SignificanceWhile widely known as the molecule of life, DNA is also an amazing building block at the nanoscale, since it allows us to design and program the structure and dynamics of functional nanomaterials. We exploit the programmability of DNA to achieve control over the rheology of self-assembled hydrogels, which have elastic or viscous behavior (similar to that of slime) that is finely regulated by temperature. Using microrheology to investigate the mechanical properties of DNA hydrogels at the microlength scale, we map the viscoelastic response over a broad range of frequencies and temperatures. The deep understanding in the fundamental physics provides a way to design DNA-based materials with precise control over the structure stability and rigidity at molecular level.
We introduce a coarse-grained numerical model that represents a generic DNA hydrogel consisting of Y-shaped building blocks. Each building block comprises three double-stranded DNA arms with single-stranded DNA sticky ends, mimicked by chains of beads and patchy particles, respectively, to allow for an accurate representation of both the basic geometry of the building blocks and the interactions between complementary units. We demonstrate that our coarse-grained model reproduces the correct melting-behaviour between the complementary ends of Y-shapes, and their self-assembly into a percolating network. Structural analysis of this network reveals three-dimensional features consistent with a uniform distribution of inter-building block dihedral angles. When applying an oscillatory shear strain to the percolating system, we show that the system exhibits a linear elastic response when fully connected. We finally discuss to what extent the system's elastic modulus may be controlled by simple changes to the building block complementarity. Our model offers a computationally
The viscosity of a dense suspension has contributions from hydrodynamics and particle interactions, both of which depend upon the flow-induced arrangement of particles into fragile structures. Here, we study the response of nearly hard sphere suspensions to oscillatory shear using simulations and experiments in the athermal, non-inertial limit. Three distinct regimes are observed as a function of the strain amplitude γ. For γ < 10, initially non-contacting particles remain separated and the suspension behaves similarly to a Newtonian fluid, with the shear stress proportional to the strain rate, and the normal stresses close to zero. For γ > 10, the microstructure becomes well-established at the beginning of each shear cycle and the rheology is quasi-Newtonian: the shear stress varies with the rate, but flow-induced structures lead to non-zero normal stresses. At intermediate γ, particle-particle contacts break and reform across entire oscillatory cycles, and we probe a non-linear regime that reveals the fragility of the material. Guided by these features, we further show that oscillatory shear may serve as a diagnostic tool to isolate specific stress contributions in dense suspensions, and more generally in those materials whose rheology has contributions with both hydrodynamic and non-hydrodynamic origin.
Rapid methods for diagnosis of bacterial infections are urgently needed to reduce inappropriate use of antibiotics, which contributes to antimicrobial resistance. In many rapid diagnostic methods, DNA oligonucleotide probes, attached to a surface, bind to specific nucleotide sequences in the DNA of a target pathogen. Typically, each probe binds to a single target sequence; i.e., target–probe binding is monovalent. Here we show using computer simulations that the detection sensitivity and specificity can be improved by designing probes that bind multivalently to the entire length of the pathogen genomic DNA, such that a given probe binds to multiple sites along the target DNA. Our results suggest that multivalent targeting of long pieces of genomic DNA can allow highly sensitive and selective binding of the target DNA, even if competing DNA in the sample also contains binding sites for the same probe sequences. Our results are robust to mild fragmentation of the bacterial genome. Our conclusions may also be relevant for DNA detection in other fields, such as disease diagnostics more broadly, environmental management, and food safety.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.