Syntheses of organic molecule-DNA hybrid structures

ACS Nano

Volumn 5, Issue 3, 2011, Pages 2067-2074

  Lee, Jungkyu K ^a   Jung, Young Hwan ^c   Tok, Jeffery B H ^b   Bao, Zhenan ^b  

^a STANFORD UNIVERSITY   (United States)

^b Stanford University   (United States)

^c Korea Bio Polytechnic   (South Korea)

Author keywords

bioconjugation of DNA; DNA extension; DNA organic molecule DNA hybrid structures; single molecule electronics

Indexed keywords

BIOCONJUGATION OF DNA; BUILDING BLOCKES; CHEMICAL LINKAGE; CROSS-COUPLINGS; DNA BUILDING BLOCKS; DNA HYBRIDIZATION; ELECTROSPRAY IONIZATION MASS SPECTROMETRY; GEL ELECTROPHORESIS; HYBRID STRUCTURE; ORGANIC MOLECULES; P-PHENYLENE; POTENTIAL APPLICATIONS; SINGLE MOLECULE; SINGLE-MOLECULE ELECTRONICS; SINGLE-STRANDED (SS) DNA; SYNTHETIC PROCEDURES; SYNTHETIC PROCESS; SYSTEMATIC INVESTIGATIONS;

DNA; ELECTROPHORESIS; ELECTROSPRAY IONIZATION; MASS SPECTROMETRY; MICROMETERS; MOLECULES; POLYETHYLENE GLYCOLS; POLYETHYLENE OXIDES;

NUCLEIC ACIDS;

DNA; NANOMATERIAL; ORGANIC COMPOUND;

ARTICLE; CHEMISTRY; CRYSTALLIZATION; MATERIALS TESTING; METHODOLOGY; PARTICLE SIZE; ULTRASTRUCTURE;

CRYSTALLIZATION; DNA; MATERIALS TESTING; NANOSTRUCTURES; ORGANIC CHEMICALS; PARTICLE SIZE;

EID: 79952925939     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn1032455     Document Type: Article

References (55)

