Using azobenzene incorporated DNA aptamers to probe molecular binding interactions

Bioconjugate Chemistry

Volumn 22, Issue 2, 2011, Pages 282-288

  Phillips, Joseph A ^a   Liu, Haipeng ^a   O'Donoghue, Meghan B ^a   Xiong, Xiangling ^a   Wang, Ruowen ^a   You, Mingxu ^a   Sefah, Kwame ^a   Tan, Weihong ^a  

^a University of Florida   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CONTROLLED DRUG DELIVERY; DNA; PHOTODYNAMIC THERAPY;

APTAMERS; BINDING AFFINITIES; BINDING INTERACTION; DNA APTAMER; MOLECULAR BINDING; MOLECULAR PROBES; RATIONAL DESIGN; RNA APTAMER; SIMPLE METHOD; STRUCTURAL ELEMENTS;

AZOBENZENE;

APTAMER; AZOBENZENE; STREPTAVIDIN;

ARTICLE; BINDING AFFINITY; BIOSENSOR; CONTROLLED STUDY; DNA BINDING; DNA STRAND; DNA STRUCTURE; DRUG DELIVERY SYSTEM; DRUG SELECTIVITY; ENZYMIC BIOSENSOR; MOLECULAR PROBE; MOLECULARLY TARGETED THERAPY; PROTEIN DNA INTERACTION;

EID: 79951696504     PISSN: 10431802     EISSN: 15204812     Source Type: Journal    
DOI: 10.1021/bc100402p     Document Type: Article

References (39)

