Label-free and real-time sequence specific DNA detection based on supramolecular self-assembly

Langmuir

Volumn 26, Issue 9, 2010, Pages 6832-6837

  Tang, Yanli ^a   Achyuthan, Komandoor E ^b   Whitten, David G ^a  

^a University of New Mexico   (United States)

^b SANDIA NATIONAL LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSORPTION PEAKS; CD SIGNALS; DNA DETECTION; DNA HYBRIDIZATION; DOUBLE HELIX; FLUORESCENCE INTENSITIES; HELIX FORMATION; HYDROPHOBIC INTERACTIONS; INDUCED CIRCULAR DICHROISM; J AGGREGATES; LABEL FREE; OPTICAL METHODS; POSITIVELY CHARGED; REAL TIME; SELF-ASSEMBLED; SIDE CHAINS; SIGNAL CHANGES; SINGLE NUCLEOTIDES; SUPRAMOLECULAR SELF-ASSEMBLIES; TEMPLATING; TIME SEQUENCES;

COMPLEXATION; DATA STORAGE EQUIPMENT; DICHROISM; DNA; DYES; HYDROPHOBICITY; LABELS; SELF ASSEMBLY; SIGNAL DETECTION; SUPRAMOLECULAR CHEMISTRY;

GENES;

DNA; POLYMER; POLYPHENYLENE SULFIDE; SINGLE STRANDED DNA;

ARTICLE; BASE MISPAIRING; CHEMISTRY; CIRCULAR DICHROISM; GENETIC PROCEDURES; GENETICS; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE SEQUENCE; SPECTROFLUOROMETRY; TIME;

BASE PAIR MISMATCH; BASE SEQUENCE; BIOSENSING TECHNIQUES; CIRCULAR DICHROISM; DNA; DNA, SINGLE-STRANDED; NUCLEIC ACID HYBRIDIZATION; POLYMERS; SPECTROMETRY, FLUORESCENCE; TIME FACTORS;

EID: 77951693863     PISSN: 07437463     EISSN: 15205827     Source Type: Journal    
DOI: 10.1021/la904008v     Document Type: Article

References (48)

