Aptamers: Versatile probes for flow cytometry

Applied Microbiology and Biotechnology

Volumn 97, Issue 16, 2013, Pages 7097-7109

  Meyer, Michael ^a   Scheper, Thomas ^a   Walter, Johanna Gabriela ^a  

^a LEIBNIZ UNIVERSITY HANNOVER   (Germany)

Author keywords

Aptamer modified nanoparticles; Aptamer modified quantum dots; Aptamers; Cell SELEX; Flow cytometry; Multivalent aptamers

Indexed keywords

APTAMERS; CANCER CELL LINES; CELL-SELEX; MOLECULAR PROBES; MOLECULAR TARGETS; NUCLEIC ACID OLIGOMERS; OLIGONUCLEOTIDE SYNTHESIS; VIRUS-INFECTED CELLS;

AMINO ACIDS; CELL CULTURE; CELLS; MOLECULES; NANOPARTICLES; NUCLEIC ACIDS; OLIGONUCLEOTIDES; PROBES; SEMICONDUCTOR QUANTUM DOTS; VIRUSES;

FLOW CYTOMETRY;

APTAMER; QUANTUM DOT;

CANCER; FLOW CYTOMETRY; NUCLEIC ACID; PHENOTYPE; SELECTION;

CANCER CELL CULTURE; CANCER DIAGNOSIS; FLOW CYTOMETRY; HUMAN; MOLECULAR PROBE; NONHUMAN; PHENOTYPE; REVIEW; SENSITIVITY ANALYSIS;

APTAMERS, NUCLEOTIDE; FLOW CYTOMETRY; SELEX APTAMER TECHNIQUE;

EID: 84881248780     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-013-5070-z     Document Type: Review

References (105)

