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Peptide-Driven Shape Control of Low-Dimensional DNA Nanostructures

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Download Hi-Res ImageDownload to MS-PowerPointCite This:ACS Nano 2020, 14, 2, 2276-2284
    Article

    Peptide-Driven Shape Control of Low-Dimensional DNA Nanostructures
    Click to copy article linkArticle link copied!

    • Chan-Jin Kim
      Chan-Jin Kim
      Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Korea
      More by Chan-Jin Kim
      Orcidhttp://orcid.org/0000-0001-8365-1295
    • Ji-eun Park
      Ji-eun Park
      Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Korea
      More by Ji-eun Park
    • Xiaole Hu
      Xiaole Hu
      Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Korea
      More by Xiaole Hu
    • Shine K. Albert
      Shine K. Albert
      Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Korea
      More by Shine K. Albert
    • So-Jung Park*
      So-Jung Park
      Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Korea
      *E-mail [email protected] (S.-J.P.).
      More by So-Jung Park
      Orcidhttp://orcid.org/0000-0002-6364-3754
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    ACS Nano

    Cite this: ACS Nano 2020, 14, 2, 2276–2284
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    https://doi.org/10.1021/acsnano.9b09312
    Published January 21, 2020
    Copyright © 2020 American Chemical Society
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    Abstract

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    We report the rational design and fabrication of unusual low-dimensional DNA nanostructures through programmable and sequence-specific peptide interactions. Dual-bioactive block copolymers composed of DNA and amino acid-based polymers (DNA-b-poly(amino acid)) were synthesized by coupling oligonucleotides to phenylalanine (Phe)-based polymers. Unlike prototypical DNA block copolymers, which typically form simple spherical micelles, DNA-b-poly(amino acid) assemble into various low-dimensional structures such as nanofibers, ribbons, and sheets through controllable amino acid interactions. Moreover, DNA-b-poly(amino acid) assemblies can undergo protease-induced fiber-to-sheet shape transformations, where the morphology change is dictated by the type of enzymes and amino acid sequences. The peptide-based self-assembly reported here provides a programmable approach to fabricate dynamic DNA assemblies with diverse and unusual low-dimensional structures.

    Copyright © 2020 American Chemical Society

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    Supporting Information

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acsnano.9b09312.

    • Materials and instrumentation, synthesis of N-acryloyl-Phe-OMe and N-acryloyl-Phe-Phe-OMe, synthesis of poly(Phe-OMe) and poly(Phe-Phe-OMe), synthesis of DNA1-b-poly(Phe-OMe) and DNA1-b-poly(Phe-Phe-OMe), determination of critical micelle concentration, circular dichroism analysis, synthesis of DNA functionalized gold nanoparticles, DNA dehybridization curves, HPLC chromatograms, NMR spectra, GPC data, DNA sequences, gel electrophoresis data, polarity index of various solvents used in this study, and additional TEM data (PDF)

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    Cited By

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    This article is cited by 28 publications.

