The shear flow processing of controlled DNA tethering and stretching for organic molecular electronics

ACS Nano

Volumn 5, Issue 1, 2011, Pages 275-282

  Yu, Guihua ^a   Kushwaha, Amit ^a   Lee, Jungkyu K ^b   Shaqfeh, Eric S G ^a   Bao, Zhenan ^a  

^a Stanford University   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

DNA stretching; Extension; Molecular electronics; Shear flow; Tethering

Indexed keywords

ARRAY STRUCTURES; BOTTOM UP APPROACH; BROWNIAN DYNAMIC SIMULATIONS; CRITICAL STEPS; DNA CHAINS; DNA MOLECULES; DNA STRETCHING; DNA TETHERING; ENZYMATIC CLEAVAGE; EXTENSION; FLOW DYNAMICS; FLOW PROCESSING; FLOW STRENGTH; METAL CONTACTS; MOLECULAR CIRCUITS; MOLECULAR LEVELS; MOLECULAR SCAFFOLDS; NANOELECTRONIC DEVICES; ORGANIC MOLECULES; SEMICONDUCTING MOLECULES; TETHERING;

BROWNIAN MOVEMENT; COMPUTER SIMULATION; DNA; MOLECULAR ELECTRONICS; MOLECULES; NANOELECTRONICS; SCAFFOLDS; SURFACE CHEMISTRY;

SHEAR FLOW;

DNA; VIRUS DNA;

ARTICLE; BACTERIOPHAGE LAMBDA; BIOMECHANICS; CHEMICAL STRUCTURE; CHEMISTRY; ELECTRONICS; MECHANICS; METHODOLOGY;

BACTERIOPHAGE LAMBDA; BIOMECHANICS; DNA; DNA, VIRAL; ELECTRONICS; MECHANICAL PROCESSES; MODELS, MOLECULAR;

EID: 79955085226     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn102669b     Document Type: Article

References (42)

