Hydrogels including oligodinucleotide (ODN) supported crosslinks alongside covalent ones in acrylamide-based networks are promising responsive soft material. The versatile molecular recognition capability of the embedded DNA strands can be transformed to affect swelling properties of the hydrogel itself. Destabilizing the hybridized ODN crosslinks in the gel by introducing target DNA strands will alter the swelling state. While the overall swelling response caused by such competitive displacement reactions has been published, insight into the molecular underlying process is not yet reported. In the present study we expand on the understanding of these materials from the overall swelling to characterization of the cascade of processes, e.g.  migration and binding of the target DNA to the ODN, the subsequent crosslink opening and the altered swelling state. These interrelated processes display a spatiotemporal evolution depending on the experimental boundary conditions.  Using a combination of interferometry and confocal laser scanning microscopy (CLSM), the spatiotemporal evolution of the migrating target ssDNA in half spherical hydrogels synthesized at the end of optical fibers was determined. The fluorescence intensity profiles were converted to concentration profiles accounting for adverse optical effects. The data indicate that the faster binding of an invading ssDNA target realized by a longer base pair toehold for the initial binding to the ODN slows down the migration of the target. As a result, only a moderate increase in the overall swelling rate is observed with longer toeholds despite their faster rate of binding.  The parameters obtained by fitting the data using a diffusion-reaction model were discussed in view of molecular parameters of the target ssDNA and ODN functionalized hydrogels. This study clearly identifies toehold length as a critical molecular parameter affecting the overall coupling between the migration and binding of this target in ODN-co-acrylamide hydrogels.

Spatiotemporal migration of target nucleotide in partly oligodinucleotide crosslinked hydrogels identifies toehold as a critical parameter in the swelling dynamics

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.