Affinity improvement of a VEGF aptamer by in silico maturation for a sensitive VEGF-detection system

Analytical Chemistry

Volumn 85, Issue 2, 2013, Pages 1132-1137

  Nonaka, Yoshihiko ^a   Yoshida, Wataru ^a   Abe, Koichi ^a   Ferri, Stefano ^a   Schulze, Holger ^b   Bachmann, Till T ^b   Ikebukuro, Kazunori ^a  

^a TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMERS; BINDING AFFINITIES; DISSOCIATION CONSTANT; G-QUADRUPLEX STRUCTURE; G-QUARTET; GUANINE-TRACTS; HIGH AFFINITY; IMPROVE-A; IN-SILICO; SENSITIVE ASSAY; SENSITIVE DETECTION; SYSTEMATIC EVOLUTION OF LIGANDS BY EXPONENTIAL ENRICHMENTS;

CHEMICAL DETECTION; DISSOCIATION; MOLECULES;

BINDING ENERGY;

APTAMER; RECOMBINANT PROTEIN; VASCULOTROPIN A; VEGFA PROTEIN, HUMAN;

ARTICLE; CHEMISTRY; CIRCULAR DICHROISM; HUMAN; SENSITIVITY AND SPECIFICITY; SURFACE PLASMON RESONANCE;

APTAMERS, NUCLEOTIDE; CIRCULAR DICHROISM; HUMANS; RECOMBINANT PROTEINS; SENSITIVITY AND SPECIFICITY; SURFACE PLASMON RESONANCE; VASCULAR ENDOTHELIAL GROWTH FACTOR A;

EID: 84872578654     PISSN: 00032700     EISSN: 15206882     Source Type: Journal    
DOI: 10.1021/ac303023d     Document Type: Article

References (45)

