Probing high affinity sequences of DNA aptamer against VEGF 165

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Kaur, Harleen ^a   Yung, Lin Yue Lanry ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; ISOPROTEIN; VASCULOTROPIN 165; DIAGNOSTIC AGENT; VASCULOTROPIN A; VEGFA PROTEIN, HUMAN;

ARTICLE; BINDING AFFINITY; CANCER CELL; COLORECTAL CANCER; CONTROLLED STUDY; DNA SEQUENCE; FETUS; FLUORESCENCE ANALYSIS; HUMAN; HUMAN CELL; IN VITRO STUDY; MOLECULAR IMAGING; MOLECULAR PROBE; PROTEIN BINDING; PROTEIN DETERMINATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN TARGETING; SPECTROSCOPY; SURFACE PLASMON RESONANCE; BINDING SITE; CHEMISTRY; COLORECTAL TUMOR; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; PATHOLOGY; SENSITIVITY AND SPECIFICITY; TUMOR CELL CULTURE;

APTAMERS, NUCLEOTIDE; BASE SEQUENCE; BINDING SITES; COLORECTAL NEOPLASMS; HUMANS; PROTEIN BINDING; SENSITIVITY AND SPECIFICITY; SURFACE PLASMON RESONANCE; TUMOR CELLS, CULTURED; VASCULAR ENDOTHELIAL GROWTH FACTOR A;

EID: 84857126821     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0031196     Document Type: Article

References (48)

