Toehold of dsDNA exchange affects the hydrogel swelling kinetics of a polymer–dsDNA hybrid hydrogel

Abstract

Hydrogel-based label-free nucleic acids sensor materials using high resolution interferometric readout of hydrogel swelling changes was prepared and characterized with respect to molecular design parameters. The DNA-sensitive hydrogel comprised sensing (S) and blocking (B) oligonucleotide pairs copolymerized with the network and formed reversible crosslinks in addition to stable covalent ones. Oligonucleotide probes (P) complementary to S with longer complementary regions comparing to B results in competitive replacement of S–B strands. The associated destabilization of DNA crosslinks results in changes of the hydrogel swelling. S–B dioligonucleotidic crosslinkers were designed with 8, 12 and 16 basepairs in complementary regions and were destabilized by probes with matching sequences with 2, 6 and 10 excess basepairs in the so-called “toe-hold” region. The kinetics of hydrogel swelling was tested at room and body temperature for hydrogels with different covalent crosslink densities. In general, the swelling kinetics was faster for longer “toe-holds” and slower for the longer and more stable blocking sequence. An increase of the covalent crosslink density resulted in a decrease of the swelling rate. The swelling of the hydrogel was faster the higher the temperature and closer to the S–B melting point. The following work shows direct correlation between the kinetics of strand displacement reaction and hydrogel swelling rates and provides a direction for further application of DNA-sensitive hydrogels.