1. Armengol CE, Schlager TA, Hendley JO (2004) Sensitivity of a rapid antigen detection test for group A streptococci in a private pediatric office setting: answering the Red Book's request for validation. Pediatrics 113:924-926 (Pubitemid 38437404)
2. Avci-Adali M, Metzger M, Perle N, Ziemer G, Wendel HP (2010) Pitfalls of cell-systematic evolution of ligands by exponential enrichment (SELEX): existing dead cells during in vitro selection anticipate the enrichment of specific aptamers. Oligonucleotides 20:317-323
3. Avci-Adali M, Wilhelm N, Perle N, Stoll H, Schlensak C, Wendel HP (2013) Absolute quantification of cell-bound DNA aptamers during SELEX. Nucleic Acid Ther 23:125-130
4. Bagalkot V, Zhang L, Levy-Nissenbaum E, Jon S, Kantoff PW, Langer R, Farokhzad OC (2007) Quantum dot - aptamer conjugates for synchronous cancer imaging, therapy, and sensing of drug delivery based on bi-fluorescence resonance energy transfer. Nano Lett 7:3065-3070 (Pubitemid 350132931)
5. Baird GS (2010) Where are all the aptamers? Am J Clin Pathol 134:529-531
6. Blank M (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
7. Boltz A, Piater B, Toleikis L, Guenther R, Kolmar H, Hock B (2011) Bi-specific aptamers mediating tumor cell lysis. J Biol Chem 286:21896-21905
8. Burzlaff A, Kalesse M, Kasper C, Scheper T (2003) Multi parameter in vitro testing of ratjadone using flow cytometry. Appl Microbiol Biotechnol 62:174-179 (Pubitemid 36995169)
9. Burzlaff A, Brethauer S, Kasper C, Jackisch B, Scheper T (2004) Flow cytometry: interesting tool for studying binding behavior of DNA on inorganic layered double hydroxide (LDH). Cytom A 62:65-69 (Pubitemid 39473455)
10. Cao X, Li S, Chen L, Ding H, Xu H, Huang Y, Li J, Liu N, Cao W, Zhu Y, Shen B, Shao N (2009) Combining use of a panel of ssDNA aptamers in the detection of Staphylococcus aureus. Nucleic Acids Res 37:4621-4628
11. Carlson R (2009) The changing economics of DNA synthesis. Nat Biotechnol 27:1091-1094
12. Chattopadhyay PK, Price DA, Harper TF, Betts MR, Yu J, Gostick E, Perfetto SP, Goepfert P, Koup RA, de Rosa SC, Bruchez MP, Roederer M (2006) Quantum dot semiconductor nanocrystals for immunophenotyping by polychromatic flow cytometry. Nat Med 12:972-977 (Pubitemid 44175152)
13. Chattopadhyay PK, Hogerkorp C, Roederer M (2008) A chromatic explosion: the development and future of multiparameter flow cytometry. Immunology 125:441-449
14. Chen CB, Chernis GA, van Hoang Q, Landgraf R (2003) Inhibition of heregulin signaling by an aptamer that preferentially binds to the oligomeric form of human epidermal growth factor receptor-3. Proc Natl Acad Sci U S A 100:9226-9231 (Pubitemid 37033911)
15. Chen F, Zhou J, Luo F, Mohammed A, Zhang X (2007) Aptamer from whole-bacterium SELEX as new therapeutic reagent against virulent Mycobacterium tuberculosis. Biochem Biophys Res Commun 357:743-748 (Pubitemid 46653843)
16. Chen HW, Medley CD, Sefah K, Shangguan D, Tang Z, Meng L, Smith JE, Tan W (2008) Molecular recognition of small-cell lung cancer cells using aptamers. ChemMedChem 3:991-1001
17. Chen X, Estévez M, Zhu Z, Huang Y, Chen Y, Wang L, Tan W (2009) Using aptamer-conjugated fluorescence resonance energy transfer nanoparticles for multiplexed cancer cell monitoring. Anal Chem 81:7009-7014
18. Chu TC, Shieh F, Lavery LA, Levy M, Richards-Kortum R, Korgel BA, Ellington AD (2006) Labeling tumor cells with fluorescent nanocrystal-aptamer bioconjugates. Biosens Bioelectron 21:1859-1866
19. Czechowska K, Johnson DR, van der Meer JR (2008) Use of flow cytometric methods for single-cell analysis in environmental microbiology. Curr Opin Microbiol 11:205-212