1. Bock LC, Griffin LC, Latham JA, Vermaas EH, Toole JJ, (1992) Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature 355: 564-566.
2. Wrzesinski J, Ciesiolka J, (2005) Characterization of structure and metal ions specificity of Co2+-binding RNA aptamers. Biochemistry 44: 6257-6268.
3. Davis JH, Szostak JW, (2002) Isolation of high-affinity GTP aptamers from partially structured RNA libraries. Proc Natl Acad Sci USA 99: 11616-11621.
4. Jayasena SD, (1999) Aptamers: An emerging class of molecules that rival antibodies in diagnostics. Clin Chem 45: 1628-1650.
5. Ruckman J, Green LS, Beeson J, Waugh S, Gillette WL, et al. (1998) 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 273: 20556-20567.
6. Sayyed SG, Hägele H, Kulkarni OP, Endlich K, Segerer S, et al. (2009) Podocytes produce homeostatic chemokine stromal cell-derived factor-1/CXCL12, which contributes to glomerulosclerosis, podocyte loss and albuminuria in a mouse model of type 2 diabetes. Diabetologia 52: 2445-2454.
7. Ninichuk V, Clauss S, Kulkarni O, Schmid H, Segerer S, et al. (2008) Late onset of Ccl2 blockade with the Spiegelmer mNOX-E36-3′-PEG prevents glomerulosclerosis and improves glomerular filtration rate in db/db mice. Am J Pathol 172: 628-637.
8. Bates PJ, Laber DA, Miller DM, Thomas SD, Trent JO, (2009) Discovery and development of the G-rich oligonucleotide AS1411 as a novel treatment for cancer. Exp Mol Pathol 86: 151-164.
9. Waters EK, Richardson J, Schaub RG, Kurz JC, (2009) Effect of NU172 and bivalirudin on ecarin clotting time in human plasma and whole blood. J Thromb Haemost 7: 683.
10. Diener JL, Daniel Lagassé HA, Duerschmied D, Merhi Y, Tanguay JF, et al. (2009) Inhibition of von Willebrand factor-mediated platelet activation and thrombosis by the anti-von Willebrand factor A1-domain aptamer ARC1779. J Thromb Haemost 7: 1155-1162.
11. Chan MY, Cohen MG, Dyke CK, Myles SK, Aberle LG, et al. (2008) Phase 1b randomized study of antidote-controlled modulation of factor IXa activity in patients with stable coronary artery disease. Circulation 117: 2865-2874.
12. Biesecker G, Dihel L, Enney K, Bendele RA, (1999) Derivation of RNA aptamer inhibitors of human complement C5. Immunopharmacology 42: 219-230.
13. Green LS, Jellinek D, Jenison R, Ostman A, Heldin CH, et al. (1996) Inhibitory DNA ligands to platelet-derived growth factor B-chain. Biochemistry 35: 14413-14424.
14. Ellington AD, Szostak JW, (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818-822.
15. Tuerk C, Gold L, (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249: 505-510.
16. Misono TS, Kumar PKR, (2005) Selection of RNA aptamers against human influenza virus hemagglutinin using surface plasmon resonance. Anal Biochem 342: 312-317.
17. Berezovski M, Drabovich A, Krylova SM, Musheev M, Okhonin V, et al. (2005) Nonequilibrium capillary electrophoresis of equilibrium mixtures: A universal tool for development of aptamers. J Am Chem Soc 127: 3165-3171.
18. Tok JB, Fischer NO, (2008) Single microbead SELEX for efficient ssDNA aptamer generation against botulinum neurotoxin. Chem Comm pp. 1883-1885.
19. Jellinek D, Green LS, Bell C, Lynott CK, Gill N, et al. (1995) Potent 2′-amino-2′-deoxypyrimidine RNA inhibitors of basic fibroblast growth factor. Biochemistry 34: 11363-11372.
20. Pagratis NC, Bell C, Chang YF, Jennings S, Fitzwater T, et al. (1997) Potent 2′-amino-, and 2′-fluoro-2′-deoxyribonucleotide RNA inhibitors of keratinocyte growth factor. Nature Biotechnol 15: 68-73.
21. Chelliserrykattil J, Ellington AD, (2004) Evolution of a T7 RNA polymerase variant that transcribes 2′-O-methyl RNA. Nature Biotechnol 22: 1155-1160.
22. Hernandez FJ, Kalra N, Wengel J, Vester B, (2009) Aptamers as a model for functional evaluation of LNA and 2′-amino LNA. Bioorg Med Chem Lett 19: 6585-6587.
23. Schmidt KS, Borkowski S, Kurreck J, Stephens AW, Bald R, et al. (2004) Application of locked nucleic acids to improve aptamer in vivo stability and targeting function. Nucleic Acids Res 32: 5757-5765.
24. Kawasaki AM, Casper MD, Freier SM, Lesnik EA, Zounes MC, et al. (1993) Uniformly modified 2′-deoxy-2′-fluoro phosphorothioate oligonucleotides as nuclease-resistant antisense compounds with high affinity and specificity for RNA targets. J Med Chem 36: 831-841.
25. Somasunderam A, Ferguson MR, Rojo DR, Thiviyanathan V, Li X, et al. (2005) Combinatorial selection, inhibition, and antiviral activity of DNA thioaptamers targeting the RNase H domain of HIV-1 reverse transcriptase. Biochemistry 44: 10388-10395.