1. Taton, T. A., Mirkin, C. A., and Letsinger, R. L. Science 2000, 289, 1757
2. Southern, E., Mir, K., and Shchepinova, M. Nat. Genet. 1999, 21
3. Palecek, E. and Jelen, F. Crit. Rev. Anal. Chem. 2002, 32
4. Wang, J., Polsky, R., Merkoci, A., and Turner, K. L. Langmuir 2003, 19, 989
5. Komurian-Pradel, F., Paranhos-Bacala, G., Sodoyer, M., Chevallier, P., Mandrand, B., Lotteau, V., and Andre, P. J. Virol. Methods 2001, 95, 111
6. Walker, N. J. Science 2002, 296, 557
7. Sevall, J. S., Prince, H., Garratty, G., Obrien, W. A., and Zack, J. A. Clin. Chem. 1993, 39, 433
8. Alfonta, L., Singh, A. K., and Willner, I. Anal. Chem. 2001, 73, 91
9. Ganguly, A., Chen, C. P., Lai, Y. T., Kuo, C. C., Hsu, C. W., Chen, K. H., and Chen, L. C. J. Mater. Chem. 2009, 19, 928
10. He, W., Huang, C. Z., Li, Y. F., Xie, J. P., Yang, R. G., Zhou, P. F., and Wang, J. Anal. Chem. 2008, 80, 8424
11. Zari, N., Amine, A., and Ennaji, M. M. Anal. Lett. 2009, 42, 519
12. Wang, J., Cai, X. H., Rivas, G., Shiraishi, H., Farias, P. A. M., and Dontha, N. Anal. Chem. 1996, 68, 2629
13. Martinez, M. T., Tseng, Y. C., Ormategui, N., Loinaz, I., Eritja, R., and Bokor, J. Nano Lett. 2009, 9, 530
14. Wang, J. Electroanal. Methods Biol. Mater. 2002, 27
15. Katz, E., Weizmann, Y., and Willner, I. J. Am. Chem. Soc. 2005, 127, 9191
16. Marrazza, G., Chiti, G., Mascini, M., and Anichini, M. Clin. Chem. 2000, 46, 31
17. Duan, X. R., Li, Z. P., He, F., and Wang, S. J. Am. Chem. Soc. 2007, 129, 4154
18. Liu, B. and Bazan, G. C. Chem. Mater. 2004, 16, 4467
19. He, F., Tang, Y. L., Wang, S., Li, Y. L., and Zhu, D. B. J. Am. Chem. Soc. 2005, 127, 12343
20. Thelwell, N., Millington, S., Solinas, A., Booth, J., and Brown, T. Nucleic Acids Res. 2000, 28, 3752
21. Feng, X. L., Duan, X. R., Liu, L. B., An, L. L., Feng, F. D., and Wang, S. Langmuir 2008, 24, 12138
22. Ren, X. S. and Xu, Q. H. Langmuir 2009, 25, 43
23. Kushon, S. A., Ley, K. D., Bradford, K., Jones, R. M., McBranch, D., and Whitten, D. Langmuir 2002, 18, 7245
24. Wang, S., Gaylord, B. S., and Bazan, G. C. J. Am. Chem. Soc. 2004, 126, 5446
25. He, F., Tang, Y. L., Yu, M. H., Feng, F., An, L. L., Sun, H., Wang, S., Li, Y. L., Zhu, D. B., and Bazan, G. C. J. Am. Chem. Soc. 2006, 128, 6764
26. Li, K. and Liu, B. Anal. Chem. 2009, 81, 4099
27. Pu, K. Y. and Liu, B. Adv. Funct. Mater. 2009, 19, 1371
28. Wang, Y. S. and Liu, B. Anal. Chem. 2007, 79, 7214
29. Gaylord, B. S., Heeger, A. J., and Bazan, G. C. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 10954
30. Tercero, N., Wang, K., Gong, P., and Levicky, R. J. Am. Chem. Soc. 2009, 131, 4953
31. Wang, J. Curr. Issues Mol. Biol. 1999, 1, 117
32. Raymond, F. R., Ho, H. A., Peytavi, R., Bissonnette, L., Boissinot, M., Picard, F. J., Leclerc, M., and Bergeron, M. G. BMC Biotechnol. 2005, 5, 10
33. Wang, H., Li, J., Liu, H. P., Liu, Q. J., Mei, Q., Wang, Y. J., Zhu, J. J., He, N. Y., and Lu, Z. H. Nucleic Acids Res. 2002, 30, e61.
34. Stender, H., Fiandaca, M., Hyldig-Nielsen, J., and Coull, J. J. Microbiol. Methods 2002, 48, 1
35. Boman, F. C., Gibbs-Davis, J. M., Heckman, L. M., Stepp, B. R., Nguyen, S. T., and Geiger, F. M. J. Am. Chem. Soc. 2009, 131, 844
36. Steichen, M., Brouette, N., Buess-Herman, C., Fragneto, G., and Sferrazza, M. Langmuir 2009, 25, 4162
37. Caruso, F., Rodda, E., Furlong, D. F., Niikura, K., and Okahata, Y. Anal. Chem. 1997, 69, 2043
38. Ho, H. A., Boissinot, M., Bergeron, M. G., Corbeil, G., Dore, K., Boudreau, D., and Leclerc, M. Angew. Chem., Int. Ed. 2002, 41, 1548
39. Tang, Y. L., Zhou, Z. J., Ogawa, K., Lopez, G. P., Schanze, K. S., and Whitten, D. G. Langmuir 2009, 25, 21
40. Tang, Y. L., Zhou, Z. J., Ogawa, K., Lopez, G. P., Schanze, K. S., and Whitten, D. G. J. Photochem. Photobiol., A 2009, 207, 4
41. -6 M) for both dsDNA and ssDNA.
42. While OPE-2 may not be planar, it is anticipated that this small oligomer should be a "rigid rod" with respect to its backbone.
43. The differences between OPE-2 complexes with dsDNA, CMC, and CMA may be caused by the size difference in the scaffolds and possibly by the ionic strength difference. CMC and CMA are larger (naturally occurring cellulose has degrees of polymerization higher than 10000) than dsDNA used in these experiments for which the largest number of base pairs is 32. The investigations in this study indicate the extent of complex fluorescence increases with an increase in the number of bases in the DNA. The present experiments were carried out in 25 mM phosphate buffer solution, whereas the self-assembly between OPE-2 and CMC or CMA was measured in water. We have found in the higher ionic strength PBS the complexes between OPE-2 and CMC and CMA exhibit similar spectra to those observed in water, but the extent of fluorescence increase is lower.
44. Martin, S. R. and Schilstra, M. J. Circular Dichroism and Its Application to the study of Biomolecules. Methods in Cell Biology; Elsevier Inc.: New York, 2008; Vol. 84, p 263
45. Nunes, J. A. and Tong, W. G. Anal. Chem. 1993, 65, 2990
46. Kim, O. K., Je, J., Jernigan, G., Buckley, L., and Whitten, D. J. Am. Chem. Soc. 2006, 128, 510
47. Liu, Y., Wang, Y., Jin, J., Wang, H., and Yang, R. Chem. Commun. 2009, 665
48. Rant, U., Arinaga, K., Scherer, S., Pringsheim, E., Fujita, S., Yokoyama, N., Tornow, M., and Abstreiter, G. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 17364