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An in Vitro Selection Strategy Identifying Naked DNA That Localizes to Cell Nuclei

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    An in Vitro Selection Strategy Identifying Naked DNA That Localizes to Cell Nuclei
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    • John Smestad
      John Smestad
      Medical Scientist Training Program, Mayo Clinic College of Medicine and Science, Rochester, Minnesota 55905, United States
      Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota 55905, United States
      More by John Smestad
    • Brandon Wilbanks
      Brandon Wilbanks
      Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota 55905, United States
      Mayo Clinic Graduate School of Biomedical Sciences, Rochester, Minnesota 55905, United States
      More by Brandon Wilbanks
    • Louis J. Maher III*
      Louis J. Maher, III
      Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota 55905, United States
      *[email protected]
      More by Louis J. Maher, III
      Orcidhttp://orcid.org/0000-0002-5043-6422
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    Journal of the American Chemical Society

    Cite this: J. Am. Chem. Soc. 2019, 141, 46, 18375–18379
    Click to copy citationCitation copied!
    https://doi.org/10.1021/jacs.9b06736
    Published November 8, 2019
    Copyright © 2019 American Chemical Society
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    Abstract

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    Combinatorial chemistry drives the biological generation of protein structural diversity in antibodies and T-cell receptors. When applied to nucleic acids, vast engineered random libraries of DNA and RNA strands allow selection of affinity reagents (“aptamers”) against molecular targets. Selection involves cycles rewarding target binding affinity with amplification. Despite the success of this approach, delivery of selected aptamers across cell membranes and to specific subcellular compartments is an unmet need in chemical biology. Here, we address this challenge, demonstrating in vitro selection of DNA aptamers capable of homing to nuclei of cultured cells without transfection agents or viral transduction. Selection of such folded karyophilic DNA aptamers (∼100 nucleotides) is achieved by a biosensor strategy that rewards exposure to nuclear DNA ligase. Identified DNA molecules are preferentially delivered to cell nuclei within minutes. Related strategies can be envisioned to select aptamers that home to other subcellular compartments.

    Copyright © 2019 American Chemical Society

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/jacs.9b06736.

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    This article is cited by 7 publications.

    1. Mo Zhou, Tianbin Xu, Kai Xia, Haiqing Gao, Wei Li, Tingting Zhai, Hongzhou Gu. Small DNAs That Specifically and Tightly Bind Transition Metal Ions. Journal of the American Chemical Society 2023, 145 (16) , 8776-8780. https://doi.org/10.1021/jacs.3c01276
    2. Brandon Wilbanks, Keenan Pearson, Shane R. Byrne, Laura B. Bickart, Peter C. Dedon, L. James Maher, III. DNA Modifications Enabling Proximity Biotinylation. Bioconjugate Chemistry 2023, 34 (4) , 611-615. https://doi.org/10.1021/acs.bioconjchem.2c00475
    3. Tianbin Xu, Canyu Zhang, Kai Xia, Wei Li, Yichun Cao, Hongzhou Gu. Small DNAs that Bind Nickel(II) Specifically and Tightly. Analytical Chemistry 2021, 93 (45) , 14912-14917. https://doi.org/10.1021/acs.analchem.1c04034
    4. Brandon Wilbanks, William Beimers, Maria Dugan, Taylor Weiskittel, L J Maher, . Peroxidase proximity selection to identify aptamers targeting a subcellular location. PNAS Nexus 2023, 2 (5) https://doi.org/10.1093/pnasnexus/pgad151
    5. Yanyan Miao, Qianqian Gao, Menghan Mao, Chao Zhang, Liqun Yang, Yang Yang, Da Han. Bispecific Aptamer Chimeras Enable Targeted Protein Degradation on Cell Membranes. Angewandte Chemie 2021, 133 (20) , 11367-11371. https://doi.org/10.1002/ange.202102170
    6. Yanyan Miao, Qianqian Gao, Menghan Mao, Chao Zhang, Liqun Yang, Yang Yang, Da Han. Bispecific Aptamer Chimeras Enable Targeted Protein Degradation on Cell Membranes. Angewandte Chemie International Edition 2021, 60 (20) , 11267-11271. https://doi.org/10.1002/anie.202102170
    7. Keisuke Tanaka, Takumi Okuda, Yuuya Kasahara, Satoshi Obika. Base-modified aptamers obtained by cell-internalization SELEX facilitate cellular uptake of an antisense oligonucleotide. Molecular Therapy - Nucleic Acids 2021, 23 , 440-449. https://doi.org/10.1016/j.omtn.2020.11.016
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    Journal of the American Chemical Society

    Cite this: J. Am. Chem. Soc. 2019, 141, 46, 18375–18379
    Click to copy citationCitation copied!
    https://doi.org/10.1021/jacs.9b06736
    Published November 8, 2019
    Copyright © 2019 American Chemical Society
    Request reuse permissions

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