Dynamics of an anti-VEGF DNA aptamer: A single-molecule study

Biochemical and Biophysical Research Communications

Volumn 373, Issue 2, 2008, Pages 213-218

  Nick Taylor, J ^a   Darugar, Qusai ^a   Kourentzi, Katerina ^b   Willson, Richard C ^b   Landes, Christy F ^a  

^a University of Houston   (United States)

^b UNIVERSITY OF HOUSTON   (United States)

Author keywords

Angiogenesis; Aptamers; Dynamics; FRET; Hidden Markov modeling; Nucleic acids; Single molecule spectroscopy; VEGF

Indexed keywords

APTAMER; DNA; MAGNESIUM ION; NUCLEIC ACID; NUCLEOTIDE; VASCULOTROPIN;

ANGIOGENESIS; ARTICLE; BASE PAIRING; CONCENTRATION RESPONSE; CONFORMATIONAL TRANSITION; DYNAMICS; ENERGY; FLUORESCENCE RESONANCE ENERGY TRANSFER; HIDDEN MARKOV MODEL; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; SINGLE MOLECULE FLUORESCENCE RESONANCE ENERGY TRANSFER; STRUCTURE ANALYSIS;

APTAMERS, NUCLEOTIDE; BASE SEQUENCE; DNA; FLUORESCENCE RESONANCE ENERGY TRANSFER; MAGNESIUM; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; VASCULAR ENDOTHELIAL GROWTH FACTOR A;

EID: 46249119401     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2008.05.191     Document Type: Article

References (34)

