Bioresponsive DNA Hydrogels: Beyond the Conventional Stimuli

Article pubs.acs.org/accounts

Bioresponsive DNA Hydrogels: Beyond the Conventional Stimuli Responsiveness Published as part of the Accounts of Chemical Research special issue “Stimuli-Responsive Hydrogels”. Dong Wang,†,‡,# Yue Hu,‡,# Peifeng Liu,*,†,§ and Dan Luo*,‡,∥,⊥ †

Central Laboratory, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States § State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200032, China ∥ Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853, United States ⊥ CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China ‡

CONSPECTUS: Bioresponsive hydrogels can respond to various biological stimuli by a macroscopic change of physical state or by converting biochemical inputs into biological or mechanical outputs. These materials are playing an increasingly important role in a wide variety of applications, especially in the biological and biomedical fields. However, the design and engineering of intriguing bioresponsive materials with adequate biocompatibility and biodegradability have proven to be a great challenge. DNA, on the other hand, possesses many unique and fascinating properties, including its indispensable genetic function, broad biocompatibility, precise molecular recognition capability, tunable multifunctionality, and convenient programmability. Therefore, DNA has provided crucial prerequisites for the exploration of novel bioresponsive hydrogels and has since become an ideal building block for the construction of novel materials. In this Account, we describe our efforts over more than a decade to develop DNAbased materials including bioresponsive hydrogels. These DNA hydrogels were created through either chemical cross-linking or physical entanglement among DNA chains. We further divided them into two categories: pure DNA-based and hybrid DNAbased hydrogels. For the pure DNA-based hydrogels, we developed the first bulk DNA hydrogel entirely from branched DNA by using enzymatic ligation. Certain drugs were encapsulated in such hydrogels in situ and released in a controllable manner under the stimulation of environmental factors such as nucleases and/or changes in ionic strength. Furthermore, we prepared a proteinproducing hydrogel (termed a “P-gel”) by ligating X-shaped DNA (X-DNA) and linear plasmids. Following the central dogma of molecular biology, this hydrogel responded to enzymes and substrate and converted them into proteins. This was the first example showing that a hydrogel could be employed to produce proteins without the involvement of live cells. This might also be the first attempt to create cell-like hydrogels that will be ultimately bioresponsive. In addition, we also constructed a DNA physical hydrogel via entanglement of DNA chains elongated by a special polymerase: Phi29. This hydrogel (termed a “metahydrogel”) exhibited a “meta” property: freely reversible change between liquidlike and solidlike states through stimulation by water molecules. Besides these pure DNA-based hydrogels, we also created a hybrid DNA-based hydrogel: a DNA−clay hybrid hydrogel utilizing electrostatic interactions between DNA and clay nanocrystals. We discovered a synergistic responsiveness in biochemical reaction in this hydrogel, suggesting that a DNA−clay hydrogel might be the environment for the origination of life and that DNA and clay might have been coevolving during early evolution. In summary, DNA links the nonbiological world with biological processes by virtue of its bioresponsiveness. We envision that bioresponsive DNA hydrogels will play an irreplaceable part in the development of future evolvable materials such as soft robots and artificial cells.

1. INTRODUCTION A proper response to stimuli from various external sources is an important characteristic of a material system called a “smart material”. Research on stimuli responsiveness will have important theoretical and practical significance for materials research in general and stimuli-responsive hydrogels in © 2017 American Chemical Society

particular in the context of drug delivery, diagnostics, catalytic reactions, actuators, sensors, etc.1−3 In this pursuit, DNA, as an essential genetic macromolecule and also a generic construction Received: November 16, 2016 Published: February 10, 2017 733

