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Toehold length of target ssDNA affects reaction-diffusion behavior in DNA-responsive DNA-co-acrylamide hydrogels

Jonasova, Eleonora Parelius; Bjørkøy, Astrid; Stokke, Bjørn Torger
Peer reviewed, Journal article
Accepted version
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URI
https://hdl.handle.net/11250/2677592
Date
2020
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  • Institutt for fysikk [1755]
  • Publikasjoner fra CRIStin - NTNU [19793]
Original version
Biomacromolecules. 2020, 21 (5), 1687-1699.   https://doi.org/10.1021/acs.biomac.9b01515
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.
Publisher
American Chemical Society
Journal
Biomacromolecules

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