20. Davis KA, Abrams B, Lin Y, Jayasena SD (1996) Use of a high affinity DNA ligand in flow cytometry. Nucleic Acids Res 24:702-706 (Pubitemid 26085845)
21. 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 (Pubitemid 28401340)
22. Di Giusto DA, King GC (2004) Construction, stability, and activity of multivalent circular anticoagulant aptamers. J Biol Chem 279:46483-46489 (Pubitemid 39518291)
23. Di Giusto DA, Wlassoff WA, Gooding JJ, Messerle BA, King GC (2005) Proximity extension of circular DNA aptamers with real-time protein detection. Nucleic Acids Res 33:e64 (Pubitemid 41748361)
24. Di Giusto DA, Knox SM, Lai Y, Tyrelle GD, Aung MT, King GC (2006) Multitasking by multivalent circular DNA aptamers. ChemBioChem 7:535-544
25. Drolet DW, Moon-McDermott L, Romig TS (1996) An enzyme-linked oligonucleotide assay. Nat Biotechnol 14:1021-1025
26. Duan N, Wu S, Chen X, Huang Y, Wang Z (2012) Selection and identification of a DNA aptamer targeted to Vibrio parahemolyticus. J Agric Food Chem 60:4034-4038
27. Duan N, Wu S, Chen X, Huang Y, Xia Y, Ma X, Wang Z (2013) Selection and characterization of aptamers against Salmonella Typhimurium using whole-bacterium systemic evolution of ligands by exponential enrichment (SELEX). J Agric Food Chem 61:3229-3234
28. Dwivedi HP, Smiley RD, Jaykus L (2010) Selection and characterization of DNA aptamers with binding selectivity to Campylobacter jejuni using whole-cell SELEX. Appl Microbiol Biotechnol 87:2323-2334
29. Dwivedi HP, Smiley RD, Jaykus L (2013) Selection of DNA aptamers for capture and detection of Salmonella Typhimurium using a whole-cell SELEX approach in conjunction with cell sorting. Appl Microbiol Biotechnol 97:3677-3686
30. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818-822 (Pubitemid 20272100)
31. Funakoshi T, Tachibana I, Hoshida Y, Kimura H, Takeda Y, Kijima T, Nishino K, Goto H, Yoneda T, Kumagai T, Osaki T, Hayashi S, Aozasa K, Kawase I (2003) Expression of tetraspanins in human lung cancer cells: frequent downregulation of CD9 and its contribution to cell motility in small cell lung cancer. Oncogene 22:674-687 (Pubitemid 36269281)
32. Glaser V (2009) Oligo market benefits from RNAi focus. Genet Eng Biotechnol News 29
33. Hamula CLA, Zhang H, Guan LL, Li X, Le XC (2008) Selection of aptamers against live bacterial cells. Anal Chem 80:7812-7819
34. Hamula CL, Le XC, Li X (2011a) DNA aptamers binding to multiple prevalent M-types of Streptococcus pyogenes. Anal Chem 83:3640-3647
35. Hamula CL, Zhang H, Li F, Wang Z, Le Chris X, Li X (2011b) Selection and analytical applications of aptamers binding microbial pathogens. TrAC Trends Anal Chem 30:1587-1597
36. Heine F, Stahl F, Sträuber H, Wiacek C, Benndorf D, Repenning C, Schmidt F, Scheper T, von Bergen M, Harms H, Müller S (2009) Prediction of flocculation ability of brewing yeast inoculates by flow cytometry, proteome analysis, and mRNA profiling. Cytom A 75:140-147
37. Herr JK, Smith JE, Medley CD, Shangguan D, Tan W (2006) Aptamer-conjugated nanoparticles for selective collection and detection of cancer cells. Anal Chem 78:2918-2924 (Pubitemid 43726108)
38. Hicke BJ, Marion C, Chang YF, Gould T, Lynott CK, Parma D, Schmidt PG, Warren S (2001) Tenascin-C aptamers are generated using tumor cells and purified protein. J Biol Chem 276:48644-48654
39. Huang Y, Chang H, Tan W (2008) Cancer cell targeting using multiple aptamers conjugated on nanorods. Anal Chem 80:567-572 (Pubitemid 351206842)
40. Hyeon J, Chon J, Choi I, Park C, Kim D, Seo K (2012) Development of RNA aptamers for detection of Salmonella Enteritidis. J Microbiol Methods 89:79-82
