On the role of flexibility in linker-mediated DNA hydrogels

Abstract

Three-dimensional DNA networks, composed of tri-or higher valent nanostars with sticky, single-stranded DNA overhangs, have been previously studied in the context of designing thermally responsive, viscoelastic hydrogels. In this work, we use linker-mediated gels, where the sticky ends of two trivalent nanostars are connected through the complementary sticky ends of a linear DNA duplex. We can design this connection to be either rigid or flexible by introducing flexible, non-binding bases. The additional flexiblity provided by these non-binding bases influences the effective elasticity of the percolating gel formed at low temperatures. Here we show that by choosing the right length of the linear duplex and non-binding flexible joints, we obtain a completely different phase behaviour to that observed for rigid linkers. In particular, we use dynamic light scattering as microrheological tool to monitor the self-assembly of DNA nanostars with linear linkers as a function of temperature. While we observe classical gelation when using rigid linkers, the presence of flexible joints leads to a cluster fluid with reduced viscosity. Using both the oxDNA model and a coarse-grained simulation to investigate the nanostar-linker topology, we hypothesise on the possible structure formed by the DNA clusters.

Mechanical Properties of DNA Hydrogels: Towards Highly Programmable Biomaterials

“…This example as well demonstrated counterintuitive results where a greater fraction of flexible linkers increased the storage moduli, which was due to an increased number of hybridized crosslinks with the flexible linkers. However, when flexible linkers were introduced to DNAns based gels they caused a decrease in the storage modulus [66]. Stoev et al studied the formation a trivalent DNAns hydrogel with rigid sticky ends and sticky ends with 6 nt poly-T region between the sticky end and the dsDNA arm of the structure [66].…”

“…However, when flexible linkers were introduced to DNAns based gels they caused a decrease in the storage modulus [66]. Stoev et al studied the formation a trivalent DNAns hydrogel with rigid sticky ends and sticky ends with 6 nt poly-T region between the sticky end and the dsDNA arm of the structure [66]. Their design allowed for enough flexibility in the linkers that they could self-hybridize with linkers from another arm on the same structure, thus also limiting the degree of connectivity between different structures.…”

“…Their design allowed for enough flexibility in the linkers that they could self-hybridize with linkers from another arm on the same structure, thus also limiting the degree of connectivity between different structures. The flexible system only showed soft gel-like rheological properties near the melting temperature (T m ) of the linker (52 • C) with a storage modulus < 1 Pa greater than the loss modulus at frequencies below 10 3 Hz, whereas the nonflexible linkers showed a high-frequency plateau modulus of 45 Pa at 10 4 Hz at 44 • C and melted at 52 • C [66].…”

“…This model was used to study the temperature and concentration-dependent degree of association, structural organization, and to dissect the rheological response, which will be discussed further in the next section. More recently, Stoev et al used a similar model in conjunction with oxDNA simulations of a single DNAns and microrheology experiments to study the role of linker flexibility in DNA hydrogels [66]. Using oxDNA the probable angle for DNA sticky ends with rigid or flexible linkers was determined.…”

“…Using oxDNA the probable angle for DNA sticky ends with rigid or flexible linkers was determined. This angle was incorporated as the range of motion for the patchy ends within the coarse-grained model and the rheological behavior acquired through simulation was validated with microrheological results, demonstrating a significant increase in the crossover frequency when flexible linkers are present, causing the gel to behave as a fluid at low frequencies [66].…”