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Selective discrimination and classification of G-quadruplex structures with a host–guest sensing array

Nature Chemistry volume 13, pages 488–495 (2021)Cite this article

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Abstract

The secondary structures of nucleic acids have an important influence on their cellular functions but can be difficult to identify and classify quickly. Here, we show that an arrayed suite of synthetic hosts and dyes is capable of fluorescence detection of oligonucleotide secondary structures. Multivariate analysis of different fluorescence enhancements—generated using cationic dyes that show affinity for both DNA G-quadruplexes and the synthetic hosts—enables discrimination between G-quadruplex structures of identical length and highly similar topological types. Different G-quadruplexes that display the same folding topology can also be easily differentiated by the number of G-quartets and sequence differences at the 3′ or 5′ ends. The array is capable of both differentiation and classification of the G-quadruplex structures at the same time. This simple non-invasive sensing method does not require the discovery and synthesis of specific G-quadruplex binding ligands, but employs a simple multicomponent approach to ensure wide applicability.

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Fig. 1: A host–guest sensor system for label-free classification and differentiation of G-quadruplex structures.
Fig. 2: Effect of DNA strands on the emission profiles of various host–dye complexes.
Fig. 3: Selective array-based sensing of variable DNA structures.
Fig. 4: Classification and discrimination of a suite of 23 G-quadruplex structures.
Fig. 5: More complex sensing with the array, which can detect structural topology switching and changing concentration of specific G4s in a mixture.

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The raw data corresponding to the supplementary figures are available as Supplementary Data. Source data are provided with this paper.

References

  1. Belmont, P., Constant, J.-F. & Demeunynck, M. Nucleic acid conformation diversity: from structure to function and regulation. Chem. Soc. Rev. 30, 70–81 (2001).

    Article  CAS  Google Scholar 

  2. Balasubramanian, S., Hurley, L. H. & Neidle, S. Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? Nat. Rev. Drug Discovery 10, 261–275 (2011).

    Article  CAS  PubMed  Google Scholar 

  3. Seeman, N. C. & Sleiman, H. F. DNA nanotechnology. Nat. Rev. Mater. 3, 17068 (2017).

    Article  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Jaeger, L. & Chworos, A. The architectonics of programmable RNA and DNA nanostructures. Curr. Opin. Struct. Biol. 16, 531–543 (2006).

    Article  CAS  PubMed  Google Scholar 

  6. Winnerdy, F. R. et al. NMR solution and X-ray crystal structures of a DNA containing both right-and left-handed parallel-stranded G-quadruplexes. Nucleic Acids Res. 47, 8272–8281 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Salgado, G. F., Cazenave, C., Kerkour, A. & Mergny, J.-L. G-quadruplex DNA and ligand interaction in living cells using NMR spectroscopy. Chem. Sci. 6, 3314–3320 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. del Villar-Guerra, R., Trent, J. O. & Chaires, J. B. G-quadruplex secondary structure obtained from circular dichroism spectroscopy. Angew. Chem. Int. Ed. 57, 7171–7175 (2018).

    Article  Google Scholar 

  9. Eubanks, C. S., Forte, J. E., Kapral, G. J. & Hargrove, A. E. Small molecule-based pattern recognition to classify RNA structure. J. Am. Chem. Soc. 139, 409–416 (2017).

    Article  CAS  PubMed  Google Scholar 

  10. You, L., Zha, D. & Anslyn, E. V. Recent advances in supramolecular analytical chemistry using optical sensing. Chem. Rev. 115, 7840–7892 (2015).

    Article  CAS  PubMed  Google Scholar 

  11. Eubanks, C. S. et al. Visualizing RNA conformational changes via pattern recognition of RNA by small molecules. J. Am. Chem. Soc. 141, 5692–5698 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Stewart, S., Ivy, M. A. & Anslyn, E. V. The use of principal component analysis and discriminant analysis in differential sensing routines. Chem. Soc. Rev. 43, 70–84 (2014).

    Article  CAS  PubMed  Google Scholar 

  13. del Villar-Guerra, R., Gray, R. D., Trent, J. O. & Chaires, J. B. A rapid fluorescent indicator displacement assay and principal component/cluster data analysis for determination of ligand–nucleic acid structural selectivity. Nucleic Acids Res. 46, e41 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  14. Huppert, J. L. Four-stranded nucleic acids: structure, function and targeting of G-quadruplexes. Chem. Soc. Rev. 37, 1375–1384 (2008).

    Article  CAS  PubMed  Google Scholar 

  15. Bochman, M. L., Paeschke, K. & Zakian, V. A. DNA secondary structures: stability and function of G-quadruplex structures. Nat. Rev. Genet. 13, 770–780 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Burge, S. et al. sequence, topology and structure. Nucleic Acids Res. 34, 5402–5415 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Dolinnaya, N. G., Ogloblina, A. M. & Yakubovskaya, M. G. Structure, properties, and biological relevance of the DNA and RNA G-quadruplexes: Overview 50 years after their discovery. Biochemistry 81, 1602–1649 (2016).

