Synthesis of DNA-organic molecule-DNA triblock oligomers using the amide coupling reaction and their enzymatic amplification

Journal of the American Chemical Society

Volumn 130, Issue 39, 2008, Pages 12854-12855

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

^a STANFORD UNIVERSITY   (United States)

^b Stanford University   (United States)

^c Korea Bio Polytechnic   (South Korea)

^d LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AGAROSE GEL ELECTROPHORESIS; ATOMIC FORCE MICROSCOPES; COUPLING REACTION; ELECTRICAL CONTACTS; ELECTROSPRAY IONIZATION MASS SPECTROMETRY; NANO-DEVICES; NANO-METER-SCALE; OLIGODEOXYNUCLEOTIDES; ORGANIC MOLECULES; POLYMERASE CHAIN REACTION; SINGLE-MOLECULE; SINGLE-MOLECULE ELECTRONICS; TRIBLOCK;

AMIDES; AMPLIFICATION; DNA; ELECTRIC CONTACTS; ELECTROPHORESIS; ELECTROSPRAY IONIZATION; GELATION; GENES; MASS SPECTROMETRY; NUCLEIC ACIDS; OLIGOMERS; THICKNESS MEASUREMENT;

MOLECULES;

AMIDE; DNA; NANOMATERIAL; OLIGONUCLEOTIDE; VIRUS DNA;

ARTICLE; BACTERIOPHAGE LAMBDA; CHEMISTRY; GENETICS; METHODOLOGY; MICROELECTRODE; POLYMERASE CHAIN REACTION; SYNTHESIS;

AMIDES; BACTERIOPHAGE LAMBDA; DNA; DNA, VIRAL; MICROELECTRODES; NANOSTRUCTURES; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION;

EID: 58149149974     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja8044458     Document Type: Article

References (37)

1. (a) Tao, N. J. Nat. Nanotechnol. 2006, 1, 173.
2. (b) Reed, M. A.; Lee, T. Molecular Nanoelectronics; American Scientific Publishers: Stevenson Ranch, CA, 2003.
3. (c) Guo, X.; et al. Science 2006, 311, 356.
4. (d) Qin, L.; Park, S.; Huang, L.; Mirkin, C. A. Science 2005, 309, 113.
5. (e) Liu, S.; Tok, J. B.-H.; Bao, Z. Nano Lett. 2005, 5, 1071.
6. (a) Patolsky, F.; Zheng, G.; Lieber, C. M. Anal. Chem. 2006, 78, 4260.
7. (b) Joachim, C.; Gimzewski, J. K.; Aviram, A. Nature 2000, 408, 541.
8. Lu, W.; Lieber, C. M. Nat. Mater. 2007, 6, 841.
9. Hipps, K. W. Science 2001, 294, 536.
10. (a) 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. Science 2001, 294, 571.
11. (b) Reddy, P.; Jang, S.-Y.; Segalman, R. A.; Majumdar, A. Science 2007, 315, 1568.
12. (c) Moore, A. M.; Dameron, A. A.; Mantooth, B. A.; Smith, R. K.; Fuchs, D. J.; Ciszek, J. W.; Maya, F.; Yao, Y.; Tour, J. M.; Weiss, P. S J. Am. Chem. Soc. 2006, 128, 1959.
13. (d) Quinn, J. R.; Foss, F. W., Jr.; Venkataraman, L.; Breslow, R. J. Am. Chem. Soc. 2007, 129, 12376.
14. (a) Reed, M. A.; Zhou, C.; Muller, C. J.; Burgin, T. P.; Tour, J. M. Science 1997, 278, 252.
15. (b) Smit, R. H. M.; Noat, Y.; Untiedt, C.; Lang, N. D.; van Hemert, M. C.; van Ruitenbeek, J. M. Nature 2002, 419, 906.
16. (a) Zhitenev, N. B.; Meng, H.; Bao, Z. Phys. Rev. Lett. 2002, 88, 226801.
17. (b) Nitzan, A.; Ratner, M. A. Science 2003, 300, 1384.
18. (c) Akkerman, H. B.; Blom, P. W. M.; de Leeuw, D. M.; de Boer, B. Nature 2006, 441, 69.
19. Martin, C. R.; Baker, L. A. Science 2005, 309, 67.
20. (a) Keren, K.; Krueger, M.; Gilad, R.; Ben-Yosep, G.; Sivan, U.; Braun, E. Science 2002, 297, 72.
21. (b) Becerril, H. A.; Stoltenberg, R. M.; Wheeler, D. R.; Davis, R. C.; Harb, J. N.; Woolley, A. T. J. Am. Chem. Soc. 2005, 127, 2828.
22. (c) Lund, J.; Dong, J. C.; Deng, Z. F.; Mao, C. D.; Parviz, B. A. Nanotechnology 2006, 17, 2752.
23. Li, X. Y.; Liu, D. R. Angew. Chem., Int. Ed. 2004, 43, 4848 and references therein.
24. Ergen, E.; Weber, M.; Jacob, J.; Herrmann, A.; Mullen, K. Chem. - Eur. J. 2006, 12, 3707.
25. (a) Alemadrouglu, F. E.; Herrmann, A. Org. Biomol. Chem. 2007, 5, 1311.
26. (b) Nielsen, M.; Dauksaite, V.; Kjems, J.; Gothelf, K. V. Bioconjugate Chem. 2005, 16, 981.
27. (c) Waybright, S. M.; Singleton, C. P.; Wachter, K.; Murphy, C. J.; Bunz, U. H. F. J. Am. Chem. Soc. 2001, 123, 1828.
28. Miller, G. P.; Kool, E. T. J. Org. Chem. 2004, 69, 2404.
29. We observed a side product from CPG-supported 24-mer ODN itself during the purification of the 24-mer ODN using 15% TBE-urea gel electrophoresis after the treatment of NH4OH. The position of the side product overlapped with desired products on the gel.
30. Abdalla, M. A.; Bayer, J.; Radler, J. O.; Mullen, K. Angew. Chem., Int. Ed. 2004, 43, 3967.
31. Clayden, J.; Greeves, N.; Warren, S.; Wothers, P. Organic Chemistry; Oxford University Press Inc.: New York, 2001; pp. 286.
32. The products were isolated by 15% TBE-urea gel electrophoresis, and then the yields were measured by the NanoDrop spectrophotometer (ND-1000, Thermo Scientific) after the purification using NAP-25 columns.
33. Instructions for DSS and BS3: http://www.piercenet.com/files/0418as4.pdf (accessed Aug 27, 2008).
34. Barnes, W. M. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 2216.
35. The 3 kbp DODs were observed as weak bands, but undesired 1.5 kbp dsDNA-organic molecule-ODN adducts were dominantly monitored. We presume that the priming ability of the remaining ODN was reduced by the increased steric hinderance from the elongated ODN. When we introduced 1.5 kbp dsDNA (synthesized in the previous PCR) in place of λ DNA-template, we observed the intensified 3 kbp bands.
36. Kuroda, T.; Sakurai, Y.; Suzuki, Y.; Nakamura, A. O.; Kuwahara, M.; Ozaki, H.; Sawai, H. Chem. Asian J. 2006, 1, 575.
37. DOD triblock architectures can also potentially be obtained using two different functional groups on a single molecule, such as-NHS and-SH to allow the attachment of different type of ODNs.