Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Analysis of aptamer discovery and technology

Abstract

Aptamers are nucleic acid molecules that mimic antibodies by folding into complex 3D shapes that bind to specific targets. Although some aptamers exist naturally as the ligand-binding elements of riboswitches, most are generated in vitro and can be tailored for a specific target. Relative to antibodies, aptamers benefit from their ease of generation, low production cost, low batch-to-batch variability, reversible folding properties and low immunogenicity. However, the true value of aptamers lies in the simplicity by which these molecules can be engineered into sensors, actuators and other devices that are often central to emerging technologies. This Review examines changing trends in aptamer technology by analysing the first quarter century of aptamer data that is available in the scientific literature (1990–2015). We highlight specific examples that showcase the use of aptamers in key applications, discuss challenges that have impeded the success of aptamers in practical applications, provide suggestions for choosing chemical modifications that can lead to enhanced activity or stability, and propose standards for the characterization of aptamers in the scientific literature.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Trends in aptamer publications.
Figure 2: Post-SELEX modifications.
Figure 3: Distribution of aptamer applications and targets.
Figure 4: Aptamer-based optical sensors.
Figure 5: L-RNA aptamers or spiegelmers.
Figure 6: Examples of aptamer applications and chemical modifications.
Figure 7: Chemical modifications used in aptamer selections.
Figure 8: Xenonucleic acids.

Similar content being viewed by others

References

  1. Venter, J. C. et al. The sequence of the human genome. Science 291, 1304–1351 (2001).

    CAS  PubMed  Google Scholar 

  2. Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).

    CAS  PubMed  Google Scholar 

  3. Doudna, J. A. & Cech, T. R. The chemical repertoire of natural ribozymes. Nature 418, 222–228 (2002).

    CAS  PubMed  Google Scholar 

  4. Sonenberg, N. & Hinnebusch, A. G. Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell 136, 731–745 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Zovoilis, A., Cifuentes-Rojas, C., Chu, H. P., Hernandez, A. J. & Lee, J. T. Destabilization of B2 RNA by EZH2 activates the stress response. Cell 167, 1788–1802 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Moore, P. B. & Steitz, T. A. The involvement of RNA in ribosome function. Nature 418, 229–235 (2002).

    CAS  PubMed  Google Scholar 

  7. Onoa, B. & Tinoco, I. Jr. RNA folding and unfolding. Curr. Opin. Struct. Biol. 14, 374–379 (2004).

    CAS  PubMed  Google Scholar 

  8. Caruthers, M. H. Gene synthesis machines: DNA chemistry and its uses. Science 230, 281–285 (1985).

    CAS  PubMed  Google Scholar 

  9. Saiki, R. et al. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239, 487–491 (1988).

    CAS  PubMed  Google Scholar 

  10. Wilson, D. S. & Szostak, J. W. In vitro selection of functional nucleic acids. Annu. Rev. Biochem. 68, 611–647 (1999).

    CAS  PubMed  Google Scholar 

  11. Ellington, A. D. & Szostak, J. W. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818–822 (1990).

    CAS  PubMed  Google Scholar 

  12. Tuerk, C. & Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505–510 (1990).

    CAS  PubMed  Google Scholar 

  13. Robertson, D. L. & Joyce, G. F. Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344, 467–468 (1990).

    CAS  PubMed  Google Scholar 

  14. Levine, H. A. & Nilsen-Hamilton, M. A mathematical analysis of SELEX. Comput. Biol. Chem. 31, 11–35 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Szostak, J. W. In vitro genetics. Trends Biochem. Sci. 17, 89–93 (1992).

    CAS  PubMed  Google Scholar 

  16. Joyce, G. F. In vitro evolution of nucleic acids. Curr. Opin. Struct. Biol. 4, 331–336 (1994).

    CAS  PubMed  Google Scholar 

  17. Jayasena, S. D. Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin. Chem. 45, 1628–1650 (1999).

    CAS  PubMed  Google Scholar 

  18. Ruigrok, V. J., Levisson, M., Eppink, M. H. M., Smidt, H. & van der Oost, J. Alternative affinity tools: more attractive than antibodies. Biochem. J. 436, 1–13 (2011).

