Streptavidin-coated magnetic beads for DNA strand separation implicate a multitude of problems during cell-SELEX

Oligonucleotides

Volumn 19, Issue 3, 2009, Pages 243-254

  Paul, Angela ^a   Avci Adali, Meltem ^a   Ziemer, Gerhard ^a   Wendel, Hans P ^a  

^a UNIVERSITY HOSPITAL TÜBINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; DOUBLE STRANDED DNA; SINGLE STRANDED DNA; STREPTAVIDIN;

ARTICLE; BIOTINYLATION; COMBINATORIAL CHEMISTRY; CONTROLLED STUDY; COVALENT BOND; DNA DENATURATION; FLOW CYTOMETRY; HUMAN; HUMAN CELL; PRIORITY JOURNAL; WESTERN BLOTTING;

APTAMERS, NUCLEOTIDE; BIOTIN; BLOOD PLATELETS; CELL LINE; DNA, SINGLE-STRANDED; FERROSOFERRIC OXIDE; HUMANS; MICROSPHERES; SELEX APTAMER TECHNIQUE; STREPTAVIDIN;

EID: 70349288034     PISSN: 15454576     EISSN: None     Source Type: Journal    
DOI: 10.1089/oli.2009.0194     Document Type: Article

References (49)

1. ALON, R., BAYER, E.A., and WILCHEK, M. (1990). Streptavidin contains an RYD sequence which mimics the RGD receptor domain of f bronectin. Biochem. Biophys. Res. Commun. 170, 1236-1241.
2. ALON, R., BAYER, E.A., and WILCHEK, M. (1992). Cell-adhesive properties of streptavidin are mediated by the exposure of an RGD-like RYD site. Eur. J. Cell Biol. 58, 271-279.
3. ALON, R., BAYER, E.A., and WILCHEK, M. (1993). Cell adhesion to streptavidin via RGD-dependent integrins. Eur. J. Cell Biol. 60, 1-11.
4. BLANK, M., and BLIND, M. (2005). Aptamers as tools for target validation. Curr. Opin. Chem. Biol. 9, 336-342.
5. BLANK, M., WEINSCHENK, T., PRIEMER, M., and SCHLUESENER, H. (2001). Systematic evolution of a DNA aptamer binding to rat brain tumor microvessels. selective targeting of endothelial regulatory protein pigpen. J. Biol. Chem. 276, 16464-16468.
6. BODARY, S.C., and McLEAN, J.W. (1990). The integrin beta 1 sub-unit associates with the vitronectin receptor alpha v subunit to form a novel vitronectin receptor in a human embryonic kidney cell line. J. Biol. Chem. 265, 5938-5941.
7. BURGSTALLER, P., GIROD, A., and BLIND, M. (2002). Aptamers as tools for target prioritization and lead identif cation. Drug Discov. Today 7, 1221-1228.
8. CERCHIA, L., and DE FRANCISCIS, V. (2007). Nucleic acid-based aptamers as promising therapeutics in neoplastic diseases. Methods Mol. Biol. 361, 187-200.
9. CERCHIA, L., DUCONGE, F., PESTOURIE, C., BOULAY, J., AISSOUNI, Y., GOMBERT, K., TAVITIAN, B., DE FRANCISCIS V., and LIBRI, D. (2005). Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol. 3, e123.
10. CHU, T.C., MARKS, J.W. III, LAVERY, L.A., FAULKNER, S., ROSENBLUM, M.G., ELLINGTON, A.D., and LEVY, M. (2006a). Aptamer:toxin conjugates that specif cally target prostate tumor cells. Cancer Res. 66, 5989-5992.
11. CHU, T.C., TWU, K.Y., ELLINGTON, A.D., and LEVY, M. (2006b). Aptamer mediated siRNA delivery. Nucleic Acids Res. 34, e73.
12. DANIELS, D.A., CHEN, H., HICKE, B.J., SWIDEREK, K.M., and GOLD, L. (2003). A tenascin-C aptamer identif ed by tumor cell SELEX: systematic evolution of ligands by exponential enrichment. Proc. Natl. Acad. Sci. USA. 100, 15416-15421.
13. ELLINGTON, A.D., and SZOSTAK, J.W. (1990). In vitro selection of RNA molecules that bind specif c ligands. Nature. 346, 818-822.
14. ESPELUND, M., STACY, R.A., and JAKOBSEN, K.S. (1990). A simple method for generating single-stranded DNA probes labeled to high activities. Nucleic Acids Res. 18, 6157-6158.
