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Rolling circle amplification (RCA)-based DNA hydrogel


DNA hydrogels have unique properties, including sequence programmability, precise molecular recognition, stimuli-responsiveness, biocompatibility and biodegradability, that have enabled their use in diverse applications ranging from material science to biomedicine. Here, we describe a rolling circle amplification (RCA)-based synthesis of 3D DNA hydrogels with rationally programmed sequences and tunable physical, chemical and biological properties. RCA is a simple and highly efficient isothermal enzymatic amplification strategy to synthesize ultralong single-stranded DNA that benefits from mild reaction conditions, and stability and efficiency in complex biological environments. Other available methods for synthesis of DNA hydrogels include hybridization chain reactions, which need a large amount of hairpin strands to produce DNA chains, and PCR, which requires temperature cycling. In contrast, the RCA process is conducted at a constant temperature and requires a small amount of circular DNA template. In this protocol, the polymerase phi29 catalyzes the elongation and displacement of DNA chains to amplify DNA, which subsequently forms a 3D hydrogel network via various cross-linking strategies, including entanglement of DNA chains, multi-primed chain amplification, hybridization between DNA chains, and hybridization with functional moieties. We also describe how to use the protocol for isolation of bone marrow mesenchymal stem cells and cell delivery. The whole protocol takes ~2 d to complete, including hydrogel synthesis and applications in cell isolation and cell delivery.

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Fig. 1: Overview of the protocol for the preparation of RCA-based DNA hydrogels.
Fig. 2: RCA-based DNA network for stem cell isolation from bone marrow.
Fig. 3: RCA-based DNA robot for cell delivery in confined space.
Fig. 4: Synthesis of DNA hydrogel by entanglement of DNA chains.
Fig. 5: Synthesis of DNA hydrogel by multi-primed chain amplification.
Fig. 6: Synthesis of DNA hydrogel by hybridization between DNA chains.
Fig. 7: Synthesis of DNA hydrogel by hybridization with functional moieties.
Fig. 8: Characterization of RCA-based hydrogels.

Data availability

The main data supporting the examples of this protocol are available in the supporting primary research papers22,23,24. Additional data are available from the corresponding author upon reasonable request.


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This work was supported in part by National Natural Science Foundation of China (21621004 and 21704074), National Key R&D Program of China (2019YFA09005800 and 2018YFA0902300) and the Tianjin Natural Science Foundation (Basic research plan, 18JCJQJC47600 and 19JCQNJC02200).

Author information




D.Y. supervised the projects; C.Y. and J.T. designed and conducted the experiments; C.Y., R.Z. and J.T. analyzed the data; C.Y., R.Z., J.T. and D.Y. wrote the manuscript.

Corresponding author

Correspondence to Dayong Yang.

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The authors declare no competing interests.

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Peer review information Nature Protocols thanks the anonymous reviewers for their contribution to the peer review of this work.

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Key references using this protocol

Tang, J. et al. Angew. Chem. Int. Ed. Engl. 132, 2511–2516 (2020):

Yao, C. et al. J. Am. Chem. Soc. 142, 3422–3429 (2020):

Lee, J. et al. Nat. Nanotechnol. 7, 816–820 (2012):

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Supplementary Data 1

CAD file for 3D printing design

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Yao, C., Zhang, R., Tang, J. et al. Rolling circle amplification (RCA)-based DNA hydrogel. Nat Protoc (2021).

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