    CAS  PubMed  Google Scholar 

  19. Binz, H. K. et al. High-affinity binders selected from designed ankyrin repeat protein libraries. Nat. Biotechnol. 22, 575–582 (2004).

    CAS  PubMed  Google Scholar 

  20. Hey, T., Fiedler, E., Rudolph, R. & Fiedler, M. Artificial, non-antibody binding proteins for pharmaceutical and industrial applications. Trends Biotechnol. 23, 514–522 (2005).

    CAS  PubMed  Google Scholar 

  21. Hoogenboom, H. R. Selecting and screening recombinant antibody libraries. Nat. Biotechnol. 23, 1105–1116 (2005).

    CAS  PubMed  Google Scholar 

  22. Sidhu, S. S. & Fellouse, F. A. Synthetic therapeutic antibodies. Nat. Chem. Biol. 2, 682–688 (2006).

    CAS  PubMed  Google Scholar 

  23. Carothers, J. M., Goler, J. A., Juminaga, D. & Keasling, J. D. Model-driven engineering of RNA devices to quantitatively program gene expression. Science 334, 1716–1719 (2011).

    CAS  PubMed  Google Scholar 

  24. Marx, V. Finding the right antibody for the job. Nat. Methods 10, 703–707 (2013).

    CAS  PubMed  Google Scholar 

  25. Keefe, A. D., Pai, S. & Ellington, A. D. Aptamers as therapeutics. Nat. Rev. Drug Discov. 9, 537–550 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Nimjee, S. M., Rusconi, C. P. & Sullenger, B. A. Aptamers: an emerging class of therapeutics. Annu. Rev. Med. 56, 555–583 (2005).

    CAS  PubMed  Google Scholar 

  27. Zhou, J. & Rossi, J. Aptamers as targeted therapeutics: current potential and challenges. Nat. Rev. Drug Discov. 16, 181–202 (2017).

    CAS  PubMed  Google Scholar 

  28. Rusconi, C. P. et al. Antidote-mediated control of an anticoagulant aptamer in vivo. Nat. Biotechnol 22, 1423–1428 (2004).

    CAS  Google Scholar 

  29. Tan, W., Donovan, M. J. & Jiang, J. Aptamers from cell-based selection for bioanalytical applications. Chem. Rev. 113, 2842–2862 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Sismour, A. M. et al. PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1. Nucleic Acids Res. 32, 728–735 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Pinheiro, A. V., Han, D., Shih, W. M. & Yan, H. Challenges and opportunities for structural DNA nanotechnology. Nat. Nanotechnol. 6, 763–772 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Lund, K. et al. Molecular robots guided by prescriptive landscapes. Nature 465, 206–210 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Mayer, G. The chemical biology of aptamers. Angew. Chem. Int. Ed. 48, 2672–2689 (2009).

    CAS  Google Scholar 

  34. Cho, E. J., Lee, J.-W. & Ellington, A. D. Applications of aptamers as sensors. Annu. Rev. Anal. Chem. 2, 241–264 (2009).

    CAS  Google Scholar 

  35. Ozer, A., Pagano, J. M. & Lis, J. T. New technologies provide quantum changes in the scale, speed, and success of SELEX methods and aptamer characterization. Mol. Ther. Nucleic Acids 3, e183 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. McKeague, M. et al. Analysis of in vitro aptamer selection parameters. J. Mol. Evol. 81, 150–161 (2015).

    CAS  PubMed  Google Scholar 

  37. Sassanfar, M. & Szostak, J. W. An RNA motif that binds ATP. Nature 364, 550–553 (1993).

    CAS  PubMed  Google Scholar 

  38. Wilson, D. S., Keefe, A. D. & Szostak, J. W. The use of mRNA display to select high-affinity protein-binding peptides. Proc. Natl Acad. Sci. USA 98, 3750–3755 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Vaish, N. K., Larralde, R., Fraley, A. W., Szostak, J. W. & McLaughlin, L. W. A novel, modification-dependent ATP-binding aptamer selected from an RNA library incorporating a cationic functionality. Biochemistry 42, 8842–8851 (2003).

