Screening and Improvement of an Anti-VEGF DNA Aptamer www.mdpi.com/journal/ molecules

Molecules

Volumn 15, Issue 1, 2010, Pages 215-225

  Nonaka, Yoshihiko ^a   Sode, Koji ^a   Ikebukuro, Kazunori ^a  

^a TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

Author keywords

Aptamer; Cancer diagnosis; Sensor element; Vegf 165; Vegf121

Indexed keywords

APTAMER; MUTANT PROTEIN; VASCULOTROPIN A;

ARTICLE; CIRCULAR DICHROISM; COMBINATORIAL CHEMISTRY; GENETICS; HUMAN; KINETICS; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SURFACE PLASMON RESONANCE;

APTAMERS, NUCLEOTIDE; BASE SEQUENCE; CIRCULAR DICHROISM; HUMANS; KINETICS; MOLECULAR SEQUENCE DATA; MUTANT PROTEINS; SELEX APTAMER TECHNIQUE; SURFACE PLASMON RESONANCE; VASCULAR ENDOTHELIAL GROWTH FACTOR A;

EID: 75749091177     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules15010215     Document Type: Article

References (21)

1. 1. Ellington, A.D.; Szostak, J. W. In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346, 818-822. (Pubitemid 20272100)
2. 2. Tuerk, C.; Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990, 249, 505-510. (Pubitemid 20248891)
3. Erdem, A.; Karadeniz, H.; Mayer, G.; Famulok, M.; Caliskan, A. Electrochemical sensing of aptamer-protein interactions using a magnetic particle assay and single-use sensor technology. Electroanalysis 2009, 21, 1278-1284.
4. Xiao, Y.; Uzawa, T.; White, R. J.; DeMartini, D.; Plaxco, K. W. On the Signaling of Electrochemical Aptamer-Based Sensors: Collision- and Folding-Based Mechanisms. Electroanalysis 2009, 21, 1267-1271.
5. Huang, Y.C.; Ge, B.X.; Sen, D.; Yu, H. Z. Immobilized DNA switches as electronic sensors for picomolar detection of plasma proteins. J. Am. Chem. Soc. 2008, 130, 8023-8029.
6. Noma, T.; Sode, K.; Ikebukuro, K. Characterization and application of aptamers for Taq DNA polymerase selected using an evolution-mimicking algorithm. Biotechnol. Lett. 2006, 28, 1939-1944.
7. 7. Hirao, I.; Madin, K.; Endo, Y.; Yokoyama, S.; Ellington, A.D. RNA aptamers that bind to and inhibit the ribosome-inactivating protein, pepocin. J. Biol. Chem. 2000, 275, 4943-4948. (Pubitemid 30108889)
8. Allali-Hassani, A.; Pereira, M.P.; Navani, N.K.; Brown, E.D.; Li, Y.F. Isolation of DNA aptamers for CDP-ribitol synthase, and characterization of their inhibitory and structural properties. Chembiochem 2007, 8, 2052-2057.
9. 9. Ruckman, J.; Green, L. S.; Beeson, J.; Waugh, S.; Gillette, W. X.; Henninger, D. D.; ClaessonWelsh, L.; Janjic, N. 2′-Fluoropyrimidine RNA-based aptamers to the 165-amino acid form of vascular endothelial growth factor (VEGF165). Inhibition of receptor binding and VEGF-induced vascular permeability through interactions requiring the exon 7-encoded domain. J. Biol. Chem. 1998, 273, 20556-20567. (Pubitemid 28377626)
10. Potty, A.S.; Kourentzi, K.; Fang, H.; Jackson, G.W.; Zhang, X.; Legge, G.B.; Willson, R.C. Biophysical characterization of DNA aptamer interactions with vascular endothelial growth factor. Biopolymers 2009, 91, 145-156.
11. 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. Direct in vitro selection of a 2′-O-methyl aptamer to VEGF. Chem. Biol. 2005, 12, 25-33.
12. Hasegawa, H.; Sode, K.; Ikebukuro, K. Selection of DNA aptamers against VEGF165 using a protein competitor and the aptamer blotting method. Biotechnol. Lett. 2008, 30, 829-834.
13. Ogasawara, D.; Hachiya, N.S.; Kaneko, K.; Sode, K.; Ikebukuro, K. Detection system based on the conformational change in an aptamer and its application to simple bound/free separation. Biosens. Bioelectron 2009, 24, 1372-1376.
14. 14. Yoshida, W.; Sode, K.; Ikebukuro, K. Aptameric enzyme subunit for biosensing based on enzymatic activity measurement. Anal. Chem. 2006, 78, 3296-3303. (Pubitemid 43748972)
15. Hasegawa, H.; Taira, K.I.; Sode, K.; Ikebukuro, K. Improvement of aptamer affinity by dimerization. Sensors 2008, 8, 1090-1098.
16. 16. Ikebukuro, K.; Kiyohara, C.; Sode, K. Novel electrochemical sensor system for protein using the aptamers in sandwich manner. Biosens. Bioelectron. 2005, 20, 2168-2172. (Pubitemid 40312118)
17. 17. Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31, 3406-3415. (Pubitemid 37442169)
18. Kikin, O.; D'Antonio, L.; Bagga, P.S. QGRS Mapper: a web-based server for predicting Gquadruplexes in nucleotide sequences. Nucleic Acids Res. 2006, 34, W676-W682.
19. Paramasivan, S.; Rujan, I.; Bolton, P.H. Circular dichroism of quadruplex DNAs: applications to structure, cation effects and ligand binding. Methods 2007,43, 324-331.
20. Jayapal, P.; Mayer, G.; Heckel, A.; Wennmohs, F. Structure-activity relationships of a caged thrombin binding DNA aptamer: insight gained from molecular dynamics simulation studies. J. Struct. Biol. 2009, 166, 241-250.
21. 21. Noma, T.; Ikebukuro, K.; Sode, K.; Ohkubo, T.; Sakasegawa, Y.; Hachiya, N.; Kaneko, K. A screening method for DNA aptamers that bind to a specific, unidentified protein in tissue samples. Biotechnol. Lett. 2006, 28, 1377-1381. (Pubitemid 44243919)