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    2. Jaepil Jeong, Grzegorz Szczepaniak, Subha R. Das, Krzysztof Matyjaszewski. Synthesis of RNA-Amphiphiles via Atom Transfer Radical Polymerization in the Organic Phase. Precision Chemistry 2023, 1 (5) , 326-331. https://doi.org/10.1021/prechem.3c00042
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    4. Chan-Jin Kim, Francesca Ercole, Eirini Goudeli, Sukhvir Kaur Bhangu, Jingqu Chen, Matthew Faria, John F. Quinn, Frank Caruso. Engineering Programmable DNA Particles and Capsules Using Catechol-Functionalized DNA Block Copolymers. Chemistry of Materials 2022, 34 (16) , 7468-7480. https://doi.org/10.1021/acs.chemmater.2c01586
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    10. Shine K. Albert, Murali Golla, Nthiyanandan Krishnan, Devanathan Perumal, Reji Varghese. DNA−π Amphiphiles: A Unique Building Block for the Crafting of DNA-Decorated Unilamellar Nanostructures. Accounts of Chemical Research 2020, 53 (11) , 2668-2679. https://doi.org/10.1021/acs.accounts.0c00492
    11. Elias Rafael de Sousa, Guilherme Colherinhas. Theoretical study on symmetric and asymmetric stacking in the self-assembly of bola-amphiphilic peptides into membranes with mixtures of EF4E and KF4K. Journal of Molecular Liquids 2024, 400 , 124535. https://doi.org/10.1016/j.molliq.2024.124535
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    14. Ryo Yonenuma, Hideharu Mori. RAFT-synthesis and self-assembly-induced emission of pendant diphenylalanine–tetraphenylethylene copolymers. Soft Matter 2023, 19 (43) , 8403-8412. https://doi.org/10.1039/D3SM00988B
    15. Muhammad Ghufran Rafique, Jacob M. Remington, Finley Clark, Haochen Bai, Violeta Toader, Dmytro F. Perepichka, Jianing Li, Hanadi F. Sleiman. Two‐Dimensional Supramolecular Polymerization of DNA Amphiphiles is Driven by Sequence‐Dependent DNA‐Chromophore Interactions. Angewandte Chemie International Edition 2023, 62 (24) https://doi.org/10.1002/anie.202217814
    16. Muhammad Ghufran Rafique, Jacob M. Remington, Finley Clark, Haochen Bai, Violeta Toader, Dmytro F. Perepichka, Jianing Li, Hanadi F. Sleiman. Two‐Dimensional Supramolecular Polymerization of DNA Amphiphiles is Driven by Sequence‐Dependent DNA‐Chromophore Interactions. Angewandte Chemie 2023, 135 (24) https://doi.org/10.1002/ange.202217814
    17. Ryo Yonenuma, Hideharu Mori. Synthesis and self-assembly of a diphenylalanine–tetraphenylethylene hybrid monomer and RAFT polymers with aggregation-induced emission. Polymer Chemistry 2023, 14 (13) , 1469-1477. https://doi.org/10.1039/D2PY01602H
    18. Mahsa Sedighi, Neha Shrestha, Zahra Mahmoudi, Zahra Khademi, Alireza Ghasempour, Hamideh Dehghan, Seyedeh Fahimeh Talebi, Maryam Toolabi, Véronique Préat, Bozhi Chen, Xindong Guo, Mohammad-Ali Shahbazi. Multifunctional Self-Assembled Peptide Hydrogels for Biomedical Applications. Polymers 2023, 15 (5) , 1160. https://doi.org/10.3390/polym15051160
    19. Rui Li, Qing-Ling Zhou, Min-Rui Tai, Kathryn Ashton-Mourney, Mathew I. Harty, Aaqil Rifai, Clare L. Parish, David R. Nisbet, Sai-Yi Zhong, Richard J. Williams. Simple Complexity: Incorporating Bioinspired Delivery Machinery within Self-Assembled Peptide Biogels. Gels 2023, 9 (3) , 199. https://doi.org/10.3390/gels9030199
    20. Chang Yoon Ji, Kyeong-Jae Heo, Rira Jeong, Minlee Kim. RNAi-based pesticides: A magic bullet to deal with plant viruses. 2023, 525-555. https://doi.org/10.1016/B978-0-323-95339-9.00001-6
    21. Elias Rafael de Sousa, Douglas Xavier de Andrade, Guilherme Colherinhas. EF4K bola-amphiphilic peptide nanomembrane: structural, energetic and dynamic properties using molecular dynamics. Journal of Molecular Liquids 2022, 368 , 120651. https://doi.org/10.1016/j.molliq.2022.120651
    22. Li Wang, Guizhi Shen, Xuehai Yan. Bio-inspired short peptide self-assembly: From particles to functional materials. Particuology 2022, 64 , 14-34. https://doi.org/10.1016/j.partic.2021.05.007
    23. Julio Bernal-Chanchavac, Md. Al-Amin, Nicholas Stephanopoulos. Nanoscale Structures and Materials from the Self-assembly of Polypeptides and DNA. Current Topics in Medicinal Chemistry 2022, 22 (8) , 699-712. https://doi.org/10.2174/1568026621666211215142916
    24. Simone I. S. Hendrikse, Rafael Contreras-Montoya, Amanda V. Ellis, Pall Thordarson, Jonathan W. Steed. Biofunctionality with a twist: the importance of molecular organisation, handedness and configuration in synthetic biomaterial design. Chemical Society Reviews 2022, 51 (1) , 28-42. https://doi.org/10.1039/D1CS00896J
    25. Min Xu, Baomei Zhou, Yan Ding, Shanshan Du, Mengke Su, Honglin Liu. Programmable Oligonucleotide-Peptide Complexes: Synthesis and Applications. Chemical Research in Chinese Universities 2021, 57 https://doi.org/10.1007/s40242-021-1265-5
    26. Chan-Jin Kim, Ga-Hyun Kim, Eun Hye Jeong, Hyukjin Lee, So-Jung Park. The core composition of DNA block copolymer micelles dictates DNA hybridization properties, nuclease stabilities, and cellular uptake efficiencies. Nanoscale 2021, 13 (32) , 13758-13763. https://doi.org/10.1039/D1NR00756D
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    ACS Nano

    Cite this: ACS Nano 2020, 14, 2, 2276–2284
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acsnano.9b09312
    Published January 21, 2020
    Copyright © 2020 American Chemical Society
    Request reuse permissions

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