Ionic permeability and mechanical properties of DNA origami nanoplates on solid-state nanopores

ACS Nano

Volumn 8, Issue 1, 2014, Pages 35-43

  Plesa, Calin ^a   Ananth, Adithya N ^a   Linko, Veikko ^b   Gülcher, Coen ^a   Katan, Allard J ^a   Dietz, Hendrik ^b   Dekker, Cees ^a  

^a DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

^b WALTER SCHOTTKY INSTITUT   (Germany)

Author keywords

DNA origami; ionic permeability; mechanical properties; nanopore

Indexed keywords

APPLIED FORCES; APPLIED VOLTAGES; BENDING DEFORMATIONS; CURRENT VOLTAGE; DNA ORIGAMIS; HONEYCOMB LATTICES; IONIC PERMEABILITY; SOLID-STATE NANOPORE;

BENDING (DEFORMATION); BUCKLING; DESIGN; DNA; IONIC STRENGTH; MECHANICAL PROPERTIES; NANOPORES;

NANOSTRUCTURES;

DNA; ION; NANOMATERIAL;

ARTICLE; CHEMISTRY; PERMEABILITY;

DNA; IONS; NANOSTRUCTURES; PERMEABILITY;

EID: 84893473971     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn405045x     Document Type: Article

References (30)