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Accounts of Chemical Research material,4−7 has many unique and fascinating properties, including its indispensable genetic function, broad biocompatibility, precise molecular recognition capability, tunable multifunctionality, and convenient programmability, just to name a few. Thus, arguably DNA is the perfect (and only) molecule capable of interfacing biology with materials and vice versa. DNA provides critical and desirable prerequisites for the creation of novel bioresponsiveness and has started to increasingly become an irreplaceable and powerful basic unit in the construction of hydrogels. Stimuli can be categorized into two types according to their sources: nonbiological stimuli and biological stimuli. To date, myriads of efforts have been made to explore hydrogels that respond to nonbiological stimuli such as heat, light, electricity, magnetism, mechanical force, pH, metallic ions, organic reagents, etc. Progress in hydrogels that respond to nonbiological stimuli has been well-documented, and interested readers are encouraged to read the relevant published reviews.8,9 This Account, on the other hand, will focus mainly on hydrogels that are responsive to biological stimuli. It is worth noting that in this Account, the term “biological stimuli” mainly refers to biomolecules, including glucose, enzymes, antigens, thrombin, nucleic acids, adenosine triphosphate (ATP), etc.10−12 A number of mechanisms have been utilized in constructing responsiveness toward biological stimuli. In the case of stimuli from glucose and certain enzymes, the responsiveness is based on the intermediates produced or consumed by enzymatic reactions. For nucleic acids, antigens, and ATP, the responsiveness stems from these biomolecules themselves. For example, Langrana13 and Tan14 demonstrated DNA− polyacrylamide hydrogels that were responsive to nucleic acids through Watson−Crick base-pairing between two DNA strands. In addition, another type of hydrogel was achieved that was responsive to an antigen; this hydrogel was based on antigen−antibody affiliation.15,16 Although many applications, including drug delivery, diagnosis, and tissue engineering, had been envisioned with these aforementioned hydrogels, the inherent non-biocompatibility and non-biodegradability of the involved synthetic polymers posed real challenges for practical medical applications. However, when synthetic polymers are replaced by DNA molecules, i.e., when DNA is used as a true polymer, not only can the DNA hydrogels themselves now respond to almost all nucleic acids, but also the DNA themselves are biocompatible and biodegradable, relieving the major concerns associated with most synthetic polymers. We have thus successfully developed responsive DNA hydrogels through two design strategies: either physical entanglement among DNA chains or chemical bonding between DNA chains. In this Account, we summarize our achievements over more than a decade in the development and applications of responsive hydrogels using DNA as a construction material. In the light of the different compositions of DNA hydrogels we have created, we divide them into two categories: pure DNA-based and hybrid DNA-based hydrogels. In each category, we detail the synthetic methodologies, characterizations, and real-world applications, including drug delivery and cell-free protein expression. We envision that DNA will link the nonbiological world with biological processes and that DNA hydrogels are bioresponsive beyond the conventional stimuli.

2. EXPLORATION OF BIORESPONSIVE DNA HYDROGELS 2.1. Pure DNA Hydrogels

Pure DNA-based hydrogels are biologically responsive to biomediated stimuli. We designed and constructed several bioresponsive DNA hydrogels with different characteristics, which were capable of responding to biological stimuli such as nuclease, lysate, and ionic strength. Our pure DNA hydrogels have become an effective and powerful platform for cell-free protein production and drug delivery. Protein-Producing DNA Hydrogel. DNA stores genetic information that can be employed as a template to synthesize messenger RNA (mRNA) through transcription; mRNA then serves as a template to be translated into proteins. On the basis of this central dogma of molecular biology, we were the first to successfully create a cell-free protein-producing hydrogel (a “Pgel”), which was composed of X-DNA and a linearized gene via enzyme ligation using T4 DNA ligase (Figure 1a).17 The

Figure 1. (a) Preparation of the P-gel and its use in protein expression. (b) In contrast to the solution phase system, the P-gel shows greater expression of Renilla luciferase (Rluc) and Aequorea coerulescens green fluorescent protein (AcGFP). Adapted with permission from ref 17. Copyright 2009 Nature Publishing Group.