    CAS  PubMed  Google Scholar 

  18. Kwok, C. K. & Merrick, C. J. G-quadruplexes: prediction, characterization, and biological application. Trends Biotechnol. 35, 997–1013 (2017).

    Article  CAS  PubMed  Google Scholar 

  19. Puig Lombardi, E. & Londoño-Vallejo, A. A guide to computational methods for G-quadruplex prediction. Nucleic Acids Res. 48, 1–15 (2020).

    Article  PubMed  Google Scholar 

  20. Zuffo, M. et al. More is not always better: finding the right trade-off between affinity and selectivity of a G-quadruplex ligand. Nucleic Acids Res. 46, e115 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  21. Felsenstein, K. M. et al. Small molecule microarrays enable the identification of a selective, quadruplex-binding inhibitor of MYC expression. ACS Chem. Biol. 11, 139–148 (2016).

    Article  CAS  PubMed  Google Scholar 

  22. Pinalli, R., Pedrini, A. & Dalcanale, E. Biochemical sensing with macrocyclic receptors. Chem. Soc. Rev. 47, 7006–7026 (2018).

    Article  CAS  PubMed  Google Scholar 

  23. Dsouza, R. N., Hennig, A. & Nau, W. M. Supramolecular tandem enzyme assays. Chem. Eur. J. 18, 3444–3459 (2012).

    Article  CAS  PubMed  Google Scholar 

  24. Hennig, A., Bakirci, H. & Nau, W. M. Label-free continuous enzyme assays with macrocycle-fluorescent dye complexes. Nat. Methods 4, 629–632 (2007).

    Article  CAS  PubMed  Google Scholar 

  25. Peacor, B. C., Ramsay, C. M. & Waters, M. L. Fluorogenic sensor platform for the histone code using receptors from dynamic combinatorial libraries. Chem. Sci. 8, 1422–1428 (2017).

    Article  CAS  PubMed  Google Scholar 

  26. Minaker, S. A., Daze, K. D., Ma, M. C. F. & Hof, F. Antibody-free reading of the histone code using a simple chemical sensor array. J. Am. Chem. Soc. 134, 11674–11680 (2012).

    Article  CAS  PubMed  Google Scholar 

  27. Florea, M. & Nau, W. M. Implementation of anion-receptor macrocycles in supramolecular tandem assays for enzymes involving nucleotides as substrates, products, and cofactors. Org. Biomol. Chem. 8, 1033–1039 (2010).

    Article  CAS  PubMed  Google Scholar 

  28. Liu, Y. et al. Selective heavy element sensing with a simple host–guest fluorescent array. Anal. Chem. 89, 11113–11121 (2017).

    Article  CAS  PubMed  Google Scholar 

  29. Gill, A. D. et al. Sensing of citrulline modifications in histone peptides by deep cavitand hosts. Chem. Commun. 55, 13259–13262 (2019).

    Article  CAS  Google Scholar 

  30. Murat, P., Singh, Y. & Defrancq, E. Methods for investigating G-quadruplex DNA/ligand interactions. Chem. Soc. Rev. 40, 5293–5307 (2011).

    Article  CAS  PubMed  Google Scholar 

  31. Biros, S. M., Ullrich, E. C., Hof, F., Trembleau, L. & Rebek, J. Kinetically stable complexes in water: the role of hydration and hydrophobicity. J. Am. Chem. Soc. 126, 2870–2876 (2004).

    Article  CAS  PubMed  Google Scholar 

  32. Liu, Y. et al. Site-selective sensing of histone methylation enzyme activity via an arrayed supramolecular tandem assay. J. Am. Chem. Soc. 139, 10964–10967 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Liu, Y. et al. Selective sensing of phosphorylated peptides and monitoring kinase and phosphatase activity with a supramolecular tandem assay. J. Am. Chem. Soc. 140, 13869–13877 (2018).

    Article  CAS  PubMed  Google Scholar 

  34. Mosca, S., Yu, Y. & Rebek, J. Preparative scale and convenient synthesis of a water-soluble, deep cavitand. Nat. Protoc. 11, 1371–1387 (2016).

    Article  CAS  PubMed  Google Scholar 

  35. Pinalli, R. et al. The origin of selectivity in the complexation of N-methyl amino acids by tetraphosphonate cavitands. J. Am. Chem. Soc. 138, 8569–8580 (2016).

    Article  CAS  PubMed  Google Scholar 

  36. Menozzi, D. et al. Thermodynamics of host–guest interactions between methylpyridinium salts and phosphonate cavitands. Supramol. Chem. 22, 768–775 (2010).