    CAS  PubMed  Google Scholar 

  40. Eaton, B. E. et al. Post-SELEX combinatorial optimization of aptamers. Bioorg. Med. Chem. 5, 1087–1096 (1997).

    CAS  PubMed  Google Scholar 

  41. Khvorova, A. & Watts, J. K. The chemical evolution of oligonucleotide therapies of clinical utility. Nat. Biotechnol. 35, 238–248 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Ng, E. W. M. et al. Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease. Nat. Rev. Drug Discov. 5, 123–132 (2006).

    CAS  PubMed  Google Scholar 

  43. Ruckman, J. 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, 20556–20567 (1998).

    CAS  PubMed  Google Scholar 

  44. Group, C. R. et al. Ranibizumab and bevacizumab for neovascular age-related macular degeneration. N. Engl. J. Med. 364, 1897–1908 (2011).

    Google Scholar 

  45. Heier, J. S. et al. Intravitreal aflibercept (VEGF trap-eye) in wet age-related macular degeneration. Ophthalmology 119, 2537–2548 (2012).

    PubMed  Google Scholar 

  46. Abeydeera, N. D. et al. Evoking picomolar binding in RNA by a single phosphorodithioate linkage. Nucleic Acids Res. 44, 8052–8064 (2016).

    PubMed  PubMed Central  Google Scholar 

  47. Williams, B. A. R. et al. Creating protein affinity reagents by combining peptide ligands on synthetic DNA scaffolds. J. Am. Chem. Soc. 131, 17233–17241 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Bittker, J. A., Phillips, K. J. & Liu, D. R. Recent advances in the in vitro evolution of nucleic acids. Curr. Opin. Chem. Biol. 6, 367–374 (2002).

    CAS  PubMed  Google Scholar 

  49. Yang, K. A. et al. Recognition and sensing of low-epitope targets via ternary complexes with oligonucleotides and synthetic receptors. Nat. Chem. 6, 1003–1008 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Ferguson, B. S. et al. Real-time, aptamer-based tracking of circulating therapeutic agents in living animals. Sci. Transl Med. 5, 213ra165 (2013).

    PubMed  PubMed Central  Google Scholar 

  51. Amaya-Gonzalez, S., de-los-Santos-Alvarez, N., Miranda-Ordieres, A. J. & Lobo-Castanon, M. J. Aptamer-based analysis: a promising alternative for food safety control. Sensors 13, 16292–16311 (2013).

    PubMed  PubMed Central  Google Scholar 

  52. Hayat, A. & Marty, J. L. Aptamer based electrochemical sensors for emerging environmental pollutants. Front. Chem. 2, 41 (2014).

    PubMed  PubMed Central  Google Scholar 

  53. Smiley, D. A. & Becker, R. C. Factor IXa as a target for anticoagulation in thrombotic disorders and conditions. Drug Discov. Today 19, 1445–1453 (2014).

    CAS  PubMed  Google Scholar 

  54. Rusconi, C. P. et al. RNA aptamers as reversible antagonists of coagulation factor IXa. Nature 419, 90–94 (2002).

    CAS  PubMed  Google Scholar 

  55. Povsic, T. J. et al. Use of the REG1 anticoagulation system in patients with acute coronary syndromes undergoing percutaneous coronary intervention: results from the phase II RADAR-PCI study. EuroIntervention 10, 431–438 (2014).

    PubMed  Google Scholar 

  56. Povsic, T. J. et al. A phase 2, randomized, partially blinded, active-controlled study assessing the efficacy and safety of variable anticoagulation reversal using the REG1 system in patients with acute coronary syndromes: results of the RADAR trial. Eur. Heart J. 34, 2481–2489 (2013).

