Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Focus Review
  • Published:

Enzyme-based fabrication of physical DNA hydrogels: new materials and applications

Abstract

Advancements in DNA nanotechnology and nanobioengineering allowed the use of DNA as a generic material, as well as a genetic material. Among various DNA-based materials, DNA hydrogels achieve a DNA-based network at the bulk scale. Notably, a recently developed enzyme-based fabrication method established a route to synthesize physically crosslinked networks from DNA. This new class of DNA networks paved the way for creating different forms of DNA materials by utilizing the characteristics of a biofunctional polymer. This Focus Review provides a brief overview of the enzyme-based fabrication method of physical DNA hydrogels and discusses the latest developments in technology and their applications.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  1. Seeman NC, Sleiman HF. DNA nanotechnology. Nat Rev Mater. 2018;3:17068. https://doi.org/10.1038/natrevmats.2017.68.

    Article  CAS  Google Scholar 

  2. Hamada S, Murata S. Substrate-assisted assembly of interconnected single-duplex DNA nanostructures. Angew Chem Int Ed Engl. 2009;48:6820–3. https://doi.org/10.1002/anie.200902662.

    Article  CAS  PubMed  Google Scholar 

  3. Cutler JI, Auyeung E, Mirkin CA. Spherical nucleic acids. J Am Chem Soc. 2012;134:1376–91. https://doi.org/10.1021/ja209351u.

    Article  CAS  PubMed  Google Scholar 

  4. Hamada S, Tan SJ, Luo D. Nanoparticle crystallization: DNA-bonded ‘atoms’. Nat Mater 2014;13:121–2. https://doi.org/10.1038/nmat3876.

    Article  CAS  PubMed  Google Scholar 

  5. Tan SJ, Campolongo MJ, Luo D, Cheng W. Building plasmonic nanostructures with DNA. Nat Nanotechnol. 2011;6:268–76. https://doi.org/10.1038/nnano.2011.49.

    Article  CAS  PubMed  Google Scholar 

  6. Um SH, Lee JB, Kwon SY, Li Y, Luo D. Dendrimer-like DNA-based fluorescence nanobarcodes. Nat Protoc. 2006;1:995–1000. https://doi.org/10.1038/nprot.2006.141.

    Article  CAS  PubMed  Google Scholar 

  7. Li F, Tang J, Geng J, Luo D, Yang D. Polymeric DNA hydrogel: design, synthesis and applications. Prog Polym Sci. 2019;98:101163. https://doi.org/10.1016/j.progpolymsci.2019.101163.

    Article  CAS  Google Scholar 

  8. Yang D, Hartman MR, Derrien TL, Hamada S, An D, Yancey KG, et al. DNA materials: bridging nanotechnology and biotechnology. Acc Chem Res. 2014;47:1902–11. https://doi.org/10.1021/ar5001082.

    Article  CAS  PubMed  Google Scholar 

  9. Wang D, Hu Y, Liu P, Luo D. Bioresponsive DNA hydrogels: beyond the conventional stimuli responsiveness. Acc Chem Res. 2017;50:733–9. https://doi.org/10.1021/acs.accounts.6b00581.

    Article  CAS  PubMed  Google Scholar 

  10. Um SH, Lee JB, Park N, Kwon SY, Umbach CC, Luo D. Enzyme-catalysed assembly of DNA hydrogel. Nat Mater. 2006;5:797–801. https://doi.org/10.1038/nmat1741.

    Article  CAS  PubMed  Google Scholar 

  11. Cheng W, Campolongo MJ, Cha JJ, Tan SJ, Umbach CC, Muller DA, et al. Free-standing nanoparticle superlattice sheets controlled by DNA. Nat Mater. 2009;8:519–25. https://doi.org/10.1038/nmat2440.

    Article  CAS  PubMed  Google Scholar 

  12. Cheng W, Park N, Walter MT, Hartman MR, Luo D. Nanopatterning self-assembled nanoparticle superlattices by moulding microdroplets. Nat Nanotechnol. 2008;3:682–90. https://doi.org/10.1038/nnano.2008.279.

    Article  CAS  PubMed  Google Scholar 

  13. Li Y, Cu YT, Luo D. Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes. Nat Biotechnol. 2005;23:885–9. https://doi.org/10.1038/nbt1106.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Derrien TL, Hamada S, Zhou M, Smilgies D-M, Luo D. Three-dimensional nanoparticle assemblies with tunable plasmonics via a layer-by-layer process. Nano Today. 2020;30:100823. https://doi.org/10.1016/j.nantod.2019.100823.