1. Tour, J. M., Molecular Electronics: Commercial Insights, Chemistry, Devices, Architectures and Programming; World Scientific: River Edge, NJ, 2003.
2. Guo, X.; Small, J. P.; Klare, J. E.; Wang, Y.; Purewal, M. S.; Tam, I. W.; Hong, B. H.; Caldwell, R.; Huang, L.; O'Brien, S.; et al. Covalently Bridging Gaps in Single-Walled Carbon Nanotubes with Conducting Molecules. Science 2006, 311, 356-359. (Pubitemid 43132655)
3. Porath, D.; Bezryadin, A.; de Vries, S.; Dekker, C. Direct Measurement of Electrical Transport through DNA Molecules. Nature 2000, 403, 635-638. (Pubitemid 30103998)
4. Heath, J. R.; Ratner, M. A. Molecular Electronics. Phys. Today 2003, 56, 43-49.
5. Kwok, K. S.; Ellenbogen, J. C. Moletronics: Future Electronics. Mater. Today 2002, 5, 28-37. (Pubitemid 40421424)
6. Lu, W.; Lieber, C. M. Nanoelectronics from the Bottom Up. Nat. Mater. 2007, 6, 841-850. (Pubitemid 350050579)
7. Tao, N. J. Electron Transport in Molecular Junctions. Nature Nanotechnol. 2006, 1, 173-181.
8. Ho Choi, S.; Kim, B.; Frisbie, C. D. Electrical Resistance of Long Conjugated Molecular Wires. Science 2008, 320, 1482-1486. (Pubitemid 351929425)
9. Moth-Poulsen, K.; Bjornholm, T. Molecular Electronics with Single Molecules in Solid-State Devices. Nature Nanotechnol. 2009, 4, 551-556.
10. Reed, M. A.; Zhou, C.; Muller, C. J.; Burgin, T. P.; Tour, J. M. Conductance of a Molecular Junction. Science 1997, 278, 252-254. (Pubitemid 27450865)
11. Smit, R. H. M.; Noat, Y.; Untiedt, C.; Lang, N. D.; van Hemert, M. C.; van Ruitenbeek, J. M. Measurement of the Conductance of a Hydrogen Molecule. Nature 2002, 419, 906-909. (Pubitemid 35339620)
12. Lee, T.-H.; Hladik, C. R.; Dickson, R. M. Asymmetric Photoconductivity within Nanoscale Break Junctions. Nano Lett. 2003, 3, 1561-1564. (Pubitemid 37518171)
13. Liang, W.; Shores, M. P.; Bockrath, M.; Long, J. R.; Park, H. Kondo Resonance in a Single-Molecule Transistor. Nature 2002, 417, 725-729. (Pubitemid 34640622)
14. Park, J.; Pasupathy, A. N.; Goldsmith, J. I.; Chang, C.; Yaish, Y.; Petta, J. R.; Rinkoski, M.; Sethna, J. P.; Abruña, H. D.; McEuen, P. L. Coulomb Blockade and the Kondo Effect in Single-Atom Transistors. Nature 2002, 417, 722-725. (Pubitemid 34649374)
15. Qin, L.; Park, S.; Huang, L.; Mirkin, C. A. On-Wire Lithography. Science 2005, 309, 113-115.
16. Cui, X. D.; Primak, A.; Zarate, X.; Tomfohr, J.; Sankey, O. F.; Moore, A. L.; Moore, T. A.; Gust, D.; Harris, G.; Lindsay, S. M. Reproducible Measurement of Single-Molecule Conductivity. Science 2001, 294, 571-574. (Pubitemid 32999549)
17. Reddy, P.; Jang, S. Y.; Segalman, R. A.; Majumdar, A. Thermoelectricity in Molecular Junctions. Science 2007, 315, 1568-1571. (Pubitemid 46449471)
18. Blum, A. S.; Kushmerick, J. G.; Long, D. P.; Patterson, C. H.; Yang, J. C.; Henderson, J. C.; Yao, Y.; Tour, J. M.; Shashidhar, R.; Ratna, B. R. Molecularly Inherent Voltage-Controlled Conductance Switching. Nat. Mater. 2005, 4, 167-172. (Pubitemid 40178718)
19. Zhitenev, N. B.; Meng, H.; Bao, Z. Conductance of Small Molecular Junctions. Phys. Rev. Lett. 2002, 88, 226801-226804.
20. Akkerman, H. B.; Blom, P. W. M.; de Leeuw, D. M.; de Boer, B. Towards Molecular Electronics with Large-Area Molecular Junctions. Nature 2006, 441, 69-72.
21. Nitzan, A.; Ratner, M. A. Electron Transport in Molecular Wire Junctions. Science 2003, 300, 1384-1389. (Pubitemid 36638150)
22. Hipps, K. W. It's All About Contacts. Science 2001, 294, 536-537.
23. Martin, C. R.; Baker, L. A. Expanding the Molecular Electronics Toolbox. Science 2005, 309, 67-68. (Pubitemid 40934951)
24. Li, X. Y.; Liu, D. R. DNA-Templated Organic Synthesis. Angew. Chem., Int. Ed. 2004, 43, 4848-4870.
25. Ustinov, A. V.; Dubnyakova, V. V.; Korshun, V. A. A Convenient 'Click Chemistry' Approach to Perylene Diimide-Oligonucleotide Conjugates. Tetrahedron 2008, 64, 1467-1473.
26. Lee, J. K.; Jung, Y. H.; Stoltenberg, R. M.; Tok, J. B. H.; Bao, Z. Synthesis of DNA-Organic Molecule-DNA Triblock Oligomers Using the Amide Coupling Reaction and Their Enzymatic Amplification. J. Am. Chem. Soc. 2008, 130, 12854-12855.
27. Braun, E.; Eichen, Y.; Sivan, U.; Ben-Yoseph, G. DNATemplated Assembly and Electrode Attachment of a Conducting Silver Wire. Nature 1998, 391, 775-778. (Pubitemid 28099671)
28. Keren, K.; Krueger, M.; Gilad, R.; Ben-Yosep, G.; Sivan, U.; Braun, E. Sequence-Specific Molecular Lithography on Single DNA Molecules. Science 2002, 297, 72-75. (Pubitemid 34743092)
29. Lee, J. K.; Jäckel, F.; Moerner, W. E.; Bao, Z. Micrometersized DNA-Single-Fluorophore-DNA Supramolecule: Synthesis and Single-Molecule Characterization. Small 2009, 5, 2418-2423.
30. Perkins, T.; Smith, D.; Larson, R.; Chu, S. Stretching of a Single Tethered Polymer in a Uniform Flow. Science 1995, 268, 83-87.
31. Kim, J. H.; Shi, W. X.; Larson, R. G. Methods of Stretching DNA Molecules Using Flow Fields. Langmuir 2007, 23, 755-764. (Pubitemid 46226589)
32. Shaqfeh, E. S. G. The Dynamics of Single-Molecule DNA in Flow. J. Non-Newtonian Fluid Mech. 2005, 130, 1-28. (Pubitemid 41478702)
33. Schroeder, C. M.; Teixeira, R. E.; Shaqfeh, E. S. G.; Chu, S. Characteristic Periodic Motion of Polymers in Shear Flow. Phys. Rev. Lett. 2005, 95, 018301-018304.
34. Jendrejack, R. M.; Schwartz, D. C.; de Pablo, J. J.; Graham, M. D. Shear-Induced Migration in Flowing Polymer Solutions: Simulation of Long-Chain DNA in Microchannels. J. Chem. Phys. 2004, 120, 2513-2529.
35. Doyle, P. S.; Ladoux, B.; Viovy, J. L. Dynamics of a Tethered Polymer in Shear Flow. Phys. Rev. Lett. 2000, 84, 4769-4772.
36. Ladoux, B.; Doyle, P. S. Stretching Tethered DNA Chains in Shear Flow. Europhys. Lett. 2000, 52, 511-517.
37. Lueth, C. A.; Shaqfeh, E. S. G. Experimental and Numerical Studies of Tethered DNA Shear Dynamics in the Flow-Gradient Plane. Macromolecules 2009, 42, 9170-9182.
38. Savage, M.; Co, P. Avidin-Biotin Chemistry: A Handbook; Pierce Chemical Co.: Rockford, IL, 1992.
39. Lambda-DNA cleaved by restriction enzymes: locations of sites. http://www.neb.com/nebecomm/tech-reference/restriction-enzymes/sites/ Lambda-sites.pdf.
40. Perkins, T.; Smith, D.; Chu, S. Direct Observation of Tube-Like Motion of a Single Polymer Chain. Science 1994, 264, 819-822. (Pubitemid 24194329)
41. Zimm, B. H. Dynamics of Polymer Molecules in Dilute Solution: Viscoelasticity Flow Birefringence and Dielectric Loss. J. Chem. Phys. 1956, 24, 269-278.
42. Chopra, M.; Larson, R. G. Brownian Dynamics Simulations of Isolated Polymer Molecules in Shear Flow Near Adsorbing and Nonadsorbing Surfaces. J. Rheol. 2002, 46, 831-862. (Pubitemid 35009843)