15. FITZWATER, T., and POLISKY, B. (1996). A SELEX primer. Methods Enzymol. 267, 275-301.
16. GREEN, N.M. (1990). Avidin and streptavidin. Methods Enzymol. 184, 51-67.
17. GUO, K.T., SCHAFER, R., PAUL, A., GERBER, A., ZIEMER, G., and WENDEL, H.P. (2006). A new technique for the isolation and surface immobilization of mesenchymal stem cells from whole bone marrow using high-specif c DNA aptamers. Stem Cells 24, 2220-2231.
18. GUO, K., WENDEL, H.P., SCHEIDELER, L., ZIEMER, G., and SCHEULE, A.M. (2005). Aptamer-based capture molecules as a novel coating strategy to promote cell adhesion. J. Cell Mol. Med. 9, 731-736.
19. GYLLENSTEN, U.B., and ERLICH, H.A. (1988). Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus. Proc. Natl. Acad. Sci. USA. 85, 7652-7656.
20. HICKE, B.J., MARION, C., CHANG, Y.F., GOULD, T., LYNOTT, C.K., PARMA, D., SCHMIDT, P.G., and WARREN, S. (2001). Tenascin-C aptamers are generated using tumor cells and purif ed protein. J. Biol. Chem. 276, 48644-48654.
21. HICKE, B.J., STEPHENS, A.W., GOULD, T., CHANG, Y.F., LYNOTT, C.K., HEIL, J., BORKOWSKI, S., HILGER, C.S., COOK, G., WARREN, S., and SCHMIDT, P.G. (2006). Tumor targeting by an aptamer. J. Nucl. Med. 47, 668-678.
22. HIGUCHI, R.G., and OCHMAN, H. (1989). Production of single-stranded DNA templates by exonuclease digestion following the polymerase chain reaction. Nucleic Acids Res. 17, 5865.
23. JAYASENA, S.D. (1999). Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin. Chem. 45, 1628-1650.
24. JONES, L.A., CLANCY, L.E., RAWLINSON, W.D., and WHITE, P.A. (2006). High-aff nity aptamers to subtype 3a hepatitis C virus polymerase display genotypic specif city. Antimicrob. Agents Chemother. 50, 3019-3027.
25. KIEFFER, N., and PHILLIPS, D.R. (1990). Platelet membrane glyco-proteins: functions in cellular interactions. Annu. Rev. Cell Biol. 6, 329-357.
26. LEFKOVITS, J., PLOW, E.F., and TOPOL, E.J. (1995). Platelet glyco-protein IIb/IIIa receptors in cardiovascular medicine. N. Engl. J. Med. 332, 1553-1559.
27. LUPOLD, S.E., HICKE, B.J., LIN, Y., and COFFEY, D.S. (2002). Identif cation and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specif c membrane antigen. Cancer Res. 62, 4029-4033.
28. MALLIKARATCHY, P., TANG, Z., KWAME, S., MENG, L., SHANGGUAN, D., and TAN, W. (2007). Aptamer directly evolved from live cells recognizes membrane bound immuno-globin heavy mu chain in Burkitt's lymphoma cells. Mol. Cell Proteomics. 6, 2230-2238.
29. McNAMARA, J.O., ANDRECHEK, E.R., WANG, Y., VILES, K.D., REMPEL, R.E., GILBOA, E., SULLENGER, B.A., and GIANGRANDE, P.H. (2006). Cell type-specif c delivery of siRNAs with aptamer-siRNA chimeras. Nat. Biotechnol. 24, 1005-1015.
30. MURPHY, M.B., FULLER, S.T., RICHARDSON, P.M., and DOYLE, S.A. (2003). An improved method for the in vitro evolution of aptamers and applications in protein detection and purif cation. Nucleic Acids Res. 31, e110.
31. NIMJEE, S.M., RUSCONI, C.P., and SULLENGER, B.A. (2005). Aptamers: an emerging class of therapeutics. Annu. Rev. Med. 56, 555-583.
32. OHUCHI, S.P., OHTSU, T., and NAKAMURA, Y. (2006). Selection of RNA aptamers against recombinant transforming growth factor-beta type III receptor displayed on cell surface. Biochimie. 88, 897-904.