covalently cross-linked X-DNA resulted in a great many pores and channels with different sizes in the P-gel structure. Notably, the P-gel was capable of responding to biological stimuli (i.e., enzymes and lysates). Transcription reactions immediately started within the P-gel to synthesize mRNA with its ultimate translations toward final protein production (Figure 1a). We demonstrated that 16 proteins were successfully produced by incubating the P-gel with a variety of lysates and enzymes (e.g., RNA polymerase, ribosomes, and other translational factors).17,18 Excitingly, the yield of protein expressed by P-gel was up to 5 mg/mL, which was approximately 300 times higher than that of a conventional solution-phase system (SPS) (Figure 1b). The effective protection of the genes, higher transcription level, increase in surface area, and improved reaction kinetics were all attributed to the enhanced protein expression in the gel format.17 Drug Delivery DNA Hydrogel. DNA, as a genetic molecule in all living organisms, is broadly biocompatible, partially because its degradation products (i.e., nucleotides) are natural compounds needed by humans (although in rare cases there might be immune reactions toward DNA). DNA 734

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Figure 2. (a) Construction of branched DNA-based hydrogels. (b) Digital photograph of a swollen X-DNA hydrogel. The inset shows a fluorescence image of the DNA hydrogel stained with SYBR I. The scale bar is 1 cm. (c) Degradation curves of DNA hydrogels. The dotted, dashed, and solid lines represent empty, insulin-loaded, and CPT-loaded hydrogels, respectively. The blue crosses, red triangles, and green squares represent X-, Y-, and T-DNA hydrogels, respectively. (d) Drug release curves. The solid and dashed lines represent the release of insulin and CPT, respectively. The diamonds, triangles, and squares represent X-, Y-, and T-DNA hydrogels, respectively. Adapted with permission from ref 19. Copyright 2006 Nature Publishing Group.

molecules are facile and flexible toward chemical modification. Thus, as a drug delivery carrier, DNA is arguably superior to conventional polymeric carriers in terms of biocompatibility, biodegradation, and multifunctionality. We synthesized a bioresponsive DNA hydrogel completely from three-dimensional branched DNA monomers (i.e., X-, Y-, and T-DNA) and showed that it can encapsulate drugs and release them in response to environmental stimuli such as changes in the ionic strength of the surrounding liquid.19 Unlike most other bioinspired hydrogels, where the gelling process requires heat, organic solvents, or other biologically harsh conditions, the DNA hydrogel was cross-linked via an enzyme-mediated reaction, which made the entire gelling process occur under physiological conditions (Figure 2a). Such mild conditions afforded the DNA hydrogel the capability to encapsulate not only small-molecule drugs but also biologicals such as proteins, RNA, and DNA drugs or even live cells. To characterize these novel drug delivery DNA gels, we stained swollen DNA hydrogels with a DNA-specific fluorescent dye (SYBR I), which revealed that the DNA hydrogels were indeed composed of DNA monomers (Figure 2b). Another important and interesting observation was that the drug was premixed with the branched DNA building blocks before the gelling process. During the gelling process, essentially 100% of the drug was automatically preloaded into the gel matrix, making the drug loading process occur entirely in situ. This “preloading” feature eliminated the postgel drug-loading step, resulting in a drug loading efficiency of almost 100%, as demonstrated with both a small-molecule drug (camptothecin, CPT) and a relatively large biological (porcine insulin).19 In addition, the DNA hydrogel exhibited a smooth, controlled release curve, and more importantly, no initial burst release was observed (Figure 2d), which was entirely different from the drug release from most other conventional drug carriers. The drug release from the DNA hydrogel was triggered by a variety