    Article  CAS  Google Scholar 

  15. Lee JB, Peng S, Yang D, Roh YH, Funabashi H, Park N, et al. A mechanical metamaterial made from a DNA hydrogel. Nat Nanotechnol. 2012;7:816–20. https://doi.org/10.1038/nnano.2012.211.

    Article  CAS  PubMed  Google Scholar 

  16. Gilbert W, Dressler D. DNA replication: the rolling circle model. Cold Spring Harb Symp Quant Biol. 1968;33:473–84. https://doi.org/10.1101/sqb.1968.033.01.055.

    Article  CAS  PubMed  Google Scholar 

  17. Demidov VV. Introduction: 20+ years of rolling the DNA minicircles—state of the art in the RCA-based nucleic acid diagnostics and therapeutics. In: Demidov VV, editor. Rolling Circle Amplification (RCA). Springer; Cham, Switzerland, 2016. p. 1–7. http://www.springer.com/gp/book/9783319422244.

  18. Johne R, Muller H, Rector A, van Ranst M, Stevens H. Rolling-circle amplification of viral DNA genomes using phi29 polymerase. Trends Microbiol. 2009;17:205–11. https://doi.org/10.1016/j.tim.2009.02.004.

    Article  CAS  PubMed  Google Scholar 

  19. Mohsen MG, Kool ET. The discovery of rolling circle amplification and rolling circle transcription. Acc Chem Res. 2016;49:2540–50. https://doi.org/10.1021/acs.accounts.6b00417.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Xu X, Jagota A, Peng S, Luo D, Wu M, Hui CY. Gravity and surface tension effects on the shape change of soft materials. Langmuir. 2013;29:8665–74. https://doi.org/10.1021/la400921h.

    Article  CAS  PubMed  Google Scholar 

  21. Park N, Um SH, Funabashi H, Xu J, Luo D. A cell-free protein-producing gel. Nat Mater. 2009;8:432–7. https://doi.org/10.1038/nmat2419.

    Article  CAS  PubMed  Google Scholar 

  22. Kahn JS, Ruiz RC, Sureka S, Peng S, Derrien TL, An D, et al. DNA microgels as a platform for cell-free protein expression and display. Biomacromolecules. 2016;17:2019–26. https://doi.org/10.1021/acs.biomac.6b00183.

    Article  CAS  PubMed  Google Scholar 

  23. Park N, Kahn JS, Rice EJ, Hartman MR, Funabashi H, Xu J, et al. High-yield cell-free protein production from P-gel. Nat Protoc. 2009;4:1759–70. https://doi.org/10.1038/nprot.2009.174.

    Article  CAS  PubMed  Google Scholar 

  24. Lee HY, Jeong H, Jung IY, Jang B, Seo YC, Lee H, et al. DhITACT: DNA hydrogel formation by isothermal amplification of complementary target in fluidic channels. Adv Mater. 2015;27:3513–7. https://doi.org/10.1002/adma.201500414.

    Article  CAS  PubMed  Google Scholar 

  25. Lin C, Wang X, Liu Y, Seeman NC, Yan H. Rolling circle enzymatic replication of a complex multi-crossover DNA nanostructure. J Am Chem Soc. 2007;129:14475–81. https://doi.org/10.1021/ja0760980.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Hamblin GD, Carneiro KM, Fakhoury JF, Bujold KE, Sleiman HF. Rolling circle amplification-templated DNA nanotubes show increased stability and cell penetration ability. J Am Chem Soc. 2012;134:2888–91. https://doi.org/10.1021/ja2107492.

    Article  CAS  PubMed  Google Scholar 

  27. Wilner OI, Willner I. Functionalized DNA nanostructures. Chem Rev. 2012;112:2528–56. https://doi.org/10.1021/cr200104q.

    Article  CAS  PubMed  Google Scholar 

  28. Wilner OI, Orbach R, Henning A, Teller C, Yehezkeli O, Mertig M, et al. Self-assembly of DNA nanotubes with controllable diameters. Nat Commun. 2011;2:540. https://doi.org/10.1038/ncomms1535.

    Article  CAS  PubMed  Google Scholar 

  29. Jang B, Kim B, Kim H, Kwon H, Kim M, Seo Y, et al. Enzymatic synthesis of self-assembled dicer substrate rna nanostructures for programmable gene silencing. Nano Lett. 2018;18:4279–84. https://doi.org/10.1021/acs.nanolett.8b01267.

    Article  CAS  PubMed  Google Scholar 

  30. Valero J, Pal N, Dhakal S, Walter NG, Famulok M. A bio-hybrid DNA rotor-stator nanoengine that moves along predefined tracks. Nat Nanotechnol. 2018;13:496–503. https://doi.org/10.1038/s41565-018-0109-z.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Ouyang X, Li J, Liu H, Zhao B, Yan J, Ma Y, et al. Rolling circle amplification-based DNA origami nanostructrures for intracellular delivery of immunostimulatory drugs. Small. 2013;9:3082–7. https://doi.org/10.1002/smll.201300458.

