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

Nucleic acid-responsive smart systems for controlled cargo delivery

Stimulus-responsive delivery systems allow controlled, highly regulated, and efficient delivery of various cargos while minimizing side effects. Owing to the unique properties of nucleic acids, including the ability to adopt complex structures by base pairing, their easy synthesis, high specificity, shape memory, and configurability, they have been employed in autonomous molecular motors, logic circuits, reconfigurable nanoplatforms, and catalytic amplifiers. Moreover, the development of nucleic acid (NA)-responsive intelligent delivery vehicles is a rapidly growing field. These vehicles have attracted much attention in recent years due to their programmable, controllable, and reversible properties. In this work, we review several types of NA-responsive controlled delivery vehicles based on locks and keys, including DNA/RNA-responsive, aptamer-responsive, and CRISPR-responsive, and summarize their advantages and limitations.

Exploiting epoxy-rich poly(ethylene glycol) films for highly selective ssDNA sensing via electrochemical impedance spectroscopy

This study introduces an alternative approach to immobilize thiolated single-stranded DNA (ssDNA) for the DNA sensing. In contrast to the standard, monomolecular assembly of such moieties on gold substrate, over the thiolate-gold anchors, we propose to use bioinert, porous polyethylene glycol (PEG) films as a 3D template for ssDNA immobilization. The latter process relies on the reaction between the thiol group of the respectively decorated ssDNA and the epoxy groups in the epoxy-rich PEG matrix. The immobilization process and subsequent hybridization ability of the resulting sensing assembly were monitored using cyclic voltammetry and electrochemical impedance spectroscopy, with the latter tool proving itself as the most suitable transduction technique. Electrochemical data confirmed the successful immobilization of thiol-decorated ssDNA probes into the PEG matrix over the thiol-epoxy linkage as well as high hybridization efficiency, selectivity, and sensitivity of the resulting DNA sensor. Whereas this sensor was equivalent to the direct ssDNA assembly in terms of the efficiency, it exhibited a better selectivity and bioinert properties in view of the bioinert character of the PEG matrix. The above findings place PEG films as a promising platform for highly selective ssDNA sensing, leveraging their flexible chemistry, 3D character, and bioinert properties.

Effects of solvent conditions on the self-assembly of heterotrimeric collagen-like peptide (CLP) triple helices: a coarse-grained simulation study

We perform coarse-grained (CG) molecular dynamics (MD) simulations to investigate the self-assembly of collagen-like peptide (CLP) triple helices into fibrillar structures and percolated networks as a function of solvent quality. The focus of this study is on CLP triple helices whose strands are different lengths (i.e., heterotrimers), leading to dangling 'sticky ends'. These 'sticky ends' are segments of the CLP strands that have unbonded hydrogen-bonding donor/acceptor sites that drive heterotrimeric CLP triple helices to physically associate with one another, leading to assembly into higher-order structures. We use a validated CG model for CLP in implicit solvent and capture varying solvent quality through changing strength of attraction between CG beads representing the amino acids in the CLP strands. Our CG MD simulations show that, at lower CLP concentrations, CLP heterotrimers assemble into fibrils and, at higher CLP concentrations, into percolated networks. At higher concentrations, decreasing solvent quality causes (i) the formation of heterogeneous network structures with a lower degree of branching at network junctions and (ii) increases in the diameter of network strands and pore sizes. We also observe a nonmonotonic effect of solvent quality on distances between network junctions due to the balance between heterotrimer end-end associations driven by hydrogen bonding and side-side associations driven by worsening solvent quality. Below the percolation threshold, we observe that decreasing solvent quality leads to the formation of fibrils composed of multiple aligned CLP triple helices, while the number of 'sticky ends' governs the spatial extent (radius of gyration) of the assembled fibrils.

Hopping Behavior Mediates the Anomalous Confined Diffusion of Nanoparticles in Porous Hydrogels

Diffusion is an essential means of mass transport in porous materials such as hydrogels, which are appealing in various biomedical applications. Herein, we investigate the diffusive motion of nanoparticles (NPs) in porous hydrogels to provide a microscopic view of confined diffusion. Based on the mean square displacement from particle tracking experiments, we elucidate the anomalous diffusion dynamics of the embedded NPs and reveal the heterogeneous pore structures in hydrogels. The results demonstrate that diffusive NPs can intermittently escape from single pores through void connective pathways and exhibit non-Gaussian displacement probability distribution. We simulate this scenario using the Monte Carlo method and clarify the existence of hopping events in porous diffusion. The resultant anomalous diffusion can be fully depicted by combining the hopping mechanism and the hydrodynamic effect. Our results highlight the hopping behavior through the connective pathways and establish a hybrid model to predict NP transport in porous environments.

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

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.

The role of the HBCU pipeline in diversifying the STEM workforce: Training the next generation of drug delivery researchers

Training the next generation of diverse drug delivery researchers is critical as there is a myriad of challenges that must be solved in the field. HBCUs have been and will continue to remain key factors in training significant numbers of diverse STEM graduates that enter a talented pool of potential drug delivery researchers. Several factors, both structural and psychosocial, play a role in preparing future African American researchers. In this review, strengths and weaknesses of the HBCU STEM pipeline are examined as well as current partnerships that better position HBCUs to recruit, train, and retain diverse researchers in drug delivery.

Development of a coarse-grained lipid model, LIME 2.0, for DSPE using multistate iterative Boltzmann inversion and discontinuous molecular dynamics simulations

We suggest an improved version of the intermediate resolution implicit solvent model for lipids, LIME, that was previously developed for use with discontinuous molecular dynamics (DMD) simulations. LIME gets its geometrical and the energy parameters between bonded and nonbonded pairs of coarse-grained (CG) sites from atomistic simulations. The improved model, LIME 2.0, uses multiple square wells rather than the single square well used in original LIME to obtain intermolecular interactions that more faithfully mimic those from atomistic simulations. The multi-state iterative Boltzmann inversion (MS-IBI) scheme is used to determine the interaction parameters. This means that a single set of interaction parameters between coarse-grained sites can be used to represent the lipid bilayers at different temperatures. The physical properties of CG DSPE lipid bilayer are calculated using CG simulations and compared to atomistic simulations results to verify the improved model. The phase transition temperature of the lipid bilayer is measured accurately and the lipid translocation phenomenon, " flip-flop" is observed through CG simulation. These results suggest that CG parameterization using multiple square-well and the MS-IBI scheme is well suited to the study of lipid bilayers cross a range of temperatures with DMD simulations.

Programmable CRISPR-responsive smart materials

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.

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

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.