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.

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

In the present study, we expand on the understanding of hydrogels with embedded deoxyribonucleic acid (DNA) cross-links, from the overall swelling to characterization of processes that precede the swelling. The hydrogels respond to target DNA strands because of a toehold-mediated strand displacement reaction in which the target strand binds to and opens the dsDNA cross-link. The spatiotemporal evolution of the diffusing target ssDNA was determined using confocal laser scanning microscopy (CLSM). The concentration profiles revealed diverse partitioning of the target DNA inside the hydrogel as compared with the immersing solution: excluding a nonbinding DNA, while accumulating a binding target. The data show that a longer toehold results in faster cross-link opening but reduced diffusion of the target, thus resulting in only a moderate increase in the overall swelling rate. The parameters obtained by fitting the data using a reaction-diffusion model were discussed in view of the molecular parameters of the target ssDNA and hydrogels.

Recovering fluorophore concentration profiles from confocal images near lateral refractive index step changes.

Optical aberrations due to refractive index mismatches occur in various types of microscopy due to refractive differences between the sample and the immersion fluid or within the sample. We study the effects of lateral refractive index differences by fluorescence confocal laser scanning microscopy due to glass or polydimethylsiloxane cuboids and glass cylinders immersed in aqueous fluorescent solution, thereby mimicking realistic imaging situations in the proximity of these materials. The reduction in fluorescence intensity near the embedded objects was found to depend on the geometry and the refractive index difference between the object and the surrounding solution. The observed fluorescence intensity gradients do not reflect the fluorophore concentration in the solution. It is suggested to apply a Gaussian fit or smoothing to the observed fluorescence intensity gradient and use this as a basis to recover the fluorophore concentration in the proximity of the refractive index step change. The method requires that the reference and sample objects have the same geometry and refractive index. The best results were obtained when the sample objects were also used for reference since small differences such as uneven surfaces will result in a different extent of aberration.