1. Nimjee S.M., Rusconi C.P., and Sullenger B.A. Aptamers: an emerging class of therapeutics. Annu. Rev. Med. 56 (2005) 555-583
2. Ellington A.D., and Szostak J.W. In vitro selection of RNA molecules that bind specific ligands. Nature 346 (1990) 818-822
3. Tuerk C., and Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage t4 DNA polymerase. Science 249 (1990) 505-510
4. 165). J. Biol. Chem. 273 (1998) 20556-20567
5. Ng E. Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease. Nat. Rev. Drug Discov. 5 (2006)
6. Leung D.W., Cachianes G., Kuang W.J., Goeddel D.V., and Ferrara N. Vascular endothelial growth factor is a secreted angiogenic mitogen. Science 246 (1989) 1306-1309
7. Millauer B., Shawver L.K., Plate K.H., Risaui W., and Ullrich A. Glioblastoma growth inhibited in vivo by a dominant-negative FLK-1 mutant. Nature 367 (1994) 576-579
8. Kim K.J., Li B., Winer J., Armanini M., Gillett N., Phillips H.S., and Ferrara N. Inhibition of vascular endothelial growth factor-induced angiogenesis suppresses tumour growth in vivo. Nature 362 (1993) 841-844
9. Ferrara N., Hillan K.J., Gerber H.-P., and Novotny W. Discovery and development of bevacizumab, an anti-VEGF antibody for treating cancer. Nat. Rev. Drug Discov. 3 (2004) 391-400
10. Holash J., Davis S., Papadopoulos N., Croll S.D., Ho L., Russell M., Boland P., Leidich R., Hylton D., Burova E., Ioffe E., Huang T., Radziejewski C., Bailey K., Fandl J.P., Daly T., Wiegand S.J., Yancopoulos G.D., and Rudge J.S. VEGF-trap: a VEGF blocker with potent antitumor effects. Proc. Natl. Acad. Sci. USA 99 (2002) 11393-11398
11. Mallikaratchy P., Stahelin R.V., Cao Z., Cho W., and Tan W. Selection of DNA ligands for protein kinase C-δ. Chem. Commun. (2006) 3229-3231
12. A. Potty, Ph.D. Thesis, University of Houston, 2007.
13. Brion P., and Westhof E. Hierarchy and dynamics of RNA folding. Annu. Rev. Biophys. Biomol. Struct. 26 (1997) 113-137
14. Misra V.K., and Draper D.E. The linkage between magnesium binding and RNA folding. J. Mol. Biol. 317 (2002) 507-521
15. Thirumalai D., Lee N., Woodson S.A., and Klimov D.K. Early events in RNA folding. Annu. Rev. Phys. Chem. 52 (2001) 751-762
16. Bokinsky G., Rueda D., Misra V.K., Rhodes M.M., Gordus A., Babcock H.P., Walter N.G., and Zhuang X. Single-molecule transition-state analysis of RNA folding. Proc. Natl. Acad. Sci. USA 100 (2003) 9302-9307
17. Draper D.E., Grilley D., and Soto A.M. Ions and RNA folding. Annu. Rev. Biophys. Biomol. Struct. 34 (2005) 221-243
18. 2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules. Proc. Natl. Acad. Sci. USA 99 (2002) 4284-4289
19. Pyle A. Metal ions in the structure and function of RNA. J. Biol. Inorg. Chem. 7 (2002) 679-690
20. Ha T. Single-molecule fluorescence resonance energy transfer. Methods 25 (2001) 78-86
21. Moerner W.E., and Orrit M. Illuminating single molecules in condensed matter. Science 283 (1999) 1670
22. Weiss S. Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy. Nat. Struct. Mol. Biol. 7 (2000) 724-729
23. Zhuang X. Single-molecule rna science. Annu. Rev. Biophys. Biomol. Struct. 34 (2005) 399-414
24. Liu S., Bokinsky G., Walter N.G., and Zhuang X. Single-molecule chemistry and biology special feature: dissecting the multistep reaction pathway of an rna enzyme by single-molecule kinetic "Fingerprinting". Proc. Natl. Acad. Sci. USA 104 (2007) 12634-12639
25. Nahas M.K., Wilson T.J., Hohng S., Jarvie K., Lilley D.M.J., and Ha T. Observation of internal cleavage and ligation reactions of a ribozyme. Nat. Struct. Mol. Biol. 11 (2004) 1107-1113
26. Bokinsky G., Nivon L.G., Liu S., Chai G., Hong M., Weeks K.M., and Zhuang X. Two distinct binding modes of a protein cofactor with its target RNA. J. Mol. Biol. 361 (2006) 771-784
27. Cosa G., Zeng Y., Liu H.W., Landes C.F., Makarov D.E., Musier-Forsyth K., and Barbara P.F. Evidence for non-two-state kinetics in the nucleocapsid protein chaperoned opening of DNA hairpins. J. Phys. Chem. B 110 (2006) 2419-2426
28. Landes C.F., Zeng Y., Liu H.W., Musier-Forsyth K., and Barbara P.F. Single-molecule study of the inhibition of hiv-1 transactivation response region DNA/DNA annealing by argininamide. J. Am. Chem. Soc. 129 (2007) 10181-10188
29. Nir E., Michalet X., Hamadani K.M., Laurence T.A., Neuhauser D., Kovchegov Y., and Weiss S. Shot-noise limited single-molecule FRET histograms: comparison between theory and experiments. J. Phys. Chem. B 110 (2006) 22103-22124
30. Sabanayagam C.R., Eid J.S., and Meller A. Long time scale blinking kinetics of cyanine fluorophores conjugated to DNA and its effect on Förster resonance energy transfer. J. Chem. Phys. 123 (2005) 224708
31. McKinney S.A., Joo C., and Ha T. Analysis of single-molecule fret trajectories using hidden markov modeling. Biophys. J. 91 (2006) 1941-1951
32. Rasnik I., McKinney S.A., and Ha T. Nonblinking and long-lasting single-molecule fluorescence imaging. Nat. Methods 3 (2006) 891-893
33. X. Zhang, A.S.R. Potty, G.W. Jackson, V. Stepanov, A. Tang, Y. Liu, K. Kourentzi, U. Strych, G.E. Fox, R.C. Willson, Engineered 5S ribosomal RNAs displaying aptamers recognizing vascular endothelial growth factor and malachite green, J. Mol. Recognit., in press.
34. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (2003) 3406-3415