Skip to main content

Thank you for visiting 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.

Recognition and sensing of low-epitope targets via ternary complexes with oligonucleotides and synthetic receptors


Oligonucleotide-based receptors or aptamers can interact with small molecules, but the ability to achieve high-affinity and specificity of these interactions depends strongly on functional groups or epitopes displayed by the binding targets. Some classes of targets are particularly challenging: for example, monosaccharides have scarce functionalities and no aptamers have been reported to recognize, let alone distinguish from each other, glucose and other hexoses. Here we report aptamers that differentiate low-epitope targets such as glucose, fructose or galactose by forming ternary complexes with high-epitope organic receptors for monosaccharides. In a follow-up example, we expand this method to isolate high-affinity oligonucleotides against aromatic amino acids complexed in situ with a nonspecific organometallic receptor. The method is general and enables broad clinical use of aptamers for the detection of small molecules in mix-and-measure assays, as demonstrated by monitoring postprandial waves of phenylalanine in human subjects.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Basic principles of glucose recognition with boronic acid receptors and of the isolation of aptamers against complexes with receptors.
Figure 2: Results of three selection procedures against monosaccharides.
Figure 3: Results of three selection procedures against amino acids.
Figure 4: Measurement in human serum and real-time monitoring of postprandial waves.


  1. 1

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

    CAS  Article  Google Scholar 

  2. 2

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

    CAS  Article  Google Scholar 

  3. 3

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

    CAS  Article  Google Scholar 

  4. 4

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

    CAS  Article  Google Scholar 

  5. 5

    McKeague, M. & Derosa, M. C. Challenges and opportunities for small molecule aptamer development. J. Nucleic Acids 748913 (2012).

  6. 6

    Imaizumi, Y. et al. Efficacy of base-modification on target binding of small molecule DNA aptamers. J. Am. Chem. Soc. 135, 9412–9419 (2013).

    CAS  Article  Google Scholar 

  7. 7

    Manimala, J. C., Wiskur, S. L., Ellington, A. D. & Anslyn, E. V. Tuning the specificity of a synthetic receptor using a selected nucleic acid receptor. J. Am. Chem. Soc. 126, 16515–16519 (2004).

    CAS  Article  Google Scholar 

  8. 8

    Klonoff, D. C. The need for separate performance goals for glucose sensors in the hypoglycemic, normoglycemic, and hyperglycemic ranges. Diabetes Care 27, 834–836 (2004).

    Article  Google Scholar 

  9. 9

    James, T. D., Samankumara Sandanayake, K. R. A. & Shinkai, S. A glucose-selective molecular fluorescence sensor. Angew. Chem. Int. Ed. 33, 2207–2209 (1994).

    Article  Google Scholar 

  10. 10

    Larkin, J. D., Frimat, K. A., Fyles, T. M., Flower, S. E. & James, T. D. Boronic acid based photoinduced electron transfer (PET) fluorescence sensors for saccharides. New J. Chem. 34, 2922–2931 (2010).

    CAS  Article  Google Scholar 

  11. 11

    Yang, K-A., Pei, R., Stefanovic, D. & Stojanovic, M. N. Optimizing cross-reactivity with evolutionary search for sensors. J. Am. Chem. Soc. 134, 1642–1647 (2012).

    CAS  Article  Google Scholar 

  12. 12

    Nutiu, R. & Li, Y. In vitro selection of structure-switching signaling aptamers. Angew. Chem. Int. Ed. 44, 1061–1065 (2005).

    CAS  Article  Google Scholar 

  13. 13

    Rajendran, M. & Ellington, A. D. Selection of fluorescent aptamer beacons that light up in the presence of zinc. Anal. Bioanal. Chem. 390, 1067–1075 (2008).

    CAS  Article  Google Scholar 

  14. 14

    Blau, N., van Spronsen, F. J. & Levy, H. L. Phenylketonuria. Lancet 376, 1417–1427 (2010).

    CAS  Article  Google Scholar 

  15. 15

    Hanley, W. B. et al. ‘Hypotyrosinemia’ in phenylketonuria. Mol. Genet. Metab. 69, 286–294 (2000).

    CAS  Article  Google Scholar 

  16. 16

    Snedden, W., Mellor, C. S. & Martin, J. R. Familial hypertryptophanemia, tryptophanuria and indoleketonuria. Clin. Chim. Acta 131, 247–256 (1983).

    CAS  Article  Google Scholar 

  17. 17

    Yarus, M., Widmann, J. J. & Knight, R. RNA–amino acid binding: a stereochemical era for the genetic code. J. Mol. Evol. 69, 406–429 (2009).

    CAS  Article  Google Scholar 

  18. 18

    Illangasekare, M. & Yarus, M. Phenylalanine-binding RNAs and genetic code evolution. J. Mol. Evol. 54, 298–311 (2002).

    CAS  Article  Google Scholar 

  19. 19

    Manironi, C., Scerch, C., Fruscoloni, P. & Tocchini-Valentini, G. P. Molecular recognition of amino acids by RNA aptamers: the evolution into an L-tyrosine binder of a dopamine-binding RNA motif. RNA 6, 520–527 (2000).

    Article  Google Scholar 

  20. 20

    Yang, X. et al. Characterization and application of a DNA aptamer binding to L-tryptophan. Analyst 136, 577–585 (2011).

    CAS  Article  Google Scholar 

  21. 21

    Buryak, A. & Severin, K. A chemosensor array for the colorimetric identification of 20 natural amino acids. J. Am. Chem. Soc. 127, 3700–3701 (2005).

    CAS  Article  Google Scholar 

  22. 22

    Rampini, S., Anders, P. W., Curtius, H. C. & Marthaler, T. Detection of heterozygotes for phenylketonuria by column chromatography and discriminatory analysis. Pediatr. Res. 3, 287–297 (1969).

    CAS  Article  Google Scholar 

  23. 23

    Taylor, S. & Stojanovic, M. N. Is there a future for DNA-based molecular devices in diabetes management? J. Diabetes Sci. Technol. 1, 440–444 (2007).

    Article  Google Scholar 

  24. 24

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

    CAS  Article  Google Scholar 

Download references


We are grateful to the National Science Foundation (CBET-1033288 and CBET-1026592), National Institutes of Health (RGM104960) and the Juvenile Diabetes Research Foundation (Innovative Program) for funding this research. We thank J. Loeb for help in correcting initial drafts of our manuscript.

Author information




M.N.S. proposed and led the project. K-A.Y. isolated the aptamers listed in this report. S.P. and S.T. performed the synthetic and characterization work on the organic receptors. T.S.W. provided the clinical context and organized self-experiments, with B.K. providing technical support in these. M.B., M.H., P.P. and D.M.K. performed earlier experiments on glucose aptamers that eventually led to the development of the method described here. All co-authors participated in the design of their own experiments and analysis of data. M.N.S., T.S.W., K-A.Y. and S.T. wrote the manuscript, with the exception of synthetic procedures written by S.P.

Corresponding authors

Correspondence to Tilla S. Worgall or Milan N. Stojanovic.

Ethics declarations

Competing interests

The authors declare competing financial interests in the form of patent application(s).

Supplementary information

Supplementary information

Supplementary information (PDF 1396 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Yang, KA., Barbu, M., Halim, M. et al. Recognition and sensing of low-epitope targets via ternary complexes with oligonucleotides and synthetic receptors. Nature Chem 6, 1003–1008 (2014).

Download citation

Further reading


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