Toehold Length of Target ssDNA Affects Its Reaction-Diffusion Behavior in DNA-Responsive DNA-co-Acrylamide Hydrogels

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.

Toward highly effective loading of DNA in hydrogels for high-density and long-term information storage

Digital information, when converted into a DNA sequence, provides dense, stable, energy-efficient, and sustainable data storage. The most stable method for encapsulating DNA has been in an inorganic matrix of silica, iron oxide, or both, but are limited by low DNA uptake and complex recovery techniques. This study investigated a rationally designed thermally responsive functionally graded (TRFG) hydrogel as a simple and cost-effective method for storing DNA. The TRFG hydrogel shows high DNA uptake, long-term protection, and reusability due to nondestructive DNA extraction. The high loading capacity was achieved by directly absorbing DNA from the solution, which is then retained because of its interaction with a hyperbranched cationic polymer loaded into a negatively charged hydrogel matrix used as a support and because of its thermoresponsive nature, which allows DNA concentration within the hydrogel through multiple swelling/deswelling cycles. We were able to achieve a high DNA data density of 7.0 × 10⁹ gigabytes per gram using a hydrogel-based system.

Interrelation between swelling, mechanical constraints and reaction-diffusion processes in molecular responsive hydrogels

The net swelling dynamics in molecular responsive hydrogels can be viewed as an integrated effect of discernible processes involving transport of actuating species, reaction with network components like destabilization of physical crosslinks or cleavage of network strands and concomitant network relaxation. Here, we describe a finite element modeling approach coupling these interdependent, underlying processes in hydrogels including oligonucleotide duplexes as physical crosslinks that can be destabilized by a particular molecule. These molecular responsive hydrogels based on acrylamide including either DNA or oligomorpholinos (MO), a DNA analogue, as functional elements can be made with various content of dsDNA or dsMO supported cross-links. The dsDNA or dsMO integrated in the hydrogel can be fabricated with ssDNA designed to competitively displace the connectivity of the dsDNA supported crosslinks, and similar for the MO hydrogels. The overall processes can be framed in a diffusion-reaction scheme. This process is dependent on the concentration of the diffusing species, their diffusion coefficients and their location. Thus, the reaction taking place in particular molecular responsive hydrogels is coupled with the deformations due to swelling and mechanical constraints undergone by the gel. Numerical examples show the importance of coupling reaction-diffusion with mechanical deformations for such gels. Finally, our model is compared to swelling experiments of hemi-spheroidal molecular responsive hydrogels bound to an optical fiber. Parameters of the reaction-diffusion model were obtained by fitting the model to reported experimental data where molecular stimuli designed with different molecular parameters for the competitive displacement reaction were employed in the swelling experiments.

Photo-induced programmable degradation of carboxymethyl chitosan-based hydrogels

Hydrogels are widely used in the biomedical field, due to their high similarity to native extracellular matrix (ECM). Most responsive hydrogels could only passively receive stimuli and independently change their properties. In this study, a photosensitive o-nitrobenzyl (NB) ester linker of polyethylene glycol (PEG) with maleimido (Mal) as terminal groups (PEG-NB-Mal) and a 5-methylfurfuryl (mF) grafted carboxymethyl chitosan (CMCS) derivative (CMCS-mF) were synthesized and used to prepare functional hydrogels via Diels-Alder (DA) reactions. The hydrogel exhibited programmable degradation properties after sequential exposure to UV light and acid treatments. It can maintain high integrity upon the single stimuli, the cascade acid and UV light treatments or the cascade UV light and alkaline treatments. Moreover, the hydrogel exhibited well controlled release profile of rhodamine B (RB). In summary, such CMCS-based hydrogels show great potential in biomedical applications. In addition, the usage of photo-induced cascade reaction in sequential degradation hydrogels can be extended to design other types of programmable smart materials.

Donnan Contribution and Specific Ion Effects in Swelling of Cationic Hydrogels are Additive: Combined High-Resolution Experiments and Finite Element Modeling

Finite element modeling applied to analyze experimentally determined hydrogel swelling data provides quantitative description of the hydrogel in the aqueous solutions with well-defined ionic content and environmental parameters. In the present study, we expand this strategy to analysis of swelling of hydrogels over an extended concentration of salt where the Donnan contribution and specific ion effects are dominating at different regimes. Dynamics and equilibrium swelling were determined for acrylamide and cationic acrylamide-based hydrogels by high-resolution interferometry technique for step-wise increase in NaCl and NaBr concentration up to 2 M. Although increased hydrogel swelling volume with increasing salt concentration was the dominant trend for the uncharged hydrogel, the weakly charged cationic hydrogel was observed to shrink for increasing salt concentration up to 0.1 M, followed by swelling at higher salt concentrations. The initial shrinking is due to the ionic equilibration accounted for by a Donnan term. Comparison of the swelling responses at high NaCl and NaBr concentrations between the uncharged and the cationic hydrogel showed similar specific ion effects. This indicates that the ion non-specific Donnan contribution and specific ion effects are additive in the case where they are occurring in well separated ranges of salt concentration. We develop a novel finite element model including both these mechanisms to account for the observed swelling in aqueous salt solution. In particular, a salt-specific, concentration-dependent Flory-Huggins parameter was introduced for the specific ion effects. This is the first report on finite element modeling of hydrogels including specific ionic effects and underpins improvement of the mechanistic insight of hydrogel swelling that can be used to predict its response to environmental change.