Introduction to Aptamer and Cell-SELEX

  • Libo Zhao
  • Weihong Tan
  • Xiaohong FangEmail author


Aptamers are functional oligonucleic acids that bind to specific targets with high affinity. They have demonstrated their unique advantages as chemical antibodies in molecular recognition for many applications in biomedicine and biotechnology such as biosensing, bioimaging, and drug. In particular, a recently developed method of live cell-based in vitro selection, termed cell-SELEX, has successfully isolated aptamers without prior knowledge of a cell’s molecular signature, making such aptamers promising for applications in molecular medicine. This chapter reviews the evolution of cell-SELEX technology and introduces the content of this book, which surveys the advancements in cell-SELEX DNA aptamer selection, characterization, modification, and application for theranostics.


Aptamer DNA/RNA oligonucleotide Antibody Cell-SELEX Theranostics 


  1. 1.
    Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505–510CrossRefGoogle Scholar
  2. 2.
    Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818–822CrossRefGoogle Scholar
  3. 3.
    Feigon J, Dieckmann T, Smith FW (1996) Aptamer structures from A to zeta. Chem Biol 3:611–617CrossRefGoogle Scholar
  4. 4.
    Patel DJ, Suri AK, Jiang F, Jiang L, Fan P, Kumar RA, Nonin S (1997) Structure, recognition and adaptive binding in RNA aptamer complexes. J Mol Biol 272:645–664CrossRefGoogle Scholar
  5. 5.
    Fang XH, Tan WH (2010) Aptamers generated from cell-SELEX for molecular medicine: a chemical biology approach. Acc Chem Res 43:48–57CrossRefGoogle Scholar
  6. 6.
    Jayasena SD (1999) Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin Chem 45:1628–1650Google Scholar
  7. 7.
    Spiegelman S (1971) An approach to the experimental analysis of precellular evolution. Q Rev Biophys 4:213–253CrossRefGoogle Scholar
  8. 8.
    Mills DR, Peterson RL, Spiegelman S (1967) An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule. Proc Natl Acad Sci U S A 58:217–224CrossRefGoogle Scholar
  9. 9.
    Ellington AD, Szostak JW (1992) Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures. Nature 355:850–852CrossRefGoogle Scholar
  10. 10.
    Ng EWM, Shima DT, Calias P, Cunningham ET, Guyer DR, Adamis AP (2006) Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease. Nat Rev Drug Discov 5:123–132CrossRefGoogle Scholar
  11. 11.
    Dhar S, Gu FX, Langer R, Farokhzad OC, Lippard SJ (2008) Targeted delivery of cisplatin to prostate cancer cells by aptamer functionalized Pt(IV) prodrug-PLGA-PEG nanoparticles. Proc Natl Acad Sci U S A 105:17356–17361CrossRefGoogle Scholar
  12. 12.
    Liu YM, Kuan CT, Mi J, Zhang XW, Clary BM, Bigner DD, Sullenger BA (2009) Aptamers selected against the unglycosylated EGFRvIII ectodomain and delivered intracellularly reduce membrane-bound EGFRvIII and induce apoptosis, Biol Chem 390:137–144Google Scholar
  13. 13.
    Shangguan D, Li Y, Tang ZW, Cao ZHC, Chen HW, Mallikaratchy P, Sefah K, Yang CYJ, Tan WH (2006) Aptamers evolved from live cells as effective molecular probes for cancer study. Proc Natl Acad Sci U S A 103:11838–11843CrossRefGoogle Scholar
  14. 14.
    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 276:48644–48654CrossRefGoogle Scholar
  15. 15.
    Tan Y, Shi YS, Wu XD, Liang HY, Gao YB, Li SJ, Zhang XM, Wang F, Gao TM (2013) DNA aptamers that target human glioblastoma multiforme cells overexpressing epidermal growth factor receptor variant III in vitro. Acta Pharmacol Sin 34:1491–1498CrossRefGoogle Scholar