of environmental conditions, including a change in ionic strength, which affected the stability of branched DNA formation. The drug release rate was controlled by adjusting the internal microstructures of the hydrogels, which were dependent on the type of branched DNA. This was partially due to the fact that DNA hydrogels with different types of branched DNA possessed quite different resistances to hydrolysis, with X-DNA gels > T-DNA gels > Y-DNA gels (Figure 2c). In addition, the type of drug also affected the release rate. For example, CPT, a DNA-binding drug, showed zeroth-order release from the DNA hydrogels because of the smaller size of CPT and its high binding capability for the grooves of the DNA molecules (Figure 2d). In a separate follow-up work, the X-DNA hydrogel was loaded with doxorubicin (DXR) through its intercalation with DNA. Meanwhile, the incorporation of a specific cytosine− phosphate−guanine (CpG) motif afforded the DNA hydrogel immunological activity. The CpG/DXR DNA hydrogel was first slowly degraded by serum nucleases, and DXR and the CpG immunostimulatory signals were slowly released.20 Further in vivo experiments demonstrated that the CpG/ DXR DNA hydrogel remarkably inhibited the growth of colon26/Luc tumor in mice, which was attributed to the increased immune activity triggered by the GpC DNA hydrogel and the effective killing activity of DXR for tumor cells.20 Interestingly, because DXR was intercalated between the adjacent DNA base pairs, it was possible to control their melting temperature (Tm) by encoding DNA with appropriate sequences and lengths.21 In addition, DNA is a particularly ideal delivery carrier for small interfering RNA (siRNA) because of its unique advantage of inherent DNA−RNA base-pairing. The base-pairing strength depends strongly on the surrounding solution environment, including the ionic strength and temperature, and the RNA release from the DNA chains could be programmed 735

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Figure 3. DNA meta-hydrogel. (a) Scheme of the fabrication pathway. (b) Liquid- and solidlike metaproperties of hydrogels with D, N, and A shapes upon removing and reintroducing water. (c) SEM image of the meta-hydrogel. (d) DNA meta-hydrogel doped with 10 nm Au nanoparticles in the electric circuit. Adapted with permission from ref 25. Copyright 2012 Nature Publishing Group. (e) Cell-free wtGFP expression from a DNA metahydrogel compared with an SPS control. BN: bird nests. Adapted from ref 27. Copyright 2016 American Chemical Society.

accordingly.21,22 We successfully developed a multiplexed delivery carrier, termed a “DNAsome”, through self-assembly of numerous Y-DNAs into liposome-like core−shell structures. As an alternative to DNA hydrogels, DNAsomes efficiently transfected glyceraldehyde 3-phosphate dehydrogenase (GAPDH) siRNA to Chinese hamster ovary (CHO) cells by themselves without any use of transfection reagents, leading to a substantial gene knockdown, while at the same it still possessed very low cytotoxicity.23 Finally, we have also successfully used DNA hydrogels to encapsulate live cells for cell 3D culture (unpublished data). Meta-Hydrogel. Most DNA hydrogels are based on chemical cross-linking of branched DNA, either by ligation19 or hybridization.24 Developing a novel method other than chemical cross-linking to create DNA hydrogels may greatly expand the DNA hydrogel reservoir. We designed a new approach, physical entanglement, to achieve a new type of DNA hydrogel by linearly elongating and non-covalently weaving DNA chains into a physical hydrogel, termed a “meta-hydrogel” (Figure 3).25 The DNA meta-hydrogel was formed by DNA chain elongation and displacement via a bacteria phage polymerase, Φ29, followed by a combination of two sequential processes, rolling circle amplification (RCA) and multiprimed chain amplification (MCA) (Figure 3a). Strikingly, this meta-hydrogel exhibited unexpected properties that were not found in nature: both solidlike and liquidlike properties. The solid-to-liquid transition process occurred in response to the gel dispersion medium (i.e., water) and was repeated many times. When the gel was dispersed in water, it memorized its original shape and behaved as a solid in water. However, when the surrounding water was taken away from the gel, surface

tension and gravity dominated the strain energy because of its low modulus (E ≈ 10 Pa),26 leading to the deformation of the gel at the water−air interface as free-flowing liquid. More interestingly, after the water was reintroduced, the effect of gravity was canceled by the buoyant stress, leading to the recovery of the exact original shape of the gel via elastic stress (Figure 3b). Scanning electron microscopy (SEM) also revealed that our DNA meta-hydrogel had unique hierarchical internal structures with densely packed bird-nest-like microstructures (Figure 3c), which had never been seen before in any other hydrogels. For a potential application of these special water-responsive mechanical properties, we designed a DNA-meta-hydrogelbased electric circuit using water as a switch (Figure 3d). By removal of the surrounding water, the liquidlike DNA metahydrogel doped with 10 nm gold nanoparticles was placed into contact with two electrodes. Once water was present, the metahydrogel was stimulated to return to its original shape (a shorter gel), consequently switching off the circuit. This shows the potential of preventing water-induced short-circuit damage that might be needed in future soft robots. In addition, many other applications of the meta-hydrogel in the context of bioresponsiveness can be envisioned. A unique advantage is that both the DNA building blocks and physical gel enclosure itself can be potentially utilized as drug reservoirs. We have successfully coloaded DXR and insulin into our meta-hydrogel by chemical intercalation and physical entrapment, respectively. As expected, in the presence of aqueous solution the chemically interacted DXR showed a much slower release profile than physically entrapped insulin. This differential performance suggested great potential not only in the aspect of controlling 736