1. Kanan, M. W.; Rozenman, M. M.; Sakurai, K.; Snyder, T. M.; Liu, D. R. Reaction Discovery Enabled by DNA-Templated Synthesis and In Vitro Selection Nature 2004, 431, 545-549 (Pubitemid 39336330)
2. Gartner, Z. J.; Tse, B. N.; Grubina, R.; Doyon, J. B.; Snyder, T. M.; Liu, D. R. DNA-Templated Organic Synthesis and Selection of a Library of Macrocycles Science 2004, 305, 1601-1605 (Pubitemid 39296351)
3. Zheng, M.; Jagota, A.; Strano, M. S.; Santos, A. P.; Barone, P.; Chou, S. G.; Diner, B. A.; Dresselhaus, M. S.; McLean, R. S.; Onoa, G. B. et al. Structure-Based Carbon Nanotube Sorting by Sequence-Dependent DNA Assembly Science 2003, 302, 1545-1548 (Pubitemid 37475693)
4. Maune, H. T.; Han, S. P.; Barish, R. D.; Bockrath, M.; Goddard, W. A.; Rothemund, P. W. K.; Winfree, E. Self-Assembly of Carbon Nanotubes into Two-Dimensional Geometries Using DNA Origami Templates Nat. Nanotechnol. 2010, 5, 61-66
5. Seeman, N. C. DNA in a Material World Nature 2003, 421, 427-431 (Pubitemid 36157949)
6. Rothemund, P. W. K. Folding DNA To Create Nanoscale Shapes and Patterns Nature 2006, 440, 297-302
7. LaBean, T. H.; Li, H. Y. Constructing Novel Materials with DNA Nano Today 2007, 2, 26-35
8. Shih, W. Biomolecular Assembly-Dynamic DNA Nat. Mater. 2008, 7, 98-100
9. Aldaye, F. A.; Palmer, A. L.; Sleiman, H. F. Assembling Materials with DNA as the Guide Science 2008, 321, 1795-1799
10. Lin, C.; Liu, Y.; Yan, H. Designer DNA Nanoarchitectures Biochemistry 2009, 48, 1663-1674
11. Braun, E.; Eichen, Y.; Sivan, U.; Ben-Yoseph, G. DNA-Templated Assembly and Electrode Attachment of a Conducting Silver Wire Nature 1998, 391, 775-778 (Pubitemid 28099671)
12. Deng, Z. X.; Mao, C. D. DNA-Templated Fabrication of 1D Parallel and 2D Crossed Metallic Nanowire Arrays Nano Lett. 2003, 3, 1545-1548
13. Stoltenberg, R. M.; Woolley, A. T. DNA-Templated Nanowire Fabrication Biomed. Microdevices 2004, 6, 105-111 (Pubitemid 38801850)
14. Lund, J.; Dong, J. C.; Deng, Z. X.; Mao, C. D.; Parviz, B. A. Electrical Conduction in 7 nm Wires Constructed on ?-DNA Nanotechnology 2006, 17, 2752-2757 (Pubitemid 43814925)
15. Nguyen, K.; Monteverde, M.; Filoramo, A.; Goux-Capes, L.; Lyonnais, S.; Jegou, P.; Viel, P.; Goffman, M.; Bourgoin, J. P. Synthesis of Thin and Highly Conductive DNA-Based Palladium Nanowires Adv. Mater. 2008, 20, 1099-1104
16. Becerril, H. A.; Woolley, A. T. DNA-Templated Nanofabrication Chem. Soc. Rev. 2009, 38, 329-337
17. Austin, R. Nanopores-The Art of Sucking Spaghetti Nat. Mater. 2003, 2, 567-568
18. Woolley, A. T.; Kelly, R. T. Deposition and Characterization of Extended Single-Stranded DNA Molecules on Surfaces Nano Lett. 2001, 1, 345-348 (Pubitemid 33673001)
19. Yokota, H.; Sunwoo, J.; Sarikaya, M.; van den Engh, G.; Aebersold, R. Spin-Stretching of DNA and Protein Molecules for Detection by Fluorescence and Atomic Force Microscopy Anal. Chem. 1999, 71, 4418-4422 (Pubitemid 29466429)
20. KorriYoussoufi, H.; Garnier, F.; Srivastava, P.; Godillot, P.; Yassar, A. Toward Bioelectronics: Specific DNA Recognition Based on an Oligonucleotide-Functionalized Polypyrrole J. Am. Chem. Soc. 1997, 119, 7388-7389 (Pubitemid 27348598)
21. Nilsson, K. P. R.; Inganas, O. Chip and Solution Detection of DNA Hybridization Using a Luminescent Zwitterionic Polythiophene Derivative Nat. Mater. 2003, 2, 419-424
22. Lee, J. K.; Jackel, F.; Moerner, W. E.; Bao, Z. A. Micrometer-Sized DNA-Single-Fluorophore-DNA Supramolecule: Synthesis and Single-Molecule Characterization Small 2009, 5, 2418-2423
23. Li, X. Y.; Liu, D. R. DNA-Templated Organic Synthesis: Natures Strategy for Controlling Chemical Reactivity Applied to Synthetic Molecules Angew. Chem., Int. Ed. 2004, 43, 4848-4870 (Pubitemid 39312132)
24. Nielsen, M.; Dauksaite, V.; Kjems, J.; Gothelf, K. V. DNA-Directed Coupling of Organic Modules by Multiple Parallel Reductive Aminations and Subsequent Cleavage of Selected DNA Sequences Bioconjugate Chem. 2005, 16, 981-985 (Pubitemid 41026183)
25. Kuroda, T.; Sakurai, Y.; Suzuki, Y.; Nakamura, A. O.; Kuwahara, M.; Ozaki, H.; Sawai, H. Assembly of DNA Nanostructures with Branched Tris-DNA Chem. Asian J. 2006, 1, 575-580 (Pubitemid 44682877)
26. Jacobsen, M. F.; Ravnsbaek, J. B.; Gothelf, K. V. Small Molecule Induced Control in Duplex and Triplex DNA-Directed Chemical Reactions Org. Biomol. Chem. 2010, 8, 50-52
27. Lee, J. K.; Jung, Y. H.; Stoltenberg, R. M.; Tok, J. B. H.; Bao, Z. N. 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
28. Ustinov, A. V.; Dubnyakova, V. V.; Korshun, V. A. A Convenient 'Click Chemistry' Approach to Perylene Diimide-Oligonucleotide Conjugates Tetrahedron 2008, 64, 1467-1473