    CAS  PubMed  Google Scholar 

  57. Hoellenriegel, J. et al. The Spiegelmer NOX-A12, a novel CXCL12 inhibitor, interferes with chronic lymphocytic leukemia cell motility and causes chemosensitization. Blood 123, 1032–1039 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Marasca, R. & Maffei, R. NOX-A12: mobilizing CLL away from home. Blood 123, 952–953 (2014).

    CAS  PubMed  Google Scholar 

  59. Vater, A. & Klussmann, S. Turning mirror-image oligonucleotides into drugs: the evolution of Spiegelmer therapeutics. Drug Discov. Today 20, 147–155 (2015).

    CAS  PubMed  Google Scholar 

  60. Klussmann, S., Nolte, A., Bald, R., Erdmann, V. A. & Furste, J. P. Mirror-image RNA that binds D-adenosine. Nat. Biotechnol. 14, 1112–1115 (1996).

    CAS  PubMed  Google Scholar 

  61. Sczepanski, J. T. & Joyce, G. F. Specific inhibition of microRNA processing using L-RNA aptamers. J. Am. Chem. Soc. 137, 16032–16037 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  62. Kruspe, S., Mittelberger, F., Szameit, K. & Hahn, U. Aptamers as drug delivery vehicles. ChemMedChem 9, 1998–2011 (2014).

    CAS  PubMed  Google Scholar 

  63. Olson, W. C., Heston, W. D. & Rajasekaran, A. K. Clinical trials of cancer therapies targeting prostate-specific membrane antigen. Rev. Recent Clin. Trials 2, 182–190 (2007).

    CAS  PubMed  Google Scholar 

  64. Lupold, S. E., Hicke, B. J., Lin, Y. & Coffey, D. S. 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 (2002).

    CAS  PubMed  Google Scholar 

  65. Pastor, F., Kolonias, D., Giangrande, P. H. & Gilboa, E. Induction of tumour immunity by targeted inhibition of nonsense-mediated mRNA decay. Nature 465, 227–230 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. Liang, C. et al. Aptamer-functionalized lipid nanoparticles targeting osteoblasts as a novel RNA interference-based bone anabolic strategy. Nat. Med. 21, 288–294 (2015).

    PubMed  PubMed Central  Google Scholar 

  67. Douek, D. C., Roederer, M. & Koup, R. A. Emerging concepts in the immunopathogenesis of AIDS. Annu. Rev. Med. 60, 471–484 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Tang, J. & Kaslow, R. A. The impact of host genetics on HIV infection and disease progression in the era of highly active antiretroviral therapy. AIDS 17 (Suppl. 4), 51–60 (2003).

    Google Scholar 

  69. Zhou, J. et al. Selection, characterization and application of new RNA HIV gp 120 aptamers for facile delivery of Dicer substrate siRNAs into HIV infected cells. Nucleic Acids Res. 37, 3094–3109 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Zhou, J., Li, H., Li, S., Zaia, J. & Rossi, J. J. Novel dual inhibitory function aptamer–siRNA delivery system for HIV-1 therapy. Mol. Ther. 16, 1481–1489 (2008).

    CAS  PubMed  Google Scholar 

  71. Zhou, J. et al. Functional in vivo delivery of multiplexed anti-HIV-1 siRNAs via a chemically synthesized aptamer with a sticky bridge. Mol. Ther 21, 192–200 (2013).

    CAS  PubMed  Google Scholar 

  72. Kahsai, A. W. et al. Conformationally selective RNA aptamers allosterically modulate the β2-adrenoceptor. Nat. Chem. Biol. 12, 709–716 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Lefkowitz, R. J. A brief history of G-protein coupled receptors (Nobel Lecture). Angew. Chem. Int. Ed. 52, 6366–6378 (2013).

    CAS  Google Scholar 

  74. Koehn, F. E. & Carter, G. T. The evolving role of natural products in drug discovery. Nat. Rev. Drug Discov. 4, 206–220 (2005).

