The selective hybridization of DNA is of key importance for many practical applications such as gene detection and DNA-mediated self-assembly. These applications require a quantitative prediction of the hybridization free energy. Existing methods ignore the effects of non-complementary ssDNA tails beyond the first unpaired base. We use experiments and simulations to show that the binding strength of complementary ssDNA oligomers is altered by these sequences of non-complementary nucleotides. Even a small number of non-binding bases are enough to raise the hybridization free energy by approximately 1 kcal/mol at physiological salt concentrations. We propose a simple analytical expression that accounts quantitatively for this variation as a function of tail length and salt concentration.
Understanding the impact of curvature on the self-assembly of elongated microscopic building blocks, such as molecules and proteins, is key to engineering functional materials with predesigned structure. We develop model “banana-shaped” colloidal particles with tunable dimensions and curvature, whose structure and dynamics are accessible at the particle level. By heating initially straight rods made of SU-8 photoresist, we induce a controllable shape deformation that causes the rods to buckle into banana-shaped particles. We elucidate the phase behavior of differently curved colloidal bananas using confocal microscopy. Although highly curved bananas only form isotropic phases, less curved bananas exhibit very rich phase behavior, including biaxial nematic phases, polar and antipolar smectic-like phases, and even the long-predicted, elusive splay-bend nematic phase.
The glassy state is known to undergo slow structural relaxation, where the system progressively explores lower free-energy minima which are either amorphous (ageing) or crystalline (devitrification). Recently, there is growing interest in the unusual intermittent collective displacements of a large number of particles known as ‘avalanches’. However, their structural origin and dynamics are yet to be fully addressed. Here, we study hard-sphere glasses which either crystallize or age depending on the degree of size polydispersity, and show that a small number of particles are thermodynamically driven to rearrange in regions of low density and bond orientational order. This causes a transient loss of mechanical equilibrium which facilitates a large cascade of motion. Combined with previously identified phenomenology, we have a complete kinetic pathway for structural change which is common to both ageing and crystallization. Furthermore, this suggests that transient force balance is what distinguishes glasses from supercooled liquids.
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