    Article  CAS  Google Scholar 

  37. Yang, Q. et al. Verification of specific G-quadruplex structure by using a novel cyanine dye supramolecular assembly: II. The binding characterization with specific intramolecular G-quadruplex and the recognizing mechanism. Nucleic Acids Res. 38, 1022–1033 (2010).

    Article  CAS  PubMed  Google Scholar 

  38. Früh, A. E., Artoni, F., Brighenti, R. & Dalcanale, E. Strain field self-diagnostic Poly(dimethylsiloxane) elastomers. Chem. Mater. 29, 7450–7467 (2017).

    Article  Google Scholar 

  39. Thordarson, P. Determining association constants from titration experiments in supramolecular chemistry. Chem. Soc. Rev. 40, 1305–1323 (2011).

    Article  CAS  PubMed  Google Scholar 

  40. Sengar, A., Heddi, B. & Phan, A. T. Formation of G-quadruplexes in poly-G sequences: structure of a propeller-type parallel-stranded G-quadruplex formed by a G15 stretch. Biochemistry 53, 7718–7723 (2014).

    Article  CAS  PubMed  Google Scholar 

  41. Ambrus, A. et al. Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution. Nucleic Acids Res. 34, 2723–2735 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank the National Science Foundation (CHE-1707347 to W.Z and R.J.H.) and MIUR (PRIN 20179BJNA2 to E.D.) for funding.

Author information

Authors and Affiliations

  1. Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA

    Junyi Chen & Wenwan Zhong

  2. Department of Chemistry, University of California, Riverside, CA, USA

    Briana L. Hickey, Linlin Wang, Jiwon Lee, Richard J. Hooley & Wenwan Zhong

  3. Department of Biochemistry and Molecular Biology, University of California, Riverside, CA, USA

    Adam D. Gill & Richard J. Hooley

  4. Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy

    Alessia Favero, Roberta Pinalli & Enrico Dalcanale

  5. INSTM, UdR, Parma, Italy

    Alessia Favero, Roberta Pinalli & Enrico Dalcanale

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Contributions

R.J.H. and W.Z. conceived and designed the experiments and wrote the paper. J.C. performed the arrayed sensing experiments and statistical analysis with help from L.W. and J.L. Chemical synthesis and optical analysis of hosts and dyes were performed by B.L.H., A.D.G, A.F., R.P. and E.D. All authors contributed to manuscript creation and proofreading.

Corresponding authors

Correspondence to Richard J. Hooley or Wenwan Zhong.

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Peer review information Nature Chemistry thanks the anonymous reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Host•dye structures.

Molecular-minimized structures of three host–guest complexes between guest DSMI and hosts 1, 2 and 5 (SPARTAN, Hartree-Fock). Lower rim substituents removed for clarity.

Extended Data Fig. 2 Effect of DNA strands on the emission profile of various host–dye complexes.

Comparison between the raw fluorescence response curves (left) and normalized fluorescence response curves (right) corresponding to the emission of DSMI dye in the presence of different DNA strands upon titration of hosts a,b) 1; c,d) 2; e,f) 5, illustrating the effect of the DNA structure on the emission of the various host–guest complexes. [DSMI] = 0.625 μM, [DNA] = 0.1 μM, [host] = 0–8 μM, 10 mM KH2PO4/K2HPO4 buffer, 1 mM EDTA, pH 7.4, Ex/Em = 485 nm/605 nm. The normalization process defines F0 as the emission at [DNA] = 0. Plots a, c, e are extended versions of those shown in Fig. 2. For the full suite of titration plots with all hosts 1–5 and both dyes, see Supplementary Figs. 18 and 19. Error bars represent the standard deviation of 3 repeated measurements.

Extended Data Fig. 3 Discrimination of a suite of 23 G-quadruplex structures.

2D PCA scores plot of the first two principal components (PC) generated from the fluorescence responses of 23 G4 strands to the sensing array. The data is identical to that shown in Fig. 4a, but rather than using the average of 5 repeats for each DNA in PCA, herein each repeat is treated as one individual sample. The first two principal components in total summarize more than 88% of the variation contained in the data, and their scores plot provides a visualization of how the 23 DNA strands are grouped by our array. Ellipses indicate 95% confidence.

Source data

Supplementary information

Supplementary Information

Supplementary Figs. 1–40 and Tables 1–3.

Supplementary Data 1

Source data for the figures within the Supplementary Information file.

Source data

Source Data Fig. 1

Fluorescence response curve source data.

Source Data Fig. 3

Array-based sensing and statistical source data.

Source Data Fig. 4

Array-based sensing and statistical source data.

Source Data Fig. 5

Array-based sensing and statistical source data.

Source Data Extended Data Fig. 3

Statistical source data.

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Chen, J., Hickey, B.L., Wang, L. et al. Selective discrimination and classification of G-quadruplex structures with a host–guest sensing array. Nat. Chem. 13, 488–495 (2021). https://doi.org/10.1038/s41557-021-00647-9

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