    CAS  PubMed  Google Scholar 

  75. Bastian, A. A., Marcozzi, A. & Herrmann, A. Selective transformations of complex molecules are enabled by aptameric protective groups. Nat. Chem. 4, 789–793 (2012).

    CAS  PubMed  Google Scholar 

  76. Sefah, K. et al. In vitro selection with artificial expanded genetic information systems. Proc. Natl Acad. Sci. USA 111, 1449–1454 (2014).

    CAS  PubMed  Google Scholar 

  77. Kimoto, M., Yamashige, R., Matsunaga, K. I., Yokoyama, S. & Hirao, I. Generation of high-affinity DNA aptamers using an expanded genetic alphabet. Nat. Biotechnol. 31, 453–457 (2013).

    CAS  PubMed  Google Scholar 

  78. Matsunaga, K. I., Kimoto, M. & Hirao, I. High-affinity DNA aptamer generation targeting von Willebrand factor A1-domain by genetic alphabet expansion for systematic evolution of ligands by exponential enrichment using two types of libraries composed of five different bases. J. Am. Chem. Soc. 139, 324–334 (2017).

    CAS  PubMed  Google Scholar 

  79. Tolle, F., Brändle, G. M., Natzner, D. & Mayer, G. A versatile approach towards nucleobase-modified aptamers. Angew. Chem. Int. Ed. 54, 10971–10974 (2015).

    CAS  Google Scholar 

  80. Shui, B. et al. RNA aptamers that functionally interact with green fluorescent protein and its derivatives. Nucleic Acids Res. 40, e39 (2012).

    CAS  PubMed  Google Scholar 

  81. Gold, L. et al. Aptamer-based multiplexed proteomic technology for biomarker discovery. PLoS One 5, e15004 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  82. Vaught, J. D. et al. Expanding the chemistry of DNA for in vitro selection. J. Am. Chem. Soc. 132, 4141–4151 (2010).

    CAS  PubMed  Google Scholar 

  83. Gupta, S. et al. Chemically modified DNA aptamers bind interleukin-6 with high affinity and inhibit signaling by blocking its interaction with interleukin-6 receptor. J. Biol. Chem. 289, 8706–8719 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  84. Gelinas, A. D., Davies, D. R. & Janjic, N. Embracing proteins: structural themes in aptamer–protein complexes. Curr. Opin. Struct. Biol. 36, 122–132 (2016).

    CAS  PubMed  Google Scholar 

  85. Gawande, B. N. et al. Selection of DNA aptamers with two modified bases. Proc. Natl Acad. Sci. USA 114, 2898–2903 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  86. Ostroff, R. M. et al. Unlocking biomarker discovery: large scale application of aptamer proteomic technology for early detection of lung cancer. PLoS One 5, e15003 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. Hili, R., Niu, J. & Liu, D. R. DNA ligase-mediated translation of DNA into densely functionalized nucleic acid polymers. J. Am. Chem. Soc. 135, 98–101 (2013).

    CAS  PubMed  Google Scholar 

  88. Guo, C., Watkins, C. P. & Hili, R. Sequence-defined scaffolding of peptides on nucleic acid polymers. J. Am. Chem. Soc. 137, 11191–11196 (2015).

    CAS  PubMed  Google Scholar 

  89. Kong, D., Lei, Y., Yeung, W. & Hili, R. Enzymatic synthesis of sequence-defined synthetic nucleic acid polymers with diverse functional groups. Angew. Chem. Int. Ed. 55, 13164–13168 (2016).

    CAS  Google Scholar 

  90. Zhao, H. & Arnold, F. H. Combinatorial protein design: strategies for screening protein libraries. Curr. Opin. Struct. Biol. 7, 480–485 (1997).

    CAS  PubMed  Google Scholar 

  91. Bordeaux, J. et al. Antibody validation. Biotechniques 48, 197–209 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  92. Marx, V. Calling the next generation of affinity reagents. Nat. Methods 10, 829–833 (2013).

