How to measure the affinity of aptamers for membrane proteins expressed on the surface of living adherent cells

Methods

Volumn 97, Issue , 2016, Pages 35-43

  Quang, Nam Nguyen ^a,b   Pestourie, Carine ^c,d   Cibiel, Agnès ^e   Ducongé, Frédéric ^a,b  

^a INSTITUT DE RADIOPROTECTION ET DE SÛRETÉ NUCLÉAIRE   (France)

^b UNIVERSITÉ PARIS SACLAY   (France)

^c INSERM   (France)

^d UNIVERSITÉ PAUL SABATIER   (France)

^e Genomic Vision   (France)

Author keywords

Aptamers; Binding; Cell SELEX; Kd; Liquid handling robot

Indexed keywords

APTAMER; MEMBRANE PROTEIN; PHOSPHORUS 32; TRANSFER RNA; PROTEIN BINDING;

APPARENT DISSOCIATION CONSTANT; ARTICLE; BINDING AFFINITY; BINDING ASSAY; CELL ADHESION; CELL COUNT; CELL SURFACE; CONTROLLED STUDY; INCUBATION TIME; ISOTOPE LABELING; LABORATORY AUTOMATION; NUCLEIC ACID ANALYSIS; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN BINDING; PROTEIN EXPRESSION; REPRODUCIBILITY; TEMPERATURE SENSITIVITY; ANIMAL; CHEMISTRY; GENETIC PROCEDURES; HUMAN; PC12 CELL LINE; RAT; SENSITIVITY AND SPECIFICITY; SINGLE CELL ANALYSIS; SYSTEMATIC EVOLUTION OF LIGANDS BY EXPONENTIAL ENRICHMENT APTAMER TECHNIQUE;

ANIMALS; APTAMERS, NUCLEOTIDE; BIOSENSING TECHNIQUES; CELL ADHESION; HUMANS; MEMBRANE PROTEINS; PC12 CELLS; PROTEIN BINDING; RATS; SELEX APTAMER TECHNIQUE; SENSITIVITY AND SPECIFICITY; SINGLE-CELL ANALYSIS;

EID: 84959898736     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2015.11.011     Document Type: Article

References (32)