26. Boomer RM, Lewis SD, Healy JM, Kurz M, Wilson C, et al. (2005) Conjugation to polyethylene glycol polymer promotes aptamer biodistribution to healthy and inflamed tissues. Oligonucleotides 15: 183-195.
27. Kato T, Yano K, Ikebukuro K, Karube I, (2000) Interaction of three-way DNA junctions with steroids. Nucleic Acids Res 28: 1963-1968.
28. Shangguan D, Tang Z, Mallikaratchy P, Xiao Z, Tan W, (2007) Optimization and modifications of aptamers selected from live cancer cell lines. ChemBioChem 8: 603-606.
29. Sayer NM, Cubin M, Rhie A, Bullock M, Tahiri-Alaoui A, et al. (2004) Structural determinants of conformationally selective, prion-binding aptamers. J Biol Chem 279: 13102-13109.
30. Katilius E, Flores C, Woodbury NW, (2007) Exploring the sequence space of a DNA aptamer using microarrays. Nucleic Acids Res 35: 7626-7635.
31. Houck KA, Ferrara N, Winer J, Cachianes G, Li B, et al. (1991) The vascular endothelial growth factor family: Identification of a fourth molecular species and characterization of alternative splicing of RNA. Mol Endocrinol 5: 1806-1814.
32. Park JE, Keller GA, Ferrara N, (1993) The vascular endothelial growth factor (VEGF) isoforms: Differential deposition into the subepithelial extracellular matrix and bioactivity of extracellular matrix-bound VEGF. Mol Biol Cell 4: 1317-1326.
33. Cohen T, Gitay-Goren H, Sharon R, Shibuya M, Halaban R, et al. (1995) VEGF121, a vascular endothelial growth factor (VEGF) isoform lacking heparin binding ability, requires cell-surface heparan sulfates for efficient binding to the VEGF receptors of human melanoma cells. J Biol Chem 270: 11322-11326.
34. Keyt BA, Berleau LT, Nguyen HV, Chen H, Heinsohn H, et al. (1996) The carboxyl-terminal domain (111-165) of vascular endothelial growth factor is critical for its mitogenic potency. J Biol Chem 271: 7788-7795.
35. Hasegawa H, Sode K, Ikebukuro K, (2008) Selection of DNA aptamers against VEGF165 using a protein competitor and the aptamer blotting method. Biotechnol Lett 30: 829-834.
36. Hasegawa H, Taira KI, Sode K, Ikebukuro K, (2008) Improvement of aptamer affinity by dimerization. Sensors 8: 1090-1098.
37. Zuker M, (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
38. Potty ASR, Kourentzi K, Fang H, Jackson GW, Zhang X, et al. (2009) Biophysical characterization of DNA aptamer interactions with vascular endothelial growth factor. Biopolymers 91: 145-156.
39. Davis KA, Lin Y, Abrams B, Jayasena SD, (1998) Staining of cell surface human CD4 with 2′-F-pyrimidine-containing RNA aptamers for flow cytometry. Nucleic Acids Res 26: 3915-3924.
40. Daniels DA, Chen H, Hicke BJ, Swiderek KM, Gold L, (2003) A tenascin-C aptamer identified by tumor cell SELEX: Systematic evolution of ligands by exponential enrichment. Proc Natl Acad Sci USA 100: 15416-15421.
41. Waleh NS, Brody MD, Knapp MA, Mendonca HL, Lord EM, et al. (1995) Mapping of the vascular endothelial growth factor-producing hypoxie cells in multicellular tumor spheroids using a hypoxia-specific marker. Cancer Res 55: 6222-6226.
42. Oswald J, Treite F, Haase C, Kampfrath T, Mäding P, et al. (2007) Experimental hypoxia is a potent stimulus for radiotracer uptake in vitro: Comparison of different tumor cells and primary endothelial cells. Cancer Lett 254: 102-110.
43. Calvani M, Trisciuoglio D, Bergamaschi C, Shoemaker RH, Melillo G, (2008) Differential involvement of vascular endothelial growth factor in the survival of hypoxic colon cancer cells. Cancer Res 68: 285-291.
44. Vaupel P, Mayer A, (2007) Hypoxia in cancer: Significance and impact on clinical outcome. Cancer Metast Rev 26: 225-239.
45. Minchenko A, Bauer T, Salceda S, Caro J, (1994) Hypoxic stimulation of vascular endothelial growth factor expression in vitro and in vivo. Lab Invest 71: 374-379.
46. Neufeld G, Cohen T, Gengrinovitch S, Poltorak Z, (1999) Vascular endothelial growth factor (VEGF) and its receptors. FASEB J 13: 9-22.
47. Ikeda E, Achen MG, Breier G, Risau W, (1995) Hypoxia-induced transcriptional activation and increased mRNA stability of vascular endothelial growth factor in C6 glioma cells. J Biol Chem 270: 19761-19766.
48. Shima DT, Deutsch U, D'Amore PA, (1995) Hypoxic induction of vascular endothelial growth factor (VEGF) in human epithelial cells is mediated by increases in mRNA stability. FEBS Lett 370: 203-208.