29. Abdalla, M. A.; Bayer, J.; Radler, J. O.; Mullen, K. Synthesis and Self-Assembly of Perylenediimide-Oligonucleotide Conjugates Angew. Chem., Int. Ed. 2004, 43, 3967-3970 (Pubitemid 39257483)
30. Keller, S.; Wang, J.; Chandra, M.; Berger, R.; Marx, A. DNA Polymerase-Catalyzed DNA Network Growth J. Am. Chem. Soc. 2008, 130, 13188-13189
31. Jung, Y. H.; Chi, Y. S.; Kim, M. R.; Lee, H. M.; Choi, I. S.; Kim, Y. G. Pore Size Variability of DNA Nanomeshes by Polymerase Chain Reaction Bull. Korean Chem. Soc. 2009, 30, 1365-1367
32. Alemdaroglu, F. E.; Zhuang, W.; Zophel, L.; Wang, J.; Berger, R.; Rabe, J. P.; Herrmann, A. Generation of Multiblock Copolymers by PCR: Synthesis, Visualization and Nanomechanical Properties Nano Lett. 2009, 9, 3658-3662
33. Pound, E.; Ashton, J. R.; Becerril, H. A.; Woolley, A. T. Polymerase Chain Reaction Based Scaffold Preparation for the Production of Thin, Branched DNA Origami Nanostructures of Arbitrary Sizes Nano Lett. 2009, 9, 4302-4305
34. Keren, K.; Berman, R. S.; Buchstab, E.; Sivan, U.; Braun, E. DNA-Templated Carbon Nanotube Field-Effect Transistor Science 2003, 302, 1380-1382 (Pubitemid 37452176)
35. Becerril, H. A.; Stoltenberg, R. M.; Wheeler, D. R.; Davis, R. C.; Harb, J. N.; Woolley, A. T. DNA-Templated Three-Branched Nanostructures for Nanoelectronic Devices J. Am. Chem. Soc. 2005, 127, 2828-2829 (Pubitemid 40349841)
36. Hermanson, G. T. Bioconjugate Techniques; Academic Press: San Diego, CA, 1996; p xxv, 785 pp.
37. Overview of the Amide-Coupling Reaction. http://www.piercenet.com/ Products/Browse.cfm?fldID=CE4D6C5C-5946-4814-9904-C46E01232683#nhsester (accessed November 17, 2010).
38. Kolb, H. C.; Finn, M. G.; Sharpless, K. B. Click Chemistry: Diverse Chemical Function from a Few Good Reactions Angew. Chem., Int. Ed. 2001, 40, 2004-2021
39. Devaraj, N. K.; Miller, G. P.; Ebina, W.; Kakaradov, B.; Collman, J. P.; Kool, E. T.; Chidsey, C. E. D. Chemoselective Covalent Coupling of Oligonucleotide Probes to Self-Assembled Monolayers J. Am. Chem. Soc. 2005, 127, 8600-8601 (Pubitemid 40868236)
40. Jain, T.; Westerlund, F.; Johnson, E.; Moth-Poulsen, K.; Bjornholm, T. Self-Assembled Nanogaps via Seed-Mediated Growth of End-to-End Linked Gold Nanorods ACS Nano 2009, 3, 828-834
41. Bunz, U. H. F. Poly(aryleneethynylene)s: Syntheses, Properties, Structures, and Applications Chem. Rev. 2000, 100, 1605-1644
42. Tour, J. M. Conjugated Macromolecules of Precise Length and Constitution. Organic Synthesis for the Construction of Nanoarchitectures Chem. Rev. 1996, 96, 537-554
43. Hu, W. P.; Nakashima, H.; Furukawa, K.; Kashimura, Y.; Ajito, K.; Liu, Y. Q.; Zhu, D. B.; Torimitsu, K. A Self-Assembled Nano Optical Switch and Transistor Based on a Rigid Conjugated Polymer, Thioacetyl-End-Functionalized Poly(para -phenylene ethynylene) J. Am. Chem. Soc. 2005, 127, 2804-2805 (Pubitemid 40349829)
44. Dong, H. L.; Li, H. X.; Wang, E. J.; Wei, Z. M.; Xu, W.; Hu, W. P.; Yan, S. K. Ordering Rigid Rod Conjugated Polymer Molecules for High Performance Photoswitchers Langmuir 2008, 24, 13241-13244
45. Lahiri, J.; Isaacs, L.; Tien, J.; Whitesides, G. M. A strategy for the Generation of Surfaces Presenting Ligands for Studies of Binding Based on an Active Ester as a Common Reactive Intermediate: A Surface Plasmon Resonance Study Anal. Chem. 1999, 71, 777-790
46. Tian, Y.; He, Y.; Ribbe, A. E.; Mao, C. D. Preparation of Branched Structures with Long DNA Duplex Arms Org. Biomol. Chem. 2006, 4, 3404-3405 (Pubitemid 44319625)
47. Manual of Lambda DNA/ HindIII Fragments. http://tools.invitrogen.com/ content/sfs/manuals/15612013.pdf (accessed November 17, 2010).
48. Description of E. coli DNA Ligase. http://www.neb.com/nebecomm/products/ productM0205.asp (accessed November 17, 2010).
49. Description of 9°N DNA Ligase. http://www.neb.com/nebecomm/products/ productM0238.asp (accessed November 17, 2010).
50. Description of T4 DNA Ligase. http://www.neb.com/nebecomm/products/ productM0202.asp (accessed November 17, 2010).
51. Measurement of DNA Concentration. http://www.nanodrop.com/Library/nd- 1000-v3.7-users-manual-8.5x11.pdf (accessed November 17, 2010).
52. Seo, T. S.; Li, Z. M.; Ruparel, H.; Ju, J. Y. Click Chemistry To Construct Fluorescent Oligonucleotides for DNA Sequencing J. Org. Chem. 2003, 68, 609-612 (Pubitemid 36126000)
53. Megens, R. P.; van den Berg, T. A.; de Bruijn, A. D.; Feringa, B. L.; Roelfes, G. Multinuclear Non-Heme Iron Complexes for Double-Strand DNA Cleavage Chem.-Eur. J. 2009, 15, 1723-1733
54. Description of SfoI. http://www.neb.com/nebecomm/products/productR0606. asp (accessed November 17, 2010).
55. Description of Alkaline Phosphatase. http://www.neb.com/nebecomm/ products/productM0290.asp (accessed November 17, 2010).