1. Savory, N.; Abe, K.; Sode, K.; Ikebukuro, K. Biosens. Bioelectron. 2010, 26, 1386-1391
2. Ferrara, N.; Henzel, W. J. Biochem. Biophys. Res. Commun. 1989, 161, 851-858
3. Peirce, S. M.; Price, R. J.; Skalak, T. C. Am. J. Physiol. Heart Circ. Physiol. 2004, 286, H918-925
4. Kim, K. J.; Li, B.; Winer, J.; Armanini, M.; Gillett, N.; Phillips, H. S.; Ferrara, N. Nature 1993, 362, 841-844
5. Kondo, S.; Asano, M.; Matsuo, K.; Ohmori, I.; Suzuki, H. Biochim. Biophys. Acta 1994, 1221, 211-214
6. Stacker, S. A.; Baldwin, M. E.; Achen, M. G. FASEB J. 2002, 16, 922-934
7. Rini, B. I.; Michaelson, M. D.; Rosenberg, J. E.; Bukowski, R. M.; Sosman, J. A.; Stadler, W. M.; Hutson, T. E.; Margolin, K.; Harmon, C. S.; DePrimo, S. E.; Kim, S. T.; Chen, I.; George, D. J. J. Clin. Oncol. 2008, 26, 3743-3748
8. Tolentino, M. Surv. Ophthalmol. 2011, 56, 95-113
9. Tuerk, C.; Gold, L. Science 1990, 249, 505-510
10. Ellington, A. D.; Szostak, J. W. Nature 1990, 346, 818-822
11. Ikebukuro, K.; Kiyohara, C.; Sode, K. Anal. Lett. 2004, 37, 2901-2909
12. Ikebukuro, K.; Kiyohara, C.; Sode, K. Biosens. Bioelectron. 2005, 20, 2168-2172
13. Potyrailo, R. A.; Conrad, R. C.; Ellington, A. D.; Hieftje, G. M. Anal. Chem. 1998, 70, 3419-3425
14. Lee, M.; Walt, D. R. Anal. Biochem. 2000, 282, 142-146
15. Bruno, J. G.; Kiel, J. L. Biotechniques 2002, 32, 178-183
16. Xiao, Y.; Lubin, A. A.; Heeger, A. J.; Plaxco, K. W. Angew. Chem., Int. Ed. 2005, 44, 5456-5459
17. Yoshida, W.; Sode, K.; Ikebukuro, K. Anal. Chem. 2006, 78, 3296-3303
18. Ogasawara, D.; Hachiya, N. S.; Kaneko, K.; Sode, K.; Ikebukuro, K. Biosens. Bioelectron. 2009, 24, 1372-1376
19. Carrasquillo, K. G.; Ricker, J. A.; Rigas, I. K.; Miller, J. W.; Gragoudas, E. S.; Adamis, A. P. Invest. Ophthalmol. Visual Sci. 2003, 44, 290-299
20. Burmeister, P. E.; Lewis, S. D.; Silva, R. F.; Preiss, J. R.; Horwitz, L. R.; Pendergrast, P. S.; McCauley, T. G.; Kurz, J. C.; Epstein, D. M.; Wilson, C.; Keefe, A. D. Chem. Biol. 2005, 12, 25-33
21. Ng, E. W. M.; Shima, D. T.; Calias, P.; Cunningham, E. T.; Guyer, D. R.; Adamis, A. P. Nat. Rev. Drug Discov. 2006, 5, 123-132
22. Nick, T. J.; Darugar, Q.; Kourentzi, K.; Willson, R. C.; Landes, C. F. Biochem. Biophys. Res. Commun. 2008, 373, 213-218
23. Zhao, S.; Yang, W.; Lai, R. Y. Biosens. Bioelectron. 2011, 26, 2442-2447
24. Zhao, J.; He, X.; Bo, B.; Liu, X.; Yin, Y.; Li, G. Biosens. Bioelectron. 2012, 34, 249-252
25. Freeman, R.; Girsh, J.; Jou, A. F.; Ho, J. A.; Hug, T.; Dernedde, J.; Willner, I. Anal. Chem. 2012, 84, 6192-6198
26. Hasegawa, H.; Sode, K.; Ikebukuro, K. Biotechnol. Lett. 2008, 30, 829-834
27. Nonaka, Y.; Sode, K.; Ikebukuro, K. Molecules 2010, 15, 215-225
28. Nonaka, Y.; Abe, K.; Ikebukuro, K. Electrochemistry 2012, 80, 363-366
29. Klug, S. J.; Famulok, M. Mol. Biol. Rep. 1994, 20, 97-107
30. Polz, M.; Cavanaugh, C. Appl. Environ. Microb. 1998, 64, 3724-3730
31. Kanagawa, T. J. Biosci. Bioeng. 2003, 96, 317-323
32. Kim, Y.; Cao, Z.; Tan, W. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 5664-5669
33. Mallikaratchy, P. R.; Ruggiero, A.; Gardner, J. R.; Kuryavyi, V.; Maguire, W. F.; Heaney, M. L.; McDevitt, M. R.; Patel, D. J.; Scheinberg, D. A. Nucleic Acids Res. 2011, 39, 2458-2469
34. Hasegawa, H.; Taira, K.; Sode, K.; Ikebukuro, K. Sensors 2008, 8, 1090-1098
35. Smith, D.; Collins, B. D.; Heil, J.; Koch, T. H. Mol. Cell. Proteomics. 2003, 2, 11-18
36. Famulok, M. J. Am. Chem. Soc. 1994, 116, 1698-1706
37. Tsiang, M.; Gibbs, C. S.; Griffin, L. C.; Dunn, K. E.; Leung, L. L. K. J. Biol. Chem. 1995, 270, 19370-19376
38. Zhang, D.; Lu, M.; Wang, H. J. Am. Chem. Soc. 2011, 133, 9188-9191
39. Ikebukuro, K.; Okumura, Y.; Sumikura, K.; Karube, I. Nucleic Acids Res. 2005, 33, e108
40. Noma, T.; Ikebukuro, K. Biochem. Biophys. Res. Commun. 2006, 347, 226-231
41. Noma, T.; Sode, K.; Ikebukuro, K. Biotechnol. Lett. 2006, 28, 1939-1944
42. Ikebukuro, K.; Yoshida, W.; Noma, T.; Sode, K. Biotechnol. Lett. 2006, 28, 1933-1937
43. Kikin, O.; D'Antonio, L.; Bagga, P. S. Nucleic Acids Res. 2006, 34, W676-682
44. Ruckman, J.; Green, L. S.; Beeson, J.; Waugh, S.; Gillette, W. L.; Henninger, D. D.; Claesson-Welsh, L.; Janjić, N. J. biol. Chem. 1998, 273, 20556-20567
45. Wen, J. D.; Gray, D. M. Biochemistry 2002, 41, 11438-11448