33. PAGRATIS, N.C. (1996). Rapid preparation of single stranded DNA from PCR products by streptavidin induced electrophoretic mobility shift. Nucleic Acids Res. 24, 3645-3646.
34. PETRENKO, V.A., and SMITH, G.P. (2000). Phages from landscape libraries as substitute antibodies. Protein Eng. 13, 589-592.
35. RADDATZ, M.S., DOLF, A., ENDL, E., KNOLLE, P., FAMULOK, M., and MAYER, G. (2008). Enrichment of cell-targeting and popu-lation-specif c aptamers by f uorescence-activated cell sorting. Angew. Chem. Int. Ed Engl. 47, 5190-5193.
36. SCHÄFER, R., WISKIRCHEN, J., GUO, K., NEUMANN, B., KEHLBACH, R., PINTASKE, J., VOTH, V., WALKER, T., SCHEULE, A.M., GREINER, T.O., HERMANUTZ-KLEIN, U., CLAUSSEN, C.D., NORTHOFF, H., ZIEMER, G., and WENDEL, H.P. (2007). Aptamer-based isolation and subsequent imaging of mesenchymal stem cells in ischemic myocard by magnetic resonance imaging. Rofo 179, 1009-1015.
37. SHANGGUAN, D., CAO, Z.C., LI, Y., and TAN, W. (2007). Aptamers evolved from cultured cancer cells reveal molecular differences of cancer cells in patient samples. Clin. Chem. 53, 1153-1155.
38. SHANGGUAN, D., LI, Y., TANG, Z., CAO, Z.C., CHEN, H.W., MALLIKARATCHY, P., SEFAH, K., YANG, C.J., and TAN, W. (2006). Aptamers evolved from live cells as effective molecular probes for cancer study. Proc. Natl. Acad. Sci. USA. 103, 11838-11843.
39. SMITH, J.E., MEDLEY, C.D., TANG, Z., SHANGGUAN, D., LOFTON, C., and TAN, W. (2007). Aptamer-conjugated nanoparticles for the collection and detection of multiple cancer cells. Anal. Chem. 79, 3075-3082.
40. SOOTER, L.J., RIEDEL, T., DAVIDSON, E.A., LEVY, M., COX, J.C., and ELLINGTON, A.D. (2001). Toward automated nucleic acid enzyme selection. Biol. Chem. 382, 1327-1334.
41. SRISAWAT, C., and ENGELKE, D.R. (2001). Streptavidin aptam-ers: aff nity tags for the study of RNAs and ribonucleoproteins. RNA. 7, 632-641.
42. STOLTENBURG, R., REINEMANN, C., and STREHLITZ, B. (2005). FluMag-SELEX as an advantageous method for DNA aptamer selection. Anal. Bioanal. Chem. 383, 83-91.
43. TAHIRI-ALAOUI, A., FRIGOTTO, L., MANVILLE, N., IBRAHIM, J., ROMBY, P., and JAMES, W. (2002). High aff nity nucleic acid aptamers for streptavidin incorporated into bi-specif c capture ligands. Nucleic Acids Res. 30, e45.
44. TAKEMURA, K., WANG, P., VORBERG, I., SUREWICZ, W., PRIOLA, S.A., KANTHASAMY, A., POTTATHIL, R., CHEN, S.G., and SREEVATSAN, S. (2006). DNA aptamers that bind to PrP(C) and not PrP(Sc) show sequence and structure specif city. Exp. Biol. Med. (Maywood) 231, 204-214.
45. TANG, Z., SHANGGUAN, D., WANG, K., SHI, H., SEFAH, K., MALLIKRATCHY, P., CHEN, H.W., LI, Y., and TAN, W. (2007). Selection of aptamers for molecular recognition and characterization of cancer cells. Anal. Chem. 79, 4900-4907.
46. TUERK, C., EDDY, S., PARMA, D., and GOLD, L. (1990). Autogenous translational operator recognized by bacteriophage T4 DNA polymerase. J. Mol. Biol. 213, 749-761
47. ULRICH, H., MAGDESIAN, M.H., ALVES, M.J., and COLLI, W. (2002). In vitro selection of RNA aptamers that bind to cell adhesion receptors of Trypanosoma cruzi and inhibit cell invasion. J. Biol. Chem. 277, 20756-20762.
48. WILLIAMS, K.P., and BARTEL, D.P. (1995). PCR product with strands of unequal length. Nucleic Acids Res. 23, 4220-4221.
49. WU, L., and CURRAN, J.F. (1999). An allosteric synthetic DNA. Nucleic Acids Res. 27, 1512-1516.