ABSTRACT
In this paper we investigate the effects of varying cation valency and concentration on the rheology of entangled λDNA solutions. We show that monovalent cations moderately increase the viscoelasticty of the solutions mainly by stabilising linear concatenation of λDNA "monomers" via hybridisation of their sticky ends. On the contrary, divalent cations have a far more complex and dramatic effect on the rheology of the solution and we observe evidence of inter-molecular DNA-DNA bridging by Mg2+. We argue that these results may be interesting in the context of dense solutions of single and double stranded DNA, e.g. in vivo or in biotechnology applications such as DNA origami and DNA hydrogels.
Subject(s)
Cations, Divalent , DNA , Rheology , DNA/chemistry , Cations, Divalent/chemistry , Cations, Monovalent/chemistry , Viscosity , Magnesium/chemistryABSTRACT
In spite of the nanoscale and single-molecule insights into nucleoid associated proteins (NAPs), their role in modulating the mesoscale viscoelasticity of entangled DNA has been overlooked so far. By combining microrheology and molecular dynamics simulation, we find that the abundant NAP "integration host factor" (IHF) lowers the viscosity of entangled λDNA 20-fold at physiological concentrations and stoichiometries. Our results suggest that IHF may play a previously unappreciated role in resolving DNA entanglements and in turn may be acting as a "genomic fluidizer" for bacterial genomes.
Subject(s)
DNA , Genome, Bacterial , Integration Host Factors/genetics , Integration Host Factors/metabolism , Bacterial Proteins/metabolism , DNA, Bacterial/genetics , DNA, Bacterial/metabolismABSTRACT
Caramel is a mixture of sugars, milk proteins, fat and water cooked at high temperatures to initiate Maillard reactions. We study caramels as 'active emulsion-filled protein gels', in which fat droplets are chemically-bonded to a background gel matrix of cross-linked proteins in a concentrated aqueous sugar solution. We delimit a 'caramel region' in composition space. Oscillatory rheology within this region reveals that we can superpose the mechanical spectra of our caramels onto a single pair of G'(ω), G''(ω) master curves using time-composition superposition (tCS) over 12 decades of frequency, so that these caramels are instances of an underlying 'universal material'. This insight constrains the molecular mechanisms for structure formation, and implies that measuring a couple of parameters will suffice to predict the rheology of our caramels over 12 orders of magnitude in frequency.
