Computational Study of DNA-Cross-Linked Hydrogel Formation for Drug Delivery Applications

Wang, Kye Won; Betancourt, Tania; Hall, Carol K.

doi:10.1021/acs.macromol.8b01505

Cited by 14 publications

(9 citation statements)

References 55 publications

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“…S11); conversely, for a given level of input, the response dynamics can be hard-coded into the system by altering the properties of the starting material. For example, pore size is expected to alter the mobility of macromolecules in polymer networks (24). On the basis of our macroscopic observations of programmed anchor hydrolysis (fig.…”

Section: Collateral Cas12a Activity Releases Ssdna-anchored Cargos Fr...mentioning

confidence: 85%

“…In these hydrogels, degradation of DNA crosslinks physically disrupts the polymer networks (fig. S1B) (24,26). The Cas12a-induced degradation of PA-based CRISPR gels was initially evaluated with a DNAintercalating dye to label bridge sequences in PA-DNA gels and track gel integrity.…”

Section: Collateral Cas12a Activity Alters the Large-scale Mechanical Properties Of Dna Hydrogelsmentioning

confidence: 99%

“…In these hydrogels, degradation of DNA crosslinks physically disrupts the polymer networks (fig. S1B) (24,26).…”

Section: Collateral Cas12a Activity Alters the Large-scale Mechanical...mentioning

confidence: 99%

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Programmable CRISPR-responsive smart materials

English

Soenksen

Gayet

et al. 2019

Science

290

256

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Stimuli-responsive materials activated by biological signals play an increasingly important role in biotechnology applications. We exploit the programmability of CRISPR-associated nucleases to actuate hydrogels containing DNA as a structural element or as an anchor for pendant groups. After activation by guide RNA–defined inputs, Cas12a cleaves DNA in the gels, thereby converting biological information into changes in material properties. We report four applications: (i) branched poly(ethylene glycol) hydrogels releasing DNA-anchored compounds, (ii) degradable polyacrylamide-DNA hydrogels encapsulating nanoparticles and live cells, (iii) conductive carbon-black–DNA hydrogels acting as degradable electrical fuses, and (iv) a polyacrylamide-DNA hydrogel operating as a fluidic valve with an electrical readout for remote signaling. These materials allow for a range of in vitro applications in tissue engineering, bioelectronics, and diagnostics.

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Section: Collateral Cas12a Activity Releases Ssdna-anchored Cargos Fr...mentioning

confidence: 85%

Section: Collateral Cas12a Activity Alters the Large-scale Mechanical Properties Of Dna Hydrogelsmentioning

confidence: 99%

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Programmable CRISPR-responsive smart materials

English

Soenksen

Gayet

et al. 2019

Science

290

256

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“…Along with OEG-decorated SAMs, all-PEG materials can also be used, such as PEG brushes and polymer films [ 27 , 28 , 29 , 30 ]. Alternatively, porous PEG and PEG-based films can be used, taking advantage of 3D immobilization of ssDNA in contrast to the standard 2D assemblies provided by SAM supports and usual OEG-based polymers [ 31 , 32 , 33 , 34 ]. In particular, such porous films can be efficiently formed by thermally activated crosslinking of multi-armed STAR-PEG precursors, decorated with amine (STAR-NH 2 ) or epoxy (STAR-EPX) groups, which build ethanol-amine bridges between individual arms of the precursors upon the crosslinking ( Figure 1 ) [ 35 ].…”

Section: Introductionmentioning

confidence: 99%

Rational Design of Porous Poly(ethylene glycol) Films as a Matrix for ssDNA Immobilization and Hybridization

2022

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Poly(ethylene glycol) (PEG) films, fabricated by thermally induced crosslinking of amine- and epoxy-terminated four-arm STAR-PEG precursors, were used as porous and bioinert matrix for single-stranded DNA (ssDNA) immobilization and hybridization. The immobilization relied on the reaction between the amine groups in the films and N-hydroxy succinimide (NHS) ester groups of the NHS-ester-decorated ssDNA. Whereas the amount of reactive amine groups in the films with the standard 1:1 composition of the precursors turned out to be too low for efficient immobilization, it could be increased noticeably using an excess (2:1) concentration of the amine-terminated precursor. The respective films retained the bioinertness of the 1:1 prototype and could be successfully decorated with probe ssDNA, resulting in porous, 3D PEG-ssDNA sensing assemblies. These assemblies exhibited high selectivity with respect to the target ssDNA strands, with a hybridization efficiency of 78–89% for the matching sequences and full inertness for non-complementary strands. The respective strategy can be applied to the fabrication of DNA microarrays and DNA sensors. As a suitable transduction technique, requiring no ssDNA labeling and showing high sensitivity in the PEG-ssDNA case, electrochemical impedance spectroscopy is suggested.

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“…For the programmable self-assembly kinetics of multivalent DNA-NPs, it is straightforward to evaluate the time-dependent hybridization extent p of DNA strands (Figures c and S4.1c of the SI). − During the coarse-grained simulations, the value of p rapidly increases in the initial stage and gradually reaches its equilibrium value p e in the late stage. Because the programmable self-assembly of multivalent DNA-NPs shares conceptual similarities with the reversible step-growth polymerization of multifunctional molecules, the analytical expression of hybridization extent p can be derived from our proposed model of step-growth polymerization (Part 2 of the SI).…”

Section: Resultsmentioning

confidence: 99%

Reversible Polymerization-like Kinetics for Programmable Self-Assembly of DNA-Encoded Nanoparticles with Limited Valence

Zhang

et al. 2019

J. Am. Chem. Soc.

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A similarity between the polymerization reaction of molecules and the self-assembly of nanoparticles provides a unique way to reliably predict structural characteristics of nanoparticle ensembles. However, the quantitative elucidation of programmable self-assembly kinetics of DNA-encoded nanoparticles is still challenging due to the existence of hybridization and dehybridization of DNA strands. Herein, a joint theoretical–computational method is developed to explicate the mechanism and kinetics of programmable self-assembly of limited-valence nanoparticles with surface encoding of complementary DNA strands. It is revealed that the DNA-encoded nanoparticles are programmed to form a diverse range of self-assembled superstructures with complex architecture, such as linear chains, sols, and gels of nanoparticles. It is theoretically demonstrated that the programmable self-assembly of DNA-encoded nanoparticles with limited valence generally obeys the kinetics and statistics of reversible step-growth polymerization originally proposed in polymer science. Furthermore, the theoretical–computational method is applied to capture the programmable self-assembly behavior of bivalent DNA–protein conjugates. The obtained results not only provide fundamental insights into the programmable self-assembly of DNA-encoded nanoparticles but also offer design rules for the DNA-programmed superstructures with elaborate architecture.

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Computational Study of DNA-Cross-Linked Hydrogel Formation for Drug Delivery Applications

Cited by 14 publications

References 55 publications

Programmable CRISPR-responsive smart materials

Programmable CRISPR-responsive smart materials

Rational Design of Porous Poly(ethylene glycol) Films as a Matrix for ssDNA Immobilization and Hybridization

Reversible Polymerization-like Kinetics for Programmable Self-Assembly of DNA-Encoded Nanoparticles with Limited Valence

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