    CAS  PubMed  Google Scholar 

  93. Mi, J. et al. In vivo selection of tumor-targeting RNA motifs. Nat. Chem. Biol. 6, 22–24 (2010).

    CAS  PubMed  Google Scholar 

  94. Cheng, C., Chen, Y. H., Lennox, K. A., Behlke, M. A. & Davidson, B. L. In vivo SELEX for identification of brain-penetrating aptamers. Mol. Ther. Nucleic Acids 2, e67 (2013).

    PubMed  PubMed Central  Google Scholar 

  95. Wang, J. et al. Multiparameter particle display (MPPD): a quantitative screening method for the discovery of highly specific aptamers. Angew. Chem. Int. Ed. 56, 744–747 (2017).

    CAS  Google Scholar 

  96. Wang, J. et al. Particle display: a quantitative screening method for generating high-affinity aptamers. Angew. Chem. Int. Ed. 126, 4896–4901 (2014).

    Google Scholar 

  97. Griffin, L. C., Tidmarsh, G. F., Bock, L. C., Toole, J. J. & Leung, L. L. In vivo anticoagulant properties of a novel nucleotide-based thrombin inhibitor and demonstration of regional anticoagulation in extracorporeal circuits. Blood 81, 3271–3276 (1993).

    CAS  PubMed  Google Scholar 

  98. Keefe, A. D. & Cload, S. T. SELEX with modified nucleotides. Curr. Opin. Chem. Biol. 12, 448–456 (2008).

    CAS  PubMed  Google Scholar 

  99. Lin, Y., Qiu, Q., Gill, S. C. & Jayasena, S. D. Modified RNA sequence pools for in vitro selection. Nucleic Acids Res. 22, 5229–5234 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  100. Burmeister, P. E. et al. Direct in vitro selection of a 2′-O-methyl aptamer to VEGF. Chem. Biol. 12, 25–33 (2005).

    CAS  PubMed  Google Scholar 

  101. Burmeister, P. E. et al. 2′-Deoxy purine, 2′-O-methyl pyrimidine (dRmY) aptamers as candidate therapeutics. Oligonucleotides 16, 337–351 (2006).

    CAS  PubMed  Google Scholar 

  102. Thirunavukarasu, D., Chen, T., Liu, Z., Hongdilokkul, N. & Romesberg, F. E. Selection of 2′-fluoro-modified aptamers with optimized properties. J. Am. Chem. Soc. 139, 2892–2895 (2017).

    CAS  PubMed  Google Scholar 

  103. Cummins, L. L. et al. Characterization of fully 2′-modified oligoribonucleotide hetero- and homoduplex hybridization and nuclease sensitivity. Nucleic Acids Res. 23, 2019–2024 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  104. Noronha, A. M. et al. Synthesis and biophysical properties of arabinonucleic acids (ANA): circular dichroic spectra, melting temperatures, and ribonuclease H susceptibility of ANA•RNA hybrid duplexes. Biochemistry 39, 7050–7062 (2000).

    CAS  PubMed  Google Scholar 

  105. Joyce, G. F. Toward an alternative biology. Science 336, 307–308 (2012).

    CAS  PubMed  Google Scholar 

  106. Legrain, P. et al. The human proteome project: current state and future direction. Mol. Cell. Proteomics 10, M111.009993 (2011).

    PubMed  PubMed Central  Google Scholar 

  107. Wang, Z., Xu, W., Liu, L. & Zhu, T. F. A synthetic molecular system capable of mirror-image genetic replication and transcription. Nat. Chem. 8, 698–704 (2016).

    CAS  PubMed  Google Scholar 

  108. Pech, A. et al. A thermostable D-polymerase for mirror-image PCR. Nucleic Acids Res. 45, 3997–4005 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  109. Larsen, A. C. et al. A general strategy for expanding polymerase function by droplet microfluidics. Nat. Commun. 7, 11235 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  110. Ghadessy, F. J., Ong, J. L. & Holliger, P. Directed evolution of polymerase function by compartmentalized self-replication. Proc. Natl Acad. Sci. USA 98, 4552–4557 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  111. Houlihan, G., Arangundy-Franklin, S. & Holliger, P. Exploring the chemistry of genetic information storage and propagation through polymerase engineering. Acc. Chem. Res. 50, 1079–1087 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  112. Chen, T. & Romesberg, F. E. Directed polymerase evolution. FEBS Lett. 588, 219–229 (2014).

