Kinetic Analysis of Site-specific Photoaptamer-Protein Cross-linking

Journal of Molecular Biology

Volumn 336, Issue 5, 2004, Pages 1159-1173

  Koch, Tad H ^a   Smith, Drew ^b   Tabacman, Eduardo ^b   Zichi, Dominic A ^b  

^a UNIVERSITY OF COLORADO   (United States)

^b SomaLogic Inc   (United States)

Author keywords

Aptamer; Kinetic analysis; Photocross link; Protein microarray; SELEX

Indexed keywords

APTAMER; FIBROBLAST GROWTH FACTOR;

ANALYTIC METHOD; ARTICLE; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CROSS LINKING; PROTEIN MICROARRAY; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; QUANTUM YIELD; REACTION ANALYSIS;

EID: 1242317033     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.01.001     Document Type: Article

References (25)

1. Meisenheimer K.M., Koch T.H. Photocross-linking of nucleic acids to associated proteins. Crit. Rev. Biochem. Mol. Biol. 32:1997;101-140.
2. Meisenheimer K.M., Meisenheimer P.L., Koch T.H. Nucleoprotein photocross-linking using halopyrimidine-substituted RNAs. Methods Enzymol. 318:2000;88-104.
3. Dietz T.M., Koch T.H. Photochemical coupling of 5-bromouracil to tryptophan, tyrosine and histidine, peptide-like derivatives in aqueous fluid solution. Photochem. Photobiol. 46:1987;971-978.
4. Dietz T.M., Koch T.H. Photochemical reduction of 5-bromouracil by cysteine derivatives and coupling of 5- bromouracil to cystine derivatives. Photochem. Photobiol. 49:1989;121-129.
5. Norris C.L., Meisenheimer K.M., Koch T.H. Mechanistic studies relevant to bromouridine enhanced nucleoprotein photocross-linking. Possible involvement of an excited tyrosine residue of the protein. Photochem. Photobiol. 65:1997;201-207.
6. Jensen K.B., Atkinson B.L., Willis M.C., Koch T.H., Gold L. Using in vitro selection to direct the covalent attachment of human immunodeficiency virus type 1 Rev protein to high-affinity RNA ligands. Proc. Natl Acad. Sci. USA. 92:1995;12220-12224.
7. Norris C.L., Meisenheimer P.L., Koch T.H. Mechanistic studies of the 5-iodouracil chromophore relevant to its use in nucleoprotein photocross-linking. J. Am. Chem. Soc. 118:1996;5796-5803.
8. Golden M.C., Collins B.D., Willis M.C., Koch T.H. Diagnostic potential of photoSELEX-evolved ssDNA aptamers. J. Biotechnol. 81:2000;167-178.
9. Brody E.N., Willis M.C., Smith J.D., Jayasena S., Zichi D.A., Gold L. The use of aptamers in large arrrays for molecular diagnostics. Mol. Diagn. 2:1999;381-388.
10. Brody E.N., Gold L. Aptamers as therapeutic and diagnostic agents. J. Biotechnol. 74:2000;5-13.
11. Smith D., Collins B.D., Heil J., Koch T.H. Sensitivity and specificity of photoaptamer probes. Mol. Cell. Proteomics. 2.1:2003;11-18.
12. Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4DNA polymerase. Science. 249:1990;505-510.
13. Ellington A.D., Szostak J.W. In vitro selection of RNA molecules that bind specific ligands. Nature. 346:1990;818-822.
14. Tasset D.M., Kubik M.F., Steiner W. Oligonucleotide inhibitors of human thrombin that bind distinct epitopes. J. Mol. Biol. 272:1997;688-698.
15. Ruckman J., Green L.S., Beeson J., Waugh S., Gillette W.L., Henninger D.D., et al. 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. 273:1998;20556-20567.
16. Petach H., Gold L. Dimensionality is the issue: use of photoaptamers in protein microarrays. Curr. Opin. Biotechnol. 13:2002;309-314.
17. Budowsky E.I., Abdurashidova G.G. Polynucleotide-protein cross-links induced by ultraviolet light and their use for structural investigation of nuleoproteins. Prog. Nucl. Acids Res. Mol. Biol. 37:1989;1-65.
18. Golden M.C., Resing R.A., Collins B.C., Willis M.C., Koch T.H. Mass spectral characterization of a protein-nucleic acid photocross-link. Protein Sci. 8:1999;2806-2812.
19. Golden, M. C. (1999). Photochemical systematic evolution of ligands by exponential enrichment (PhotoSELEX) employing the 5-bromo-2′ deoxyuridine chromophore for the basic fibroblast growth factor target. Ph.D. Thesis, Univ. of Colorado, Boulder, CO.
20. Sugiyama H., Tsutsumi Y., Saito I. Highly sequence selective photoreaction of 5-bromouracil-containing deoxyhexanucleotides. J. Am. Chem. Soc. 112:1990;6720-6721.
21. Fujimoto K., Ikeda Y., Ishihara S., Saito I. Deoxyribonolactone formation in photoirradiation of 5-bromouracil-containing oligonucleotides by direct C1′ hydrogen abstraction. Tetrahedron Letters. 43:2002;2243-2245.
22. Cook G.P., Greenberg M.M. A novel mechanism for the formation of direct strand breaks upon anaerobic photolysis of duplex DNA containing 5-bromodeoxyuridine. J. Am. Chem. Soc. 118:1996;10025-10030.
23. Chen T., Cook G.P., Koppisch A.T., Greenberg M.M. Investigation of the origin of the sequence selectivity for the 5-halo-2′-deoxyuridine sensitization of DNA to damage by UV-irradiation. J. Am. Chem. Soc. 122:2000;3861-3866.
24. Sugiyama H., Tsutsumi Y., Fujimoto K., Saito I. Photoinduced deoxyribose C2′ oxidation in DNA. Alkali-dependent cleavage of erythrose-containing sites via a retroaldol reaction. J. Am. Chem. Soc. 115:1993;4443-4448.
25. Valegard K., Murray J.B., Stocky P.G., Stonehouse N.J., Liljas L. Crystal structure of an RNA bacteriophage coat protein-operator complex. Nature. 371:1994;623-626.