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Designer DNA architecture offers precise and multivalent spatial pattern-recognition for viral sensing and inhibition

Nature Chemistry volume 12, pages 26–35 (2020)Cite this article

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Abstract

DNA, when folded into nanostructures with a specific shape, is capable of spacing and arranging binding sites into a complex geometric pattern with nanometre precision. Here we demonstrate a designer DNA nanostructure that can act as a template to display multiple binding motifs with precise spatial pattern-recognition properties, and that this approach can confer exceptional sensing and potent viral inhibitory capabilities. A star-shaped DNA architecture, carrying five molecular beacon-like motifs, was constructed to display ten dengue envelope protein domain III (ED3)-targeting aptamers into a two-dimensional pattern precisely matching the spatial arrangement of ED3 clusters on the dengue (DENV) viral surface. The resulting multivalent interactions provide high DENV-binding avidity. We show that this structure is a potent viral inhibitor and that it can act as a sensor by including a fluorescent output to report binding. Our molecular-platform design strategy could be adapted to detect and combat other disease-causing pathogens by generating the requisite ligand patterns on customized DNA nanoarchitectures.

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Fig. 1: Dimensional pattern analysis and scaffold design principle.
Fig. 2: DNA star sensor.
Fig. 3: Evaluation of control sensors.
Fig. 4: Evaluation of inhibitors.
Fig. 5: Confocal imaging.
Fig. 6: Design principle of DNA nanostructure-based method with pattern-recognition properties.

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Data availability

All data supporting the findings of this work are available within this paper (figures, videos and description) and its Supplementary Information. All other data are available from the corresponding authors upon request.

Code availability

The SEQUIN program used in this study is available from the corresponding authors upon reasonable request.

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Acknowledgements

We thank the core facilities at RPI-CBIS, Wadsworth Center of New York State Department of Health, Organic Electronics and Information Displays and Jiangsu Key Laboratory and Institute of Advanced Materials of Nanjing University of Posts and Telecommunications (China). This work was funded by an RPI-CBIS start-up fund and award, a gift fund from HT Materials Corporation to X.W., the Ministry of Science and Technology of China (2017YFA0205302), the National Science Foundation of China (21922408 and 61771253), the Natural Science Foundation of Jiangsu Province for Distinguished Young Scholars (BK20190038) to J.C., the Global Research Laboratory Program through the National Research Foundation of Korea (2014K1A1A2043032) to J.S.D. and S.-J.K., and the National Institute of Health (DK111958) to R.J.L. The microscopy for time-lapsed analysis is supported by the National Science Foundation (NSF-MRI-1725984).

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Author notes

  1. These authors contributed equally: Paul S. Kwon, Shaokang Ren, Seok-Joon Kwon, Megan E. Kizer, Lili Kuo.

Authors and Affiliations

  1. Key Laboratory for Organic Electronics and Information Displays and Jiangsu, Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China

    Paul S. Kwon, Shaokang Ren, Mo Xie, Dan Zhu & Jie Chao

  2. Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA

    Paul S. Kwon, Megan E. Kizer, Robert J. Linhardt & Xing Wang

  3. Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA

    Paul S. Kwon

  4. Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA

    Seok-Joon Kwon, Fuming Zhang, Domyoung Kim, Keith Fraser, Jonathan S. Dordick & Robert J. Linhardt

  5. Wadsworth Center, New York State Department of Health, Albany, NY, USA

    Lili Kuo & Laura D. Kramer

  6. Department of Chemistry, New York University, New York, NY, USA

    Feng Zhou & Nadrian C. Seeman

  7. Center for Soft Matter Research, New York University, New York, NY, USA

    Feng Zhou

  8. Department of Chemistry, Micro and Nanotechnology Laboratory (MNTL), Carl R. Woese Institute for Genomic Biology (IGB), University of Illinois at Urbana-Champaign, Urbana, IL, USA

    Xing Wang

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Contributions

P.S.K., S.-J.K., J.S.D., R.J.L. and X.W. conceived the original 2D spatial pattern-matching strategy. P.S.K., S.-J.K., R.J.L., J.C. and X.W. conceived and designed the experiments. S.R. and J.C. designed the sequences of the DNA scaffolds and performed non-denaturing PAGE. S.R., M.X., D.Z., J.C., F. Zhou and N.C.S. performed the AFM experiments. P.S.K., S.R. and M.E.K. purified and folded the DNA. L.K. and L.D.K. prepared viruses, conducted RT–qPCR detection and performed the plaque forming assays. F. Zhang performed SPR analysis. P.S.K., S.-J.K. and D.K. performed confocal microscopy. P.S.K. performed all other experiments. K.F. analysed the aptamer binding pattern of DENV. P.S.K., S.-J.K. and X.W. performed data analysis. P.S.K., S.-J.K., R.J.L. and X.W. led the preparation of the manuscript with contributions from all authors. P.S.K., S.R., S.-J.K., M.E.K. and L.K. contributed equally to this work.

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Correspondence to Jie Chao or Xing Wang.

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Supplementary information

Supplementary Information

Supplementary materials, methods, Figs. 1–9, Tables 1–11, notes and references.

Reporting Summary

Supplementary Video 1 (unbound condition)

Time-lapsed, live confocal imaging of dengue cell internalization.

Supplementary Video 2 (DNA star-bound condition)

Time-lapsed, live confocal imaging of DNA star-bound dengue losing cell internalization ability.

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Kwon, P.S., Ren, S., Kwon, SJ. et al. Designer DNA architecture offers precise and multivalent spatial pattern-recognition for viral sensing and inhibition. Nat. Chem. 12, 26–35 (2020). https://doi.org/10.1038/s41557-019-0369-8

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