41. Iliuk AB, Hu L, Tao WA (2011) Aptamer in bioanalytical applications. Anal Chem 83:4440-4452
42. Jackman DM, Johnson BE (2005) Small-cell lung cancer. Lancet 366:1385-1396 (Pubitemid 41443406)
43. Jiménez E, Sefah K, López-Colón D, van Simaeys D, Chen HW, Tockman MS, Tan W (2012) Generation of lung adenocarcinoma DNA aptamers for cancer studies. PLoS One 7:e46222
44. Kang WJ, Chae JR, Cho YL, Lee JD, Kim S (2009) Multiplex imaging of single tumor cells using quantum-dot-conjugated aptamers. Small 5:2519-2522
45. Keefe AD, Cload ST (2008) SELEX with modified nucleotides. Curr Opin Chem Biol 12:448-456
46. Kökpinar O, Walter J, Shoham Y, Stahl F, Scheper T (2011) Aptamer-based downstream processing of his-tagged proteins utilizing magnetic beads. Biotechnol Bioeng 108:2371-2379
47. Kruth HS (1982) Flow cytometry: rapid biochemical analysis of single cells. Anal Biochem 125:225-242
48. Kulbachinskiy AV (2007) Methods for selection of aptamers to protein targets. Biochemistry (Mosc) 72:1505-1518
49. Kunii T, Ogura S, Mie M, Kobatake E (2011) Selection of DNA aptamers recognizing small cell lung cancer using living cell-SELEX. Analyst 136:1310
50. Lao Y, Peck K, Chen L (2009) Enhancement of aptamer microarray sensitivity through spacer optimization and avidity effect. Anal Chem 81:1747-1754
51. Li N, Ebright JN, Stovall GM, Chen X, Nguyen HH, Singh A, Syrett A, Ellington AD (2009) Technical and biological issues relevant to cell typing with aptamers. J Proteome Res 8:2438-2448
52. Lübbecke M, Walter J, Stahl F, Scheper T (2012) Aptamers as detection molecules on reverse phase protein microarrays for the analysis of cell lysates. Eng Life Sci 12:144-151
53. Lupold SE, Hicke BJ, Lin Y, Coffey DS (2002) Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. Cancer Res 62:4029-4033 (Pubitemid 34791070)
54. Mallikaratchy P, Tang Z, Kwame S, Meng L, Shangguan D, Tan W (2007) Aptamer directly evolved from live cells recognizes membrane bound immunoglobin heavy mu chain in Burkitt's lymphoma cells. Mol Cell Proteomics 6:2230-2238
55. Mallikaratchy PR, Ruggiero A, Gardner JR, Kuryavyi V, Maguire WF, Heaney ML, McDevitt MR, Patel DJ, Scheinberg DA (2011) A multivalent DNA aptamer specific for the B cell receptor on human lymphoma and leukemia. Nucleic Acids Res 39:2458-2469
56. Mayer G, Ahmed ML, Dolf A, Endl E, Knolle PA, Famulok M (2010) Fluorescence-activated cell sorting for aptamer SELEX with cell mixtures. Nat Protoc 5:1993-2004
57. McKeague M, Derosa MC (2012) Challenges and opportunities for small molecule aptamer development. J Nucleic Acids 2012:748913
58. Medley CD, Bamrungsap S, Tan W, Smith JE (2011) Aptamer-conjugated nanoparticles for cancer cell detection. Anal Chem 83:727-734
59. Moretti P, Behr L, Walter JG, Kasper C, Stahl F, Scheper T (2010) Characterization and improvement of cell line performance via flow cytometry and cell sorting. Eng Life Sci:NA
60. Morris KN, Jensen KB, Julin CM, Weil M, Gold L (1998) High affinity ligands from in vitro selection: complex targets. Proc Natl Acad Sci U S A 95:2902-2907 (Pubitemid 28135827)
61. Müller S, Bley T (2011) High resolution microbial single cell analytics. Springer-Verlag Berlin Heidelberg, Berlin, Heidelberg
62. Ninomiya K, Kaneda K, Kawashima S, Miyachi Y, Ogino C, Shimizu N (2013) Cell-SELEX based selection and characterization of DNA aptamer recognizing human hepatocarcinoma. Bioorg Med Chem Lett 23:1797-1802
