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Single-Molecule Nanomechanical Genoty** with DNA Origami-Based Shape IDs

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DNA and RNA Origami

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2639))

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Abstract

Atomic force microscopy (AFM)-based nanomechanical imaging provides a sub-10-nm-resolution approach for imaging biomolecules under ambient conditions. Here we describe how to generate a set of DNA origami-based shape IDs (triangular and cross shape, with and without streptavidin) to site-specifically label target genomic DNA sequences containing two single-nucleotide polymorphisms (SNPs). Adjacent labeling sites separated by only 30 nucleobases (~10 nm) can be differentiated under AFM imaging. We can directly genotype single molecules of human genomic DNA.

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Acknowledgments

This work was supported by the Ministry of Science and Technology of China (2017YFA0205302, 2016YFA0201200, and 2016YFA0400900), the NSFC (61771253 and 21390414), the Program for Changjiang Scholars and Innovative Research Team in University (IRT 15R37), the Natural Science Foundation of Jiangsu Province (BK20151504), and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD, YX03001).

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Authors and Affiliations

  1. School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China

    Qian Li & Chunhai Fan

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

    Jie Chao

  3. School of Biomedical Sciences and Engineering, National Engineering Research Center for Tissue Restoration and Reconstruction, Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou, China

    Honglu Zhang

Authors
  1. Qian Li
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  2. Jie Chao
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  3. Honglu Zhang
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  4. Chunhai Fan
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Corresponding author

Correspondence to Chunhai Fan .

Editor information

Editors and Affiliations

  1. Aarhus university, Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus, Denmark

    Julián Valero

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Li, Q., Chao, J., Zhang, H., Fan, C. (2023). Single-Molecule Nanomechanical Genoty** with DNA Origami-Based Shape IDs. In: Valero, J. (eds) DNA and RNA Origami. Methods in Molecular Biology, vol 2639. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3028-0_9

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  • DOI: https://doi.org/10.1007/978-1-0716-3028-0_9

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3027-3

  • Online ISBN: 978-1-0716-3028-0

  • eBook Packages: Springer Protocols

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