1. Jhaveri, S. D., Kirby, R., Conrad, R., Maglott, E. J., Bowser, M., Kennedy, R. T., Glick, G., and Ellington, A. D. (2000) Designed signaling aptamers that transduce molecular recognition to changes in fluorescence intensity J. Am. Chem. Soc. 122, 2469-2473
2. Stojanovic, M. N., de Prada, P., and Landry, D. W. (2001) Aptamer-based folding fluorescent sensor for cocaine J. Am. Chem. Soc. 123, 4928-4931
3. Ozaki, H., Nishihira, A., Wakabayashi, M., Kuwahara, M., and Sawai, H. (2006) Biomolecular sensor based on fluorescence-labeled aptamer Bioorg. Med. Chem. Lett. 16, 4381-4384
4. Ferapontova, E. E., Olsen, E. M., and Gothelf, K. V. (2008) An RNA Aptamer-based electrochemical biosensor for detection of theophylline in serum J. Am. Chem. Soc. 130, 4256-4258
5. Hamaguchi, N., Ellington, A., and Stanton, M. (2001) Aptamer beacons for the direct detection of proteins Anal. Biochem. 294, 126-131
6. Yamamoto, R. and Kumar, P. K. R. (2000) Molecular beacon aptamer fluoresces in the presence of Tat protein of HIV-1 Genes Cells 5, 389-396
7. Jiang, Y., Fang, X., and Bai, C. (2004) Signaling aptamer/protein binding by a molecular light switch complex Anal. Chem. 76, 5230-5235
8. Li, W., Yang, X., Wang, K., Tan, W., Li, H., and Ma, C. (2008) FRET-based aptamer probe for rapid angiogenin detection Talanta 75, 770-774
9. Patel, D. J. and Suri, A. K. (2000) Structure, recognition and discrimination in RNA aptamer complexes with cofactors, amino acids, drugs and aminoglycoside antibiotics Rev. Mol. Biotechnol. 74, 39-60
10. Schwalbe, H., Buck, J., Furtig, B., Noeske, J., and Wohnert, J. (2007) Structures of RNA switches: insight into molecular recognition and tertiary structure Angew. Chem., Int. Ed. 46, 1212-1219
11. Padmanabhan, K., Padmanabhan, K. P., Ferrara, J. D., Sadler, J. E., and Tulinsky, A. (1993) The structure of α-thrombin inhibited by a 15-Mer single-stranded DNA aptamer J. Biol. Chem. 268, 17651-17654
12. Marathias, V. M., Wang, K. Y., Kumar, S., Pham, T. Q., Swaminathan, S., and Bolton, P. H. (1996) Determination of the number and location of the manganese binding sites of DNA quadruplexes in solution by EPR and NMR in the presence and absence of thrombin J. Mol. Biol. 260, 378-394
13. Padmanabhan, K. and Tulinsky, A. (1996) An ambiguous structure of a DNA 15-mer thrombin complex Acta Crystallogr. D52, 272-282
14. Long, S. B., Long, M. B., White, R. R., and Sullenger, B. A. (2008) Crystal structure of an RNA aptamer bound to thrombin RNA 14, 1-9
15. Bouvet, P., Allain, F. H-T., Finger, L. D., Deickmann, T., and Feigon, J. (2001) Recognition of pre-formed and flexible elements of an RNA stem-loop by nucleolin J. Mol. Biol. 309, 763-775
16. 2 complexed to a high-affinity RNA aptamer Proc. Natl. Acad. Sci. U.S.A. 100, 9268-9273
17. Yesodha, S. K., Pillai, C. K. S., and Tsutsumi, N. (2004) Stable polymeric materials for nonlinear optics: a review based on azobenzene systems Prog. Polym. Sci. 29, 45-74
18. Renner, C. and Moroder, L. (2006) Azobenzene as conformational switch in model peptides ChemBioChem 7, 868-878
19. Yager, G. and Barrett, C. J. (2006) Novel photo-switching using azobenzene functional materials J. Photochem. Photobiol. A 182, 250-261
20. Barrett, C. J., Mamiya, J., Yager, K. G., and Ikeda, T. (2007) Photo-mechanical effects in azobenzene-containing soft materials Soft Matter 3, 1249-1261
21. Asanuma, H., Ito, T., Yoshida, T., Liang, X., and Komiyama, M. (1999) Photoregulation of the formation and dissociation of a DNA duplex by using the cis-trans isomerization of azobenzene Angew. Chem., Int. Ed. 38, 2393-2395
22. Liang, X., Asanuma, H., and Komiyama, M. (2001) Phenylazonaphthalene as a superb photo-regulator for DNA-triplex formation Tetrahedron Lett. 42, 6723-6725
23. Liang, X., Asanuma, H., Kashida, H., Takasu, A., Sakamoto, T., Kawai, G., and Komiyama, M. (2003) NMR study on the photoresponsive DNA tethering an azobenzene. assignment of the absolute configuration of two diastereomers and structure determination of their duplexes in the trans-form J. Am. Chem. Soc. 125, 16408-16415
24. Takahashi, K., Yaegashi, S., Asanuma, H., and Hagiya, M. (2006) Photo- and Thermoregulation of DNA Nanomachines Lect. Notes Comput. Sci. 3892, 336-346
25. Liang, X., Nishioka, H., Takenaka, N., and Asanuma, H. (2008) A DNA nanomachine powered by light irradiation ChemBioChem 9, 702-705
26. Liang, X., Takenaka, N., Nishioka, H., and Asanuma, H. (2008) Light driven open/close operation of an azobenzene-modified DNA nano-pincette Nucleic Acids Symp. Ser. (Oxford) 52, 697-698
27. Kim, Y., Phillips, J. A., Liu, H. P., Kang, H. Z., and Tan, W. H. (2009) Using photons to manipulate enzyme inhibition by an azobenzene-modified nucleic acid probe Proc. Natl. Acad. Sci. U.S.A. 106, 6489-6494
28. Ogura, Y., Nishimura, T., and Tanida, J. (2009) Self-contained photonically-controlled DNA tweezers Appl. Phys. Express 2, 025004-1-025004-3
29. Dohno, C., Uno, S., Sakai, S., Oku, M., and Nakatani, K. (2009) The effect of linker length on binding affinity of a photoswitchable molecular glue for DNA Bioorg. Med. Chem. 17, 2536-2543
30. Kang, H., Liu, H., Phillips, J. A., Cao, Z., Kim, Y., Chen, Y., Yang, Z., Li, J., and Tan, W. (2009) Single-DNA molecule nanomotor regulated by photons Nano Lett. 9, 2690-2696
31. Shangguan, D., Li, Y., Tang, Z., Cao, Z. C., Chen, H. W., Mallikaratchy, P., Sefah, K., Yang, C. J., and Tan, W. (2006) Aptamers evolved from live cells as effective molecular probes for cancer study Proc. Natl. Acad. Sci. U.S.A. 103, 11838-11843
32. Shangguan, D., Tang, Z., Mallikaratchy, P., Xiao, Z., and Tan, W. (2007) Optimization and modifications of aptamers selected from live cancer cell lines ChemBioChem 8, 603-606
33. Shangguan, D., Cao, Z., Meng, L., Mallikaratchy, P., Sefah, K., Wang, H., Li, Y., and Tan, W. (2008) Cell-specific aptamer probes for membrane protein elucidation in cancer cells J. Proteome Res. 7, 2133-2139
34. Huang, Y. F., Chang, H. T., and Tan, W. (2008) Cancer cell targeting using multiple aptamers conjugated on nanorods Anal. Chem. 80, 567-572
35. Huang, Y. F., Sefah, K., Bamrungsap, S., Chang, H. T., and Tan, W. (2008) Selective photothermal therapy for mixed cancer cells using aptamer-conjugated nanorods Langmuir 24, 11860-11865
36. Ma, N., Sargent, E. H., and Kelley, S. O. (2008) One-step DNA-programmed growth of luminescent and biofunctionalized nanocrystals Nat. Nanotechnol. 4, 121-125
37. Phillips, J. A., Xu, Y., Xia, Z., Fan, Z. H., and Tan, W. (2009) Enrichment of cancer cells using aptamers immobilized on a microfluidic channel Anal. Chem. 81, 1033-1039
38. Asanuma, H., Liang, X., Nishioka, H., Matsunaga, D., Liu, M., and Komiyama, M. (2007) Synthesis of azobenzene-tethered DNA for reversible photo-regulation of DNA functions: hybridization and transcription Nat. Protoc. 2, 203-212
39. Tang, Z., Shangguan, D., Wang, K., Shi, H., Sefah, K., Mallikratchy, P., Chen, H. W., Li, Y., and Tan, W. (2007) Selection of aptamers for molecular recognition and characterization of cancer cells Anal. Chem. 79, 4900-4907