63. Nitsche A, Kurth A, Dunkhorst A, Pänke O, Sielaff H, Junge W, Muth D, Scheller F, Stöcklein W, Dahmen C, Pauli G, Kage A (2007) One-step selection of vaccinia virus-binding DNA aptamers by MonoLEX. BMC Biotechnol 7:48 (Pubitemid 47497181)
64. Nurse P, Hayles J (2011) The cell in an era of systems biology. Cell 144:850-854
65. Parekh P, Tang Z, Turner PC, Moyer RW, Tan W (2010) Aptamers recognizing glycosylated hemagglutinin expressed on the surface of vaccinia virus-infected cells. Anal Chem 82:8642-8649
66. Paul A, Avci-Adali M, Ziemer G, Wendel HP (2009) Streptavidin-coated magnetic beads for DNA strand separation implicate a multitude of problems during cell-SELEX. Oligonucleotides 19:243-254
67. Preffer F, Dombkowski D (2009) Advances in complex multiparameter flow cytometry technology: applications in stem cell research. Cytometry B Clin Cytom 76:295-314
68. Raddatz ML, Dolf A, Endl E, Knolle P, Famulok M, Mayer G (2008) Enrichment of cell-targeting and population-specific aptamers by fluorescence-activated cell sorting. Angew Chem Int Ed 47:5190-5193
69. Rieseberg M, Kasper C, Reardon KF, Scheper T (2001) Flow cytometry in biotechnology. Appl Microbiol Biotechnol 56:350-360 (Pubitemid 32763344)
70. Ringquist S, Parma D (1998) Anti-l-selectin oligonucleotide ligands recognize CD62L-positive leukocytes: binding affinity and specificity of univalent and bivalent ligands. Cytometry 33:394-405 (Pubitemid 28533189)
71. Roederer M, Bigos M, Nozaki T, Stovel RT, Parks DR, Herzenberg LA (1995) Heterogeneous calcium flux in peripheral T cell subsets revealed by five-color flow cytometry using log-ratio circuitry. Cytometry 21:187-196
72. Schütze T, Wilhelm B, Greiner N, Braun H, Peter F, Mörl M, Erdmann VA, Lehrach H, Konthur Z, Menger M, Arndt PF, Glökler J (2011) Probing the SELEX process with next generation sequencing. PLoS One 6:e29604
73. Sefah K, Tang ZW, Shangguan DH, Chen H, Lopez-Colon D, Li Y, Parekh P, Martin J, Meng L, Phillips JA, Kim YM, Tan WH (2009) Molecular recognition of acute myeloid leukemia using aptamers. Leukemia 23:235-244
74. Sefah K, Shangguan D, Xiong X, O'Donoghue MB, Tan W (2010) Development of DNA aptamers using Cell-SELEX. Nat Protoc 5:1169-1185
75. Sefah K, Bae K, Phillips JA, Siemann DW, Su Z, McClellan S, Vieweg J, Tan W (2013) Cell-based selection provides novel molecular probes for cancer stem cells. Int J Cancer 132:2578-2588
76. Shamah SM, Healy JM, Cload ST (2008) Complex target SELEX. Acc Chem Res 41:130-138
77. Shangguan D, Li Y, Tang Z, Cao ZC, Chen HW, Mallikaratchy P, Sefah K, Yang CJ, Tan W (2006) Aptamers evolved from live cells as effective molecular probes for cancer study. Proc Natl Acad Sci 103:11838-11843 (Pubitemid 44215773)
78. Shangguan D, Cao ZC, Li Y, Tan W (2007) Aptamers evolved from cultured cancer cells reveal molecular differences of cancer cells in patient samples. Clin Chem 53:1153-1155 (Pubitemid 46867534)
79. Shangguan D, Meng L, Cao ZC, Xiao Z, Fang X, Li Y, Cardona D, Witek RP, Liu C, Tan W (2008) Identification of liver cancer-specific aptamers using whole live cells. Anal Chem 80:721-728 (Pubitemid 351206860)
80. Shapiro HM (1983) Multistation multiparameter flow cytometry: a critical review and rationale. Cytometry 3:227-243 (Pubitemid 13146136)
81. Shigdar S, Lin J, Yu Y, Pastuovic M, Wei M, Duan W (2011) RNA aptamer against a cancer stem cell marker epithelial cell adhesion molecule. Cancer Sci 102:991-998
82. Shigdar S, Qiao L, Zhou S, Xiang D, Wang T, Li Y, Lim LY, Kong L, Li L, Duan W (2013) RNA aptamers targeting cancer stem cell marker CD133. Cancer Lett 330:84-95
83. Smith JE, Medley CD, Tang Z, Shangguan D, Lofton C, Tan W (2007) Aptamer-conjugated nanoparticles for the collection and detection of multiple cancer cells. Anal Chem 79:3075-3082 (Pubitemid 46640529)