    Article  CAS  PubMed  Google Scholar 

  32. Kageyama R, Kawamata I, Tanabe K, Suzuki Y, Nomura SM, Murata S. Construction of T-motif-based DNA nanostructures through enzymatic reactions. Chembiochem 2018;19:873–6. https://doi.org/10.1002/cbic.201700682.

    Article  CAS  PubMed  Google Scholar 

  33. Zhu G, Hu R, Zhao Z, Chen Z, Zhang X, Tan W. Noncanonical self-assembly of multifunctional DNA nanoflowers for biomedical applications. J Am Chem Soc. 2013;135:16438–45. https://doi.org/10.1021/ja406115e.

    Article  CAS  PubMed  Google Scholar 

  34. Lee JB, Hong J, Bonner DK, Poon Z, Hammond PT. Self-assembled RNA interference microsponges for efficient siRNA delivery. Nat Mater. 2012;11:316–22. https://doi.org/10.1038/nmat3253.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Hamada S, Yancey KG, Pardo Y, Gan M, Vanatta M, An D, et al. Dynamic DNA material with emergent locomotion behavior powered by artificial metabolism. Sci Robot. 2019;4:eaaw3512. https://doi.org/10.1126/scirobotics.aaw3512.

    Article  PubMed  Google Scholar 

  36. Lv Y, Hu R, Zhu G, Zhang X, Mei L, Liu Q, et al. Preparation and biomedical applications of programmable and multifunctional DNA nanoflowers. Nat Protoc. 2015;10:1508–24. https://doi.org/10.1038/nprot.2015.078.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Shopsowitz KE, Roh YH, Deng ZJ, Morton SW, Hammond PT. RNAi-microsponges form through self-assembly of the organic and inorganic products of transcription. Small. 2014;10:1623–33. https://doi.org/10.1002/smll.201302676.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Han D, Park Y, Kim H, Lee JB. Self-assembly of free-standing RNA membranes. Nat Commun. 2014;5:4367. https://doi.org/10.1038/ncomms5367.

    Article  CAS  PubMed  Google Scholar 

  39. Ali MM, Li F, Zhang Z, Zhang K, Kang DK, Ankrum JA, et al. Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine. Chem Soc Rev. 2014;43:3324–41. https://doi.org/10.1039/c3cs60439j.

    Article  CAS  PubMed  Google Scholar 

  40. Gu L, Yan W, Liu L, Wang S, Zhang X, Lyu M. Research progress on rolling circle amplification (RCA)-based biomedical sensing. Pharmaceuticals 2018;11:35. https://doi.org/10.3390/ph11020035.

    Article  PubMed Central  Google Scholar 

  41. Hu R, Zhang X, Zhao Z, Zhu G, Chen T, Fu T, et al. DNA nanoflowers for multiplexed cellular imaging and traceable targeted drug delivery. Angew Chem Int Ed Engl. 2014;53:5821–6. https://doi.org/10.1002/anie.201400323.

    Article  CAS  PubMed  Google Scholar 

  42. Zhang L, Zhu G, Mei L, Wu C, Qiu L, Cui C, et al. Self-assembled DNA immunonanoflowers as multivalent CpG nanoagents. ACS Appl Mater Interfaces. 2015;7:24069–74. https://doi.org/10.1021/acsami.5b06987.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Han S, Lee JS, Lee JB. Synthesis of a multi-functional DNA nanosphere barcode system for direct cell detection. Nanoscale. 2017;9:14094–102. https://doi.org/10.1039/c7nr03615a.

    Article  CAS  PubMed  Google Scholar 

  44. Rosenwasser D, Hamada S, Luo D, Sabin JE. PolyBrick 3.0: live signatures through DNA hydrogels and digital ceramics. Int J Rapid Manuf. 2018;7:203. https://doi.org/10.1504/ijrapidm.2018.092909.

    Article  Google Scholar 

Download references

Acknowledgements

This work is supported by the U.S. National Science Foundation (NSF) (RoL: EAGER: DESYN-C3: 1844310 and SNM-1530522).

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Shogo Hamada or Dan Luo.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Hamada, S., Luo, D. Enzyme-based fabrication of physical DNA hydrogels: new materials and applications. Polym J 52, 891–898 (2020). https://doi.org/10.1038/s41428-020-0340-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41428-020-0340-y

This article is cited by

Search

Quick links