Microrheology of entangled DNA solutions

Abstract

Fundamental properties of DNA-based materials, including DNA sequence, length, and topology, as well as external factors such as ionic strength and temperature, collectively influence their behaviour. However, how these factors affect the rheology of highly concentrated DNA solutions has remained largely unexplored. This thesis aims to characterise how the rheological properties of DNA-based materials are influenced by DNA topology, cation concentration and valency, and temperature.

Firstly, the influence of DNA topology on the macroscopic properties of concentrated DNA solutions was investigated. DNA can be ‘folded’ into virtually any arbitrary design by combining a single-stranded scaffold DNA with many smaller staple strands in a technique known as ‘DNA origami’. This technique allows for precise control over the topology of polymeric building blocks at the nanometer scale. Polymer topologies that simultaneously exhibit both linear and circular architectures have been shown experimentally and computationally to display viscoelastic properties influenced by topological constraints, or ‘threadings’, between the polymers. In this thesis, a linear, circular, and tadpole design of DNA origami were synthesised and characterised using gel electrophoresis and atomic force microscopy (AFM). The viscoelastic properties of concentrated solutions of these DNA origami topologies were investigated using microrheology. We discovered that the differing rheological behaviour between DNA topologies is not due to topological threadings, but rather a result of variations in the polymers’ radii of gyration across different topologies.

Since DNA is a negatively charged polyelectrolyte, it is well known that the presence of cations promotes the hybridisation of DNA strands. Therefore, we explore the impact of cations on this process in concentrated DNA solutions. We study a system of entangled DNA, which possesses two ends capable of binding to each other, allowing the formation of longer chains through hybridisation. We investigate how cation valency and concentration affect the rheology of entangled DNA solutions, and reveal that the distribution of polymer chain lengths is influenced by both the type, and concentration of cations. Furthermore, we observe indications of intermolecular bridging between DNA strands induced by divalent cations.

This thesis concludes with an extension of the initial DNA origami project, exploring the collective behaviour of DNA origami at high concentrations. We find that different staple designs influence how DNA origami responds to temperature changes, and the presence of excess staples in solution. At high concentrations, heating and cooling the solution can induce staple-mediated bridging between different scaffolds. However, this interaction can be disrupted by introducing staples corresponding to a different DNA topology. Clearly, many factors affect the rheological response of DNA origami, making it an excellent candidate for the design of smart materials with programmable viscoelasticity.

Overall, this thesis demonstrates that DNA is a versatile material building block, enabling the creation of novel topologies while also responding dynamically to external factors such as cations, temperature, and competitive DNA molecules in solution. Understanding how these fundamental properties influence rheological properties is crucial for designing the next generation of smart and programmable materials.