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Figure 4. DNA−clay hydrogel. (a) Synthesis scheme for the bulk DNA−clay hydrogel. (b) Protection of DNA in the bulk DNA−clay hydrogel. (c) Luminescence images of active Rluc protein expressed from the bulk DNA−clay hydrogel and SPS. Lysate (blank) was used as a control. Adapted with permission from ref 28. Copyright 2013 Nature Publishing Group. (d) Bright-field and fluorescence images of a donutlike DNA−clay microhydrogel. (e) Fluorescence images of GFP production with (left) or without (right) donutlike DNA−clay microhydrogels. Adapted with permission from ref 30. Copyright 2016 Nature Publishing Group.

than that of RNA/clay, which can be ascribed to the different charge densities of DNA and RNA. As a result of the unique structure of the clay hydrogel, it served as a protective microenvironment for biomolecules, especially nucleic acids; it further increased the efficiency of bioresponsive reactions. Indeed, our hybrid hydrogel had a capability to protect both DNA and RNA from DNase and RNase digestion (Figure 4b), whereas free DNA and RNA in the same amounts were quickly digested. The DNA−clay hydrogel also represented the response to E. coli lysate and performed cell-free Rluc protein expression. Remarkably, the yield of Rluc protein expression in the DNA−clay hydrogel was approximately 6-fold enhanced in comparison with that in the SPS control (Figure 4c). Besides the bulk DNA−clay hydrogel, recently we also explored a microsized DNA−clay hydrogel with a donutlike shape (Figure 4d).30 Compared with the bulk DNA−clay hydrogel, the donutlike DNA−clay microhydrogel had a larger surface area per unit volume and a shorter diffusion pathway, which was more desirable for bioresponsive stimulation, particularly, protein production. Indeed, GFP production associated with the donutlike DNA−clay microhydrogel showed 3 times greater yield than that with the SPS control (Figure 4e). Taken together, our results clearly demonstrated the feasibility of developing a DNA-based hybrid hydrogel as a biomolecule-stimulated responsive platform.

the release of different drugs in a time-controlled manner but also in the area of triggering the release in different dispersion media, including the cell medium or biological electrolytes. Meanwhile, our DNA meta-hydrogel also elucidated its bioresponsiveness in the development of cell-free protein expression. Upon exposure to Escherichia coli lysate, the wildtype GFP (wtGFP) yield from the meta-hydrogel was much higher than that from the SPS control (Figure 3e).27 This highly effective cell-free protein expression was due to the synergistic effects of high-density packing of bird-nest-like microstructures and potential gene protection. In summary, our DNA meta-hydrogel has shown great potential not only with nonbiological stimuli but also in biostimuli-related applications, including controlled drug delivery/release, DNA immunotherapy, and cell-free protein expression. 2.2. Hybrid DNA-Based Hydrogels

In addition to our pure DNA hydrogels, a hybrid DNA hydrogel provides additional molecular recognition capabilities and versatilities, greatly expanding the range of bioresponsiverelated applications. We developed a DNA hybrid hydrogel employing nanoclay, relying on the interfacing reaction between clay and DNA.28 Clay exhibits a sheetlike structure with negative charges on the sheet surface and positive charges on the rim.29 On the basis of this unique property, a DNA−clay hydrogel was generated using two approaches (Figure 4a): (1) A clay hydrogel was formed first, triggered by ionic species, resulting a “house-of-cards” structure. Subsequently, DNA was attached to the clay hydrogel via electrostatic interactions, resulting in the formation of the DNA−clay hydrogel. (2) Initially DNA was bound to clay disks at a certain ratio, and then ionic species were applied to stimulate the generation of the DNA−clay hydrogel. The same two approaches could also be applied for RNA−clay hydrogels. It is worth noting that the DNA/clay binding efficiency in the hydrogel is much higher