  16. 16.
    Chen F, Hu YL, Li DQ, Chen HD, Zhang XL (2009) CS-SELEX generates high-affinity ssDNA aptamers as molecular probes for hepatitis C virus envelope glycoprotein E2. Plos One 4:e8142. doi: 10.1371/journal.pone.0008142
  17. 17.
    Thiel KW, Hernandez LI, Dassie JP, Thiel WH, Liu XY, Stockdale KR, Rothman AM, Hernandez FJ, McNamara JO, Giangrande PH (2012) Delivery of chemo-sensitizing siRNAs to HER2(+)-breast cancer cells using RNA aptamers. Nucleic Acids Res 40:6319–6337CrossRefGoogle Scholar
  18. 18.
    Shangguan DH, Meng L, Cao ZHC, Xiao ZY, Fang XH, Li Y, Cardona D, Witek RP, Liu C, Tan WH (2008) Identification of liver cancer-specific aptamers using whole live cells. Anal Chem 80:721–728CrossRefGoogle Scholar
  19. 19.
    Wang FB, Rong Y, Fang M, Yuan JP, Peng CW, Liu SP, Li Y (2013) Recognition and capture of metastatic hepatocellular carcinoma cells using aptamer-conjugated quantum dots and magnetic particles. Biomaterials 34:3816–3827CrossRefGoogle Scholar
  20. 20.
    Cerchia L, Duconge F, Pestourie C, Boulay J, Aissouni Y, Gombert K, Tavitian B, de Franciscis V, Libri D (2005) Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol 3:697–704CrossRefGoogle Scholar
  21. 21.
    Tang ZW, Parekh P, Turner P, Moyer RW, Tan WH (2009) Generating aptamers for recognition of virus-infected cells. Clin Chem 55:813–822CrossRefGoogle Scholar
  22. 22.
    Graham JC, Zarbl H (2012) Use of cell-SELEX to generate DNA aptamers as molecular probes of HPV-associated cervical cancer cells. Plos One 7:e36103. doi: 10.1371/journal.pone.0036103
  23. 23.
    Shangguan D, Cao ZH, Meng L, Mallikaratchy P, Sefah K, Wang H, Li Y, Tan WH (2008) Cell-specific aptamer probes for membrane protein elucidation in cancer cells. J Proteome Res 7:2133–2139CrossRefGoogle Scholar
  24. 24.
    Tang ZW, Shangguan D, Wang KM, Shi H, Sefah K, Mallikratchy P, Chen HW, Li Y, Tan WH (2007) Selection of aptamers for molecular recognition and characterization of cancer cells. Anal Chem 79:4900–4907CrossRefGoogle Scholar
  25. 25.
    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 23:235–244CrossRefGoogle Scholar
  26. 26.
    Kang DZ, Wang JJ, Zhang WY, Song YL, Li XL, Zou Y, Zhu MT, Zhu Z, Chen FY, Yang CJ (2012) Selection of DNA aptamers against glioblastoma cells with high affinity and specificity. Plos One 7:e42731. doi: 10.1371/journal.pone.0042731
  27. 27.
    Bayrac AT, Sefah K, Parekh P, Bayrac C, Gulbakan B, Oktem HA, Tan WH (2011) In vitro selection of DNA aptamers to glioblastoma multiforme. ACS Chem Neurosci 2:175–181CrossRefGoogle Scholar
  28. 28.
    Zhao ZL, Xu L, Shi XL, Tan WH, Fang XH, Shangguan DH (2009) Recognition of subtype non-small cell lung cancer by DNA aptamers selected from living cells. Analyst 134:1808–1814CrossRefGoogle Scholar
  29. 29.
    Jimenez E, Sefah K, Lopez-Colon D, Van Simaeys D, Chen HW, Tockman MS, Tan WH (2012) Generation of lung adenocarcinoma DNA aptamers for cancer studies. Plos One 7:e46222. doi: 10.1371/journal.pone.0046222
  30. 30.
    Chen HW, Medley CD, Sefah K, Shangguan D, Tang ZW, Meng L, Smith JE, Tan WH (2008) Molecular recognition of small-cell lung cancer cells using aptamers. ChemMedChem 3:991–1001CrossRefGoogle Scholar
  31. 31.
    Kunii T, Ogura S, Mie M, Kobatake E (2011) Selection of DNA aptamers recognizing small cell lung cancer using living cell-SELEX. Analyst 136:1310–1312CrossRefGoogle Scholar
  32. 32.