1. Pestourie C., Tavitian B., Duconge F. Aptamers against extracellular targets for in vivo applications. Biochimie 2005, 87:921-930.
2. Cibiel A., Dupont D.M., Duconge F. Methods to identify aptamers against cell surface biomarkers. Pharmaceuticals 2011, 4:1216-1235.
3. Cibiel A., Pestourie C., Duconge F. In vivo uses of aptamers selected against cell surface biomarkers for therapy and molecular imaging. Biochimie 2012, 94:1595-1606.
4. Meyer C., Hahn U., Rentmeister A. Cell-specific aptamers as emerging therapeutics. J. Nucleic Acids 2011, 2011:904750.
5. Zhou J., Rossi J. Cell-type-specific aptamer and aptamer-small interfering RNA conjugates for targeted human immunodeficiency virus type 1 therapy. J. Investig. Med. 2014, 62:914-919.
6. Ellington A.D., Szostak J.W. In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346:818-822.
7. Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990, 249:505-510.
8. Keefe A.D., Pai S., Ellington A. Aptamers as therapeutics. Nat. Rev. Drug Discovery 2010, 9:537-550.
9. Opazo F., Levy M., Byrom M., Schafer C., Geisler C., Groemer T.W., Ellington A.D., Rizzoli S.O. Aptamers as potential tools for super-resolution microscopy. Nat. Methods 2012, 9:938-939.
10. Zhang P., Zhao N., Zeng Z., Chang C.C., Zu Y. Combination of an aptamer probe to CD4 and antibodies for multicolored cell phenotyping. Am. J. Clin. Pathol. 2010, 134:586-593.
11. Meyer M., Scheper T., Walter J.G. Aptamers: versatile probes for flow cytometry. Appl. Microbiol. Biotechnol. 2013.
12. Mayer G. The chemical biology of aptamers. Angew. Chem. Int. Ed. Engl. 2009, 48:2672-2689.
13. Farokhzad O.C., Karp J.M., Langer R. Nanoparticle-aptamer bioconjugates for cancer targeting. Expert Opin. Drug Delivery 2006, 3:311-324.
14. Thiel K.W., Giangrande P.H. Therapeutic applications of DNA and RNA aptamers. Oligonucleotides 2009, 19:209-222.
15. Jing M., Bowser M.T. Methods for measuring aptamer-protein equilibria: a review. Anal. Chim. Acta 2011, 686:9-18.
16. Deng B., Lin Y., Wang C., Li F., Wang Z., Zhang H., Li X.F., Le X.C. Aptamer binding assays for proteins: the thrombin example-A review. Anal. Chim. Acta 2014, 837C:1-15.
17. Blank M., Weinschenk T., Priemer M., Schluesener H. Systematic evolution of a DNA aptamer binding to rat brain tumor microvessels. Selective targeting of endothelial regulatory protein pigpen. J. Biol. Chem. 2001, 276:16464-16468.
18. Raddatz M.S., Dolf A., Endl E., Knolle P., Famulok M., Mayer G. Enrichment of cell-targeting and population-specific aptamers by fluorescence-activated cell sorting. Angew. Chem. Int. Ed. Engl. 2008, 47:5190-5193.
19. Hernandez L., Flenker K., Hernandez F., Klingelhutz A., McNamara J., Giangrande P. Methods for evaluating cell-specific, cell-internalizing RNA aptamers. Pharmaceuticals 2013, 6:295-319.
20. Li N., Ebright J., Stovall G., Chen X., Nguyen H., Singh A., Syrett H., Ellington A. Technical and biological issues relevant to cell typing by aptamers. J. Proteome Res. 2009.
21. Lefkowitz R.J. Seven transmembrane receptors: a brief personal retrospective. Biochim. Biophys. Acta 2007, 1768:748-755.
22. Frey K.A., Albin R.L. Receptor binding techniques. Current Protocols in Neuroscience 2001, John Wiley & Sons, Inc., (Chapter 1), Unit 1.4.
23. Bylund D.B., Murrin L.C. Radioligand saturation binding experiments over large concentration ranges. Life Sci. 2000, 67:2897-2911.
24. Hulme E.C., Trevethick M.A. Ligand binding assays at equilibrium: validation and interpretation. Br. J. Pharmacol. 2010, 161:1219-1237.
25. Lauffenburger D.A., Linderman J.J. Receptors: Models for Binding, Trafficking, and Signalling 1993, Oxford University Press.
26. Wilson K. Principles and Techniques of Practical Biochemistry 2000, Cambridge University Press, pp. 403-452.
27. Borgna J.L. Requirements for reliable determination of binding affinity constants by saturation analysis approach. J. Steroid Biochem. Mol. Biol. 2004, 92:419-433.
28. Sambrook J.F., Russell D.W. Molecular Cloning: A Laboratory Manual 2001, Cold Spring Harbor Laboratory Press, pp. 10.11-10.16. third ed.
29. Pestourie C., Cerchia L., Gombert K., Aissouni Y., Boulay J., De Franciscis V., Libri D., Tavitian B., Duconge F. Comparison of different strategies to select aptamers against a transmembrane protein target. Oligonucleotides 2006, 16:323-335.
30. Cibiel A., Quang N.Nguyen, Gombert K., Thézé B., Garofalakis A., Ducongé F. From ugly duckling to swan: unexpected identification from cell-SELEX of an anti-annexin A2 aptamer targeting tumors. PLoS One 2014, 9:e87002.
31. Califano D., D'Alessio A., Colucci-D'Amato G.L., De Vita G., Monaco C., Santelli G., Di Fiore P.P., Vecchio G., Fusco A., Santoro M., de Franciscis V. A potential pathogenetic mechanism for multiple endocrine neoplasia type 2 syndromes involves ret-induced impairment of terminal differentiation of neuroepithelial cells. Proc. Natl. Acad. Sci. USA 1996, 93:7933-7937.
32. Shigdar S., Qian C., Lv L., Pu C., Li Y., Li L., Marappan M., Lin J., Wang L., Duan W. The use of sensitive chemical antibodies for diagnosis: detection of low levels of EpCAM in breast cancer. PLoS One 2013, 8:e57613.