3. CONCLUSIONS AND FUTURE OUTLOOK DNA, as a biomacromolecule, is not only a bioresponsive entity but also a polymer that can be designed and modified by employing enzymatic and/or chemical methods. Bioresponsive DNA hydrogels possess a prominent ability to convert biological or chemical cues into biochemical outputs or mechanical variation; consequently, the conversions reconfigure the gel on both the molecular and macroscopic levels, providing enormous opportunities for the design and engineering of 737

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Accounts of Chemical Research hydrogels. In the past decade, our group has demonstrated such a DNA gel concept by using DNA as a material construction building block. We have formed chemical and physical DNA hydrogels based on covalent linkages and non-covalent entanglement, respectively. Our design strategies take full advantage of DNA molecules, and our methods are facile and flexible, endowing DNA hydrogels with specific bioresponsiveness and functionality for real-world applications as detailed in this Account and also in our publications. Overall, utilizing the unique attributes of DNA molecules provides bioresponsiveness beyond conventional stimuli. We have just started this new DNA-based bulk material journey. However, there remain certain challenges for full exploration and exploitation of DNA hydrogels. For real-world applications, the large-scale production of DNA hydrogels has not yet been realized because of the associated high cost and limited synthesis efficiency. Also, the environmental stability of DNA hydrogels needs to be improved. The synergistic multifunctional integration of DNA hydrogels is unexplored as well, such as the construction of selfsustained “smart” systems for cell-free protein expression. In the future, taking advantage of DNA to explore new types of DNA hydrogels and combining DNA hydrogels with conventional polymers may result in unprecedented novel materials that are intelligent with built-in logical decision making. DNA hydrogels may also lay the foundation for future soft robots or cell-free synthetic biology in which DNA serves as a molecule not only for genetic information storage but also for construction of the matrix. A cell-like material that is evolvable might be the ultimate goal for a bioresponsive DNA hydrogel.

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faculty in the department of biological and environmental engineering in 2001 and was promoted to full professor in 2011. His research interest focuses on engineering DNA as both a generic and genetic material for real-world applications.

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ACKNOWLEDGMENTS

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REFERENCES

The work was partially supported by various grants from the U.S. Department of Agriculture, the National Science Foundation, and the National Institutes of Health. D.W. (21473239) and P.L. (81472842) acknowledge the National Natural Science Foundation of China.

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AUTHOR INFORMATION

Corresponding Authors

*[email protected] *[email protected]. ORCID

Yue Hu: 0000-0002-1116-7303 Dan Luo: 0000-0003-2628-8391 Author Contributions #

D.W. and Y.H. contributed equally.

Notes

The authors declare no competing financial interest. Biographies Dong Wang obtained his B.S. from Inner Mongolia Normal University in 2004 and Ph.D. from Jilin University in 2009. He is presently a postdoctoral associate at Cornell University. Yue Hu obtained her B.S. (2008) from Tianjin Polytechnic University and her Ph.D. (2015) from Stevens Institute of Technology. She is presently a postdoctoral associate at Cornell University. Peifeng Liu obtained his Ph.D. in Material Science and Engineering from Donghua University in 2010. He is currently a director of the central laboratory affiliated with Renji Hospital, School of Medicine, Shanghai Jiao Tong University and also an associate professor at Shanghai Cancer Institute. His multidisciplinary research combines materials science, biology, DNA material, and microfluidics for the development of disease therapies and diagnosis technologies. Dan Luo obtained his B.S. from the University of Science and Technology of China in 1989 and his Ph.D. in 1997 from The Ohio State University. After his postdoctoral training in the School of Chemical Engineering at Cornell University, he joined the Cornell 738

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