    Sefah K, Meng L, Lopez-Colon D, Jimenez E, Liu C, Tan WH (2010) DNA aptamers as molecular probes for colorectal cancer study. Plos One 5:e14269. doi: 10.1371/journal.pone.0014269
  33. 33.
    Van Simaeys D, Lopez-Colon D, Sefah K, Sutphen R, Jimenez E, Tan WH (2010) Study of the molecular recognition of aptamers selected through ovarian cancer cell-SELEX. Plos One 5:e13770. doi: 10.1371/journal.pone.0013770
  34. 34.
    Zhang KJ, Sefah K, Tang LL, Zhao ZL, Zhu GZ, Ye M, Sun WJ, Goodison S, Tan WH (2012) A novel aptamer developed for breast cancer cell internalization. ChemMedChem 7:79–84CrossRefGoogle Scholar
  35. 35.
    Li XL, Zhang WY, Liu L, Zhu Z, Ouyang GL, An Y, Zhao CY, Yang CJ (2014) In vitro selection of DNA aptamers for metastatic breast cancer cell recognition and tissue imaging. Anal Chem 86:6596–6603CrossRefGoogle Scholar
  36. 36.
    Dua P, Kang HS, Hong SM, Tsao MS, Kim S, Lee DK (2013) Alkaline phosphatase ALPPL-2 is a novel pancreatic carcinoma-associated protein. Cancer Res 73:1934–1945CrossRefGoogle Scholar
  37. 37.
    Sefah K, Bae KM, Phillips JA, Siemann DW, Su Z, McClellan S, Vieweg J, Tan WH (2013) Cell-based selection provides novel molecular probes for cancer stem cells. Int J Cancer 132:2578–2588CrossRefGoogle Scholar
  38. 38.
    Wang YY, Luo Y, Bing T, Chen Z, Lu MH, Zhang N, Shangguan DH, Gao X (2014) DNA aptamer evolved by cell-SELEX for recognition of prostate cancer. Plos One 9:e100243. doi: 10.1371/journal.pone.0100243
  39. 39.
    Tan WH, Donovan MJ, Jiang JH (2013) Aptamers from cell-based selection for bioanalytical applications. Chem Rev 113:2842–2862CrossRefGoogle Scholar
  40. 40.
    Shen Q, Xu L, Zhao L, Wu D, Fan Y, Zhou Y, OuYang W-H, Xu X, Zhang Z, Song M, Lee T, Garcia MA, Xiong B, Hou S, Tseng H-R, Fang X (2013) Specific capture and release of circulating tumor cells using aptamer-modified nanosubstrates. Adv Mater 25:2368–2373CrossRefGoogle Scholar
  41. 41.
    Shangguan DH, Cao ZHC, Li Y, Tan WH (2007) Aptamers evolved from cultured cancer cells reveal molecular differences of cancer cells in patient samples. Clin Chem 53:1153–1155CrossRefGoogle Scholar
  42. 42.
    Yang ML, Jiang GH, Li WJ, Qiu K, Zhang M, Carter CM, Al-Quran SZ, Li Y (2014) Developing aptamer probes for acute myelogenous leukemia detection and surface protein biomarker discovery. J Hematol Oncol 7:5. doi: 10.1186/1756-8722-7-5
  43. 43.
    Daniels DA, Chen H, Hicke BJ, Swiderek KM, Gold L (2003) A tenascin-C aptamer identified by tumor cell SELEX: systematic evolution of ligands by exponential enrichment. Proc Natl Acad Sci U S A 100:15416–15421CrossRefGoogle Scholar
  44. 44.
    Liu J, Liu HX, Sefah K, Liu B, Pu Y, Van Simaeys D, Tan WH (2012) Selection of aptamers specific for adipose tissue. Plos One 7:e37789. doi: 10.1371/journal.pone.0037789
  45. 45.
    Iwagawa T, Ohuchi SP, Watanabe S, Nakamura Y (2012) Selection of RNA aptamers against mouse embryonic stem cells. Biochimie 94:250–257CrossRefGoogle Scholar
  46. 46.
    Meyer S, Maufort JP, Nie J, Stewart R, McIntosh BE, Conti LR, Ahmad KM, Soh HT, Thomson JA (2013) Development of an efficient targeted cell-SELEX procedure for DNA aptamer reagents. Plos One 8:e71798. doi: 10.1371/journal.pone.0071798

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.Key Laboratory of Molecular Nanostructure and NanotechnologyInstitute of Chemistry, Chinese Academy of SciencesBeijingChina
  2. 2.College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular MedicineHunan UniversityChangshaChina
  3. 3.Departments of ChemistryUniversity of FloridaGainesvilleUSA

Personalised recommendations