1. Wanunu, M. Nanopores: A Journey towards DNA Sequencing Phys. Life Rev. 2012, 9, 125-158
2. Haque, F.; Li, J.; Wu, H.-C.; Liang, X.-J.; Guo, P. Solid-State and Biological Nanopore for Real-Time Sensing of Single Chemical and Sequencing of DNA Nano Today 2013, 8, 56-74
3. Tabard-Cossa, V.; Trivedi, D.; Wiggin, M.; Jetha, N.; Marziali, A. Noise Analysis and Reduction in Solid-State Nanopores Nanotechnology 2007, 18, 305505
4. Venkatesan, B. M.; Bashir, R. Nanopore Sensors for Nucleic Acid Analysis Nat. Nanotechnol. 2011, 6, 615-624
5. Rotem, D.; Jayasinghe, L.; Salichou, M.; Bayley, H. Protein Detection by Nanopores Equipped with Aptamers J. Am. Chem. Soc. 2012, 134, 2781-2787
6. Hall, A. R.; Scott, A.; Rotem, D.; Mehta, K. K.; Bayley, H.; Dekker, C. Hybrid Pore Formation by Directed Insertion of [Alpha]-Hemolysin into Solid-State Nanopores Nat Nano 2010, 5, 874-877
7. Rothemund, P. W. K. Folding DNA to Create Nanoscale Shapes and Patterns Nature 2006, 440, 297-302
8. Andersen, E. S.; Dong, M.; Nielsen, M. M.; Jahn, K.; Subramani, R.; Mamdouh, W.; Golas, M. M.; Sander, B.; Stark, H.; Oliveira, C. L. P. et al. Self-Assembly of a Nanoscale DNA Box with a Controllable Lid Nature 2009, 459, 73-76
9. Douglas, S. M.; Dietz, H.; Liedl, T.; Hogberg, B.; Graf, F.; Shih, W. M. Self-Assembly of DNA into Nanoscale Three-Dimensional Shapes Nature 2009, 459, 414-418
10. Han, D.; Pal, S.; Nangreave, J.; Deng, Z.; Liu, Y.; Yan, H. DNA Origami with Complex Curvatures in Three-Dimensional Space Science 2011, 332, 342-346
11. Dietz, H.; Douglas, S. M.; Shih, W. M. Folding DNA into Twisted and Curved Nanoscale Shapes Science 2009, 325, 725-730
12. Wei, R.; Martin, T. G.; Rant, U.; Dietz, H. DNA Origami Gatekeepers for Solid-State Nanopores Angew. Chem., Int. Ed. 2012, 51, 4864-4867
13. Bell, N. A. W.; Engst, C. R.; Ablay, M.; Divitini, G.; Ducati, C.; Liedl, T.; Keyser, U. F. DNA Origami Nanopores Nano Lett. 2012, 12, 512-517
14. Hernández-Ainsa, S.; Bell, N. A. W.; Thacker, V. V.; Göpfrich, K.; Misiunas, K.; Fuentes-Perez, M. E.; Moreno-Herrero, F.; Keyser, U. F. DNA Origami Nanopores for Controlling DNA Translocation ACS Nano 2013, 7, 6024-6030
15. Langecker, M.; Arnaut, V.; Martin, T. G.; List, J.; Renner, S.; Mayer, M.; Dietz, H.; Simmel, F. C. Synthetic Lipid Membrane Channels Formed by Designed DNA Nanostructures Science 2012, 338, 932-936
16. Burns, J. R.; Stulz, E.; Howorka, S. Self-Assembled DNA Nanopores That Span Lipid Bilayers Nano Lett. 2013, 13, 2351-2356
17. Bai, X.-c.; Martin, T. G.; Scheres, S. H. W.; Dietz, H. Cryo-EM Structure of a 3d DNA-Origami Object Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 20012-20017
18. Ke, Y.; Douglas, S. M.; Liu, M.; Sharma, J.; Cheng, A.; Leung, A.; Liu, Y.; Shih, W. M.; Yan, H. Multilayer DNA Origami Packed on a Square Lattice J. Am. Chem. Soc. 2009, 131, 15903-15908
19. Castro, C. E.; Kilchherr, F.; Kim, D.-N.; Shiao, E. L.; Wauer, T.; Wortmann, P.; Bathe, M.; Dietz, H. A Primer to Scaffolded DNA Origami Nat. Methods 2011, 8, 221-229
20. Kim, D.-N.; Kilchherr, F.; Dietz, H.; Bathe, M. Quantitative Prediction of 3d Solution Shape and Flexibility of Nucleic Acid Nanostructures Nucleic Acids Res. 2012, 40, 2862-2868
21. Kowalczyk, S. W.; Grosberg, A. Y.; Rabin, Y.; Dekker, C. Modeling the Conductance and DNA Blockade of Solid-State Nanopores Nanotechnology 2011, 22, 315101
22. Arbona, J. M.; Aimé, J.-P.; Elezgaray, J. Modeling the Mechanical Properties of DNA Nanostructures Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. 2012, 86, 051912
23. Schoch, R. B.; Han, J.; Renaud, P. Transport Phenomena in Nanofluidics Rev. Mod. Phys. 2008, 80, 839-883
24. Ho, C.; Qiao, R.; Heng, J. B.; Chatterjee, A.; Timp, R. J.; Aluru, N. R.; Timp, G. Electrolytic Transport through a Synthetic Nanometer-Diameter Pore Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 10445-10450
25. Martin, T. G.; Dietz, H. Magnesium-Free Self-Assembly of Multi-Layer DNA Objects Nat. Commun. 2012, 3, 1103
26. Essevaz-Roulet, B.; Bockelmann, U.; Heslot, F. Mechanical Separation of the Complementary Strands of DNA Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 11935-11940
27. Strunz, T.; Oroszlan, K.; Schäfer, R.; Güntherodt, H.-J. Dynamic Force Spectroscopy of Single DNA Molecules Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11277-11282
28. Kowalczyk, S. W.; Tuijtel, M. W.; Donkers, S. P.; Dekker, C. Unraveling Single-Stranded DNA in a Solid-State Nanopore Nano Lett. 2010, 10, 1414-1420
29. Janssen, X. J. A.; Jonsson, M. P.; Plesa, C.; Soni, G. V.; Dekker, C.; Dekker, N. H. Rapid Manufacturing of Low-Noise Membranes for Nanopore Sensors by Trans-Chip Illumination Lithography Nanotechnology 2012, 23, 475302
30. Sobczak, J.-P. J.; Martin, T. G.; Gerling, T.; Dietz, H. Rapid Folding of DNA into Nanoscale Shapes at Constant Temperature Science 2012, 338, 1458-1461