow Thermal Conductivity in Disordered, Layered WSe2 Crystals Science 2007, 315, 351
42. Chiritescu, C.; Cahill, D. G.; Heideman, C.; Lin, Q.; Mortensen, C.; Nguyen, N. T.; Johnson, D.; Rostek, R.; Botner3, H. Low Thermal Conductivity in Nanoscale Layered Materials Synthesized by the Method of Modulated Elemental Reactants J. Appl. Phys. 2008, 104, 033533
43. Reimann, P.; Meyer, A.; Getfert, S. On the Lubensky-Nelson Model of Polymer Translocation through Nanopores Biophys. J. 2012, 103, 889-897
44. Agar, J. N.; Mou, C. Y.; Lin, J. L. Single-Ion Heat of Transport in Electrolyte Solutions: A Hydrodynamic Theory J. Phys. Chem. 1989, 93, 2079-2082
45. Majee, A.; Wurger, A. Collective Thermoelectrophoresis of Charged Colloids Phys. Rev. E 2011, 83, 061403