    CAS  PubMed  Google Scholar 

  113. Taylor, A. I. & Holliger, P. Directed evolution of artificial enzymes (XNAzymes) from diverse repertoires of synthetic genetic polymers. Nat. Protoc. 10, 1625–1642 (2015).

    CAS  PubMed  Google Scholar 

  114. Pinheiro, V. B. et al. Synthetic genetic polymers capable of heredity and evolution. Science 336, 341–344 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  115. Alves Ferreira-Bravo, I., Cozens, C., Holliger, P. & DeStefano, J. J. Selection of 2′-deoxy-2′-fluoroarabinonucleotide (FANA) aptamers that bind HIV-1 reverse transcriptase with picomolar affinity. Nucleic Acids Res. 43, 9587–9599 (2015).

    PubMed  PubMed Central  Google Scholar 

  116. Yu, H., Zhang, S. & Chaput, J. C. Darwinian evolution of an alternative genetic system provides support for TNA as an RNA progenitor. Nat. Chem. 4, 183–187 (2012).

    CAS  PubMed  Google Scholar 

  117. Dunn, M. R. & Chaput, J. C. Reverse transcription of threose nucleic acid by a naturally occurring DNA polymerase. ChemBioChem 17, 1804–1808 (2016).

    CAS  PubMed  Google Scholar 

  118. Schöning, K. U. et al. Chemical etiology of nucleic acid structure: the α-threofuranosyl-(3′→2′) oligonucleotide system. Science 290, 1347–1351 (2000).

    PubMed  Google Scholar 

  119. Ebert, M. O., Mang, C., Krishnamurthy, R., Eschenmoser, A. & Jaun, B. The structure of a TNA–TNA complex in solution: NMR study of the octamer duplex derived from α-(L)-threofuranosyl-(3′-2′)-CGAATTCG. J. Am. Chem. Soc. 130, 15105–15115 (2008).

    PubMed  Google Scholar 

  120. Culbertson, M. C. et al. Evaluating TNA stability under simulated physiological conditions. Bioorg. Med. Chem. Lett. 26, 2418–2421 (2016).

    CAS  PubMed  Google Scholar 

  121. Tizei, P. A., Csibra, E., Torres, L. & Pinheiro, V. B. Selection platforms for directed evolution in synthetic biology. Biochem. Soc. Trans. 44, 1165–1175 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  122. Mei, H. et al. Synthesis and polymerase activity of a fluorescent cytidine TNA triphosphate analogue. Nucleic Acids Res. 45, 5629–5638 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  123. Mendonsa, S. D. & Bowser, M. T. In vitro evolution of functional DNA using capillary electrophoresis. J. Am. Chem. Soc. 126, 20–21 (2004).

    CAS  PubMed  Google Scholar 

  124. Ouellet, E., Foley, J. H., Conway, E. M. & Haynes, C. Hi-Fi SELEX: a high-fidelity digital-PCR based therapeutic aptamer discovery platform. Biotechnol. Bioeng. 112, 1506–1522 (2015).

    CAS  PubMed  Google Scholar 

  125. Williams, R. et al. Amplification of complex gene libraries by emulsion PCR. Nat. Methods 3, 545–550 (2006).

    CAS  PubMed  Google Scholar 

  126. Cox, J. C. et al. Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer. Nucleic Acids Res. 30, e108 (2002).

    PubMed  PubMed Central  Google Scholar 

  127. Bradbury, A. & Pluckthun, A. Reproducibility: standardize antibodies used in research. Nature 518, 27–29 (2015).

    CAS  PubMed  Google Scholar 

  128. Barrett, S. E. et al. An in vivo evaluation of amphiphilic, biodegradable peptide copolymers as siRNA delivery agents. Int. J. Pharm. 466, 58–67 (2014).

