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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.

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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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