84. Song Y, Zhu Z, An Y, Zhang W, Zhang H, Liu D, Yu C, Duan W, Yang CJ (2013) Selection of DNA aptamers against epithelial cell adhesion molecule for cancer cell imaging and circulating tumor cell capture. Anal Chem 85:4141-4149
85. Stanlis KKH, McIntosh JR (2003) Single-strand DNA aptamers as probes for protein localization in cells. J Histochem Cytochem 51:797-808 (Pubitemid 36628861)
86. Steiner JM, Sartor M, Sanchez AB, Messmer D, Freed A, Esener S, Messmer BT (2010) DeNAno: selectable deoxyribonucleic acid nanoparticle libraries. J Biotechnol 145:330-333
87. Stoltenburg R, Reinemann C, Strehlitz B (2007) SELEX - a (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol Eng 24:381-403 (Pubitemid 47391579)
88. Tang Z, Shangguan D, Wang K, Shi H, Sefah K, Mallikratchy P, Chen HW, Li Y, Tan W (2007) Selection of aptamers for molecular recognition and characterization of cancer cells. Anal Chem 79:4900-4907 (Pubitemid 47051443)
89. Tang Z, Parekh P, Turner P, Moyer RW, Tan W (2009) Generating aptamers for recognition of virus-infected cells. Clin Chem 55:813-822
90. Tracy BP, Gaida SM, Papoutsakis ET (2010) Flow cytometry for bacteria: enabling metabolic engineering, synthetic biology and the elucidation of complex phenotypes. Curr Opin Biotechnol 21:85-99
91. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505-510
92. Ulrich H, Wrenger C (2009) Disease-specific biomarker discovery by aptamers. Cytometry 75:727-733
93. van Simaeys D, López-Colón D, Sefah K, Sutphen R, Jimenez E, Tan W (2010) Study of the molecular recognition of aptamers selected through ovarian cancer cell-SELEX. PLoS One 5:e13770
94. Walter J, Kökpinar O, Friehs K, Stahl F, Scheper T (2008) Systematic investigation of optimal aptamer immobilization for protein-microarray applications. Anal Chem 80:7372-7378
95. Walter JG, Petersen S, Stahl F, Scheper T, Barcikowski S (2010) Laser ablation-based one-step generation and bio-functionalization of gold nanoparticles conjugated with aptamers. J Nanobiotechnology 8:21
96. Walter J, Heilkenbrinker A, Austerjost J, Timur S, Stahl F, Scheper T (2012a) Aptasensors for small molecule detection. Z Naturforsch B 67:976-986
97. Walter J, Stahl F, Scheper T (2012b) Aptamers as affinity ligands for downstream processing. Eng Life Sci 12:496-506
98. World Health Organization WHO (2012a) World Health Statistics 2012
99. World Health Organization (WHO) (2012b) World Health Statistics 2012. Noncommunicable diseases: a major health challenge of the 21st century
100. Zhang P, Zhao N, Zeng Z, Feng Y, Tung C, Chang C, Zu Y (2009) Using an RNA aptamer probe for flow cytometry detection of CD30-expressing lymphoma cells. Lab Invest 89:1423-1432
101. Zhang J, Jia X, Lv X, Deng Y, Xie H (2010a) Fluorescent quantum dot-labeled aptamer bioprobes specifically targeting mouse liver cancer cells. Talanta 81:505-509
102. Zhang P, Zhao N, Zeng Z, Chang C, Zu Y (2010b) Combination of an aptamer probe to CD4 and antibodies for multicolored cell phenotyping. Am J Clin Pathol 134:586-593
103. Zhao Z, Xu L, Shi X, Tan W, Fang X, Shangguan D (2009) Recognition of subtype non-small cell lung cancer by DNA aptamers selected from living cells. Analyst 134:1808
104. Zheng D, Seferos DS, Giljohann DA, Patel PC, Mirkin CA (2009) Aptamer nano-flares for molecular detection in living cells. Nano Lett 9:3258-3261
105. Zhu G, Lübbecke M, Walter J, Stahl F, Scheper T (2011) Characterization of optimal aptamer-microarray binding chemistry and spacer design. Chem Eng Technol 34:2022-2028