    CAS  PubMed  Google Scholar 

  129. Long, S. B., Long, M. B., White, R. R. & Sullenger, B. A. Crystal structure of an RNA aptamer bound to thrombin. RNA 14, 2504–2512 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors thank members of the Chaput laboratory for helpful comments and suggestions, and N. Chim for assistance with the figures. This work was supported by the Defense Advanced Research Projects Agency (DARPA) Folded Non-Natural Polymers with Biological Function (Fold Fx) Program (Award No.N66001-16-2-4061).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to John C. Chaput.

Ethics declarations

Competing interests

The authors declare no competing interests.

Supplementary information

Supplementary information S1–S21 (tables)

Raw and normalized data for aptamer trends presented in Figure 1b. (XLSX 335 kb)

PowerPoint slides

Glossary

Phenotypes

Observable characteristics, such as binding or catalytic activity, that are encoded in the sequence of a nucleic acid or protein.

Genotypes

Genetic sequences that encode phenotypes.

Antibodies

Protein affinity reagents produced by the immune system that can be made to recognize a wide range of targets called antigens.

Aptagenic

A target that is known to produce an aptamer by in vitro selection.

Dissociation constant

The equilibrium constant for the dissociation of the target– aptamer complex (Kd = [target] [aptamer]/[target–aptamer]).

Lysate

The contents of a cell produced by cell lysis.

cDNA

The complementary DNA sequence that results when RNA (or xeno-nucleic acid (XNA)) is reverse transcribed into DNA.

Doped library

A nucleic acid library that contains variants of a single sequence, which feature a small fraction of non-wild type residues at each position. For example, if the wild-type residue is A, then the library would contain mostly A with a mixture of C with T and G.

Recombinant protein therapies

Therapies that are produced through recombinant DNA technology, which involves expressing and purifying a protein from bacterial or mammalian cells. Many biologics, such as monoclonal antibodies, are recombinant protein therapies.

Phosphodiester linkage

The chemical linkage, connecting the monomeric units in a nucleic acid polymer. In general, the linkage takes the form RO(O)P(O)OR′.

Induced-fit

A biochemistry model in which the initial interactions of an enzyme–substrate complex (or antibody–target complex) are strengthened by conformational changes that increase the strength of the intermolecular interactions involved in substrate or target recognition.

Fluorescent reporter

Molecules that elicit a fluorescent signal.

Fluorescence resonance energy transfer

A photophysical effect in which energy is transferred between fluorescent or light-sensitive moieties.

Mirror-image symmetry

Symmetry with respect to a reflection or plane of symmetry. Mirror-image molecules are non-superimposable. For example, your right hand cannot be superimposed on top of your left hand.

von Willebrand factor

A glycoprotein found in the blood that is involved in haemostasis (blood clotting).

Click chemistry

A general class of high-yielding cycloaddition reactions that occur between azide and alkyne functional groups. Click chemistry is often used to add new functional groups to biomolecules.

Primer extension

A DNA (or xeno-nucleic acid (XNA)) replication step in which a nucleic acid primer is extended by annealing the primer to a template and copying the template with a polymerase.

Fluorescence-activated cell sorting

A development of flow cytometry that enables sorting of a mixture of cells into two or more fractions based on the light scattering and fluorescence signal of each cell.

Enzyme-linked immunosorbent assay

A diagnostic test that uses affinity reagents, typically antibodies, to detect a substance.

Emulsion PCR

A variant of the polymerase chain reaction (PCR) that is performed in water-in-oil droplets.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Dunn, M., Jimenez, R. & Chaput, J. Analysis of aptamer discovery and technology. Nat Rev Chem 1, 0076 (2017). https://doi.org/10.1038/s41570-017-0076

Download citation

  • Published:

  • DOI: https://doi.org/10.1038/s41570-017-0076

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing