Nano Research

, Volume 8, Issue 12, pp 3764–3771 | Cite as

Atomic force microscopy analysis of orientation and bending of oligodeoxynucleotides in polypod-like structured DNA

  • Tomoki Shiomi
  • Mengmeng Tan
  • Natsuki Takahashi
  • Masayuki Endo
  • Tomoko Emura
  • Kumi Hidaka
  • Hiroshi Sugiyama
  • Yuki Takahashi
  • Yoshinobu Takakura
  • Makiya Nishikawa
Research Article

Abstract

We previously demonstrated that polypod-like structured DNA, or polypodna, constructed with three or more oligodeoxynucleotides (ODNs), is efficiently taken up by immune cells such as dendritic cells and macrophages, depending on its structural complexity. The ODNs comprising the polypodna should bend to form the polypod-like structure, and may do so by adopting either a bendtype conformation or a cross-type conformation. Here, we tried to elucidate the orientation and bending of ODNs in polypodnas using atomic force microscopy (AFM). We designed two types of pentapodnas (i.e., a polypodna with five pods) using 60- to 88-base ODNs, which were then immobilized on DNA origami frames. AFM imaging showed that the ODNs in the pentapodna adopted bend-type conformations. Tetrapodna and hexapodna also adopted bend-type conformations when they were immobilized on frames under unconstrained conditions. These findings provide useful information toward the coherent design of, and the structure–activity relationships for, a variety of DNA nanostructures.

Keywords

DNA nanostructure atomic force microscopy self-assembly nanotechnology structure–activity relationship 

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References

  1. [1]
    Um, S. H.; Lee, J. B.; Park, N.; Kwon, S. Y.; Umbach, C. C.; Luo, D. Enzyme-catalysed assembly of DNA hydrogel. Nat. Mater. 2006, 5, 797–801.CrossRefGoogle Scholar
  2. [2]
    Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 2006, 440, 297–302.CrossRefGoogle Scholar
  3. [3]
    He, Y.; Ye, T.; Su, M.; Zhang, C.; Ribbe, A. E.; Jiang, W.; Mao, C. D. Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature 2008, 452, 198–201.CrossRefGoogle Scholar
  4. [4]
    Smith, D; Schüller, V; Engst, C; Rädler, J; Liedl, T. Nucleic acid nanostructures for biomedical applications. Nanomedicine 2013, 8, 105–121.CrossRefGoogle Scholar
  5. [5]
    Um, S. H.; Lee, J. B.; Kwon, S. Y.; Li, Y. G.; Luo, D. Dendrimer-like DNA-based fluorescence nanobarcodes. Nat. Protoc. 2006, 1, 995–1000.CrossRefGoogle Scholar
  6. [6]
    Ke, Y. G.; Ong, L. L.; Shih, W. M.; Yin, P. Three-dimensional structures self-assembled from DNA bricks. Science 2012, 338, 1177–1183.CrossRefGoogle Scholar
  7. [7]
    Rattanakiat, S.; Nishikawa, M.; Funabashi, H.; Luo, D.; Takakura, Y. The assembly of a short linear natural cytosinephosphate-guanine DNA into dendritic structures and its effect on immunostimulatory activity. Biomaterials 2009, 30, 5701–5706.CrossRefGoogle Scholar
  8. [8]
    Mohri, K.; Nishikawa, M.; Takahashi, N.; Shiomi, T.; Matsuoka, N.; Ogawa, K.; Endo, M.; Hidaka, K.; Sugiyama, H.; Takahashi, Y. et al. Design and development of nanosized DNA assemblies in polypod-like structures as efficient vehicles for immunostimulatory CpG motifs to immune cells. ACS Nano 2012, 6, 5931–5940.CrossRefGoogle Scholar
  9. [9]
    Wemmer, D. E.; Wand, A. J.; Seeman, N. C.; Kallenbach, N. R. NMR analysis of DNA junctions: Imino proton NMR studies of individual arms and intact junction. Biochemistry 1985, 24, 5745–5749.CrossRefGoogle Scholar
  10. [10]
    Ortiz-Lombardía, M.; González, A.; Eritja, R.; Aymamí, J.; Azorín, F.; Coll, M. Crystal structure of a DNA Holliday junction. Nat. Struct. Biol. 1999, 6, 913–917.CrossRefGoogle Scholar
  11. [11]
    Lilley, D. M. Structures of helical junctions in nucleic acids. Q Rev. Biophys. 2000, 33, 109–159.CrossRefGoogle Scholar
  12. [12]
    Li, Y. G.; Tseng, Y. D.; Kwon, S. Y.; d’Espaux, L.; Bunch, J. S.; McEuen, P. L.; Luo, D. Controlled assembly of dendrimer-like DNA. Nat. Mater. 2004, 3, 38–42.CrossRefGoogle Scholar
  13. [13]
    Mizuno, R.; Haruta, H.; Morii, T.; Okada, T.; Asakawa, T.; Hayashi, K. Synthesis and AFM visualization of DNA nanostructures. Thin Solid Films 2004, 459–465.Google Scholar
  14. [14]
    Lyubchenko, Y. L.; Shlyakhtenko, L. S.; Ando, T. Imaging of nucleic acids with atomic force microscopy. Methods 2011, 54, 274–283.CrossRefGoogle Scholar
  15. [15]
    Nishikawa, M.; Mizuno, Y.; Mohri, K.; Matsuoka, N.; Rattanakiat, S.; Takahashi, Y.; Funabashi, H.; Luo, D.; Takakura, Y. Biodegradable CpG DNA hydrogels for sustained delivery of doxorubicin and immunostimulatory signals in tumor-bearing mice. Biomaterials 2011, 32, 488–494.CrossRefGoogle Scholar
  16. [16]
    Endo, M.; Katsuda, Y.; Hidaka, K.; Sugiyama, H. Regulation of DNA methylation using different tensions of double strands constructed in a defined DNA nanostructure. J. Am. Chem. Soc. 2010, 132, 1592–1597.CrossRefGoogle Scholar
  17. [17]
    Suzuki, Y.; Endo, M.; Katsuda, Y.; Ou, K.; Hidaka, K.; Sugiyama, H. DNA origami based visualization system for studying site-specific recombination events. J. Am. Chem. Soc. 2014, 136, 211–218.CrossRefGoogle Scholar
  18. [18]
    Murchie, A. I. H.; Clegg, R. M.; von Krtzing, E.; Duckett, D. R.; Diekmann, S.; Lilley, D. M. J. Fluorescence energy transfer shows that the four-way DNA junction is a righthanded cross of antiparallel molecules. Nature 1989, 341, 763–766.CrossRefGoogle Scholar
  19. [19]
    Eichman, B. F.; Vargason, J. M.; Mooers, B. H. M.; Ho, P. S. The Holliday junction in an inverted repeat DNA sequence: Sequence effects on the structure of four-way junctions. Proc. Natl. Acad. Sci. USA 2000, 97, 3971–3976.CrossRefGoogle Scholar
  20. [20]
    Sha, R.; Liu, F.; Seeman, N. C. Atomic force microscopic measurement of the interdomain angle in symmetric Holliday junctions. Biochemistry 2002, 41, 5950–5955.CrossRefGoogle Scholar
  21. [21]
    Peters 3rd, J. P.; Maher, L. J. DNA curvature and flexibility in vitro and in vivo. Q Rev. Biophys. 2010, 43, 23–63.CrossRefGoogle Scholar
  22. [22]
    Vafabakhsh, R.; Ha, T. Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization. Science 2012, 337, 1097–1101.CrossRefGoogle Scholar

Copyright information

© Tsinghua University Press and Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Tomoki Shiomi
    • 1
  • Mengmeng Tan
    • 1
  • Natsuki Takahashi
    • 1
  • Masayuki Endo
    • 2
  • Tomoko Emura
    • 3
  • Kumi Hidaka
    • 3
  • Hiroshi Sugiyama
    • 2
    • 3
  • Yuki Takahashi
    • 1
  • Yoshinobu Takakura
    • 1
  • Makiya Nishikawa
    • 1
  1. 1.Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical SciencesKyoto UniversitySakyo-ku, KyotoJapan
  2. 2.Institute for Integrated Cell-Material Sciences (WPI-iCeMS)Kyoto UniversitySakyo-ku, KyotoJapan
  3. 3.Department of Chemistry, Graduate School of ScienceKyoto UniversitySakyo-ku, KyotoJapan

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