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

Abstract

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.

Morpholino Target Molecular Properties Affect the Swelling Process of Oligomorpholino-Functionalized Responsive Hydrogels

“…This behavior cannot be explained by the association, dissociation, and crosslink opening processes as described in the reaction-diffusion model and suggests another phenomenon taking place in these hydrogels. Additional experiments mapping effects of toehold molecular parameters are also reported elsewhere [24,42]. However, an explicit comparison between the various sets of data is challenging due to differences in concentrations of immobilized dsDNA crosslinks and possible effects of the various fluoroprobe labels.…”

“…I.C. : m o (r, 0) = 0, 0 ≤r ≤ 1 (15) This system of partial differential equations can be numerically solved by applying the method of lines and discretizing the spatial dimension to reduce the problem to a system of ordinary differential equations [41,42].…”

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

“…Moreover, it can be easily chemically modified through copolymerization as well as by forming a semi-interpenetrating network (semi-IPN) and an interpenetrating network (IPN) to improve functionality and to provide versatile properties (38,39). Besides, they are considered good DNA carriers because of their excellent biocompatibility (40)(41)(42)(43)(44)(45) and blend easily with DNA protectants (25,46).…”