Understanding and controlling the rheology of polymeric complex fluids that are pushed out-of-equilibrium is a fundamental problem in both industry and biology. For example, to package, repair, and replicate DNA, cells use enzymes to constantly manipulate DNA topology, length, and structure. Inspired by this feat, here we engineer and study DNA-based complex fluids that undergo enzymatically-driven topological and architectural alterations via restriction endonuclease (RE) reactions. We show that these systems display time-dependent rheological properties that depend on the concentrations and properties of the comprising DNA and REs. Through time-resolved microrheology experiments and Brownian Dynamics simulations, we show that conversion of supercoiled to linear DNA topology leads to a monotonic increase in viscosity. On the other hand, the viscosity of entangled linear DNA undergoing fragmentation displays a universal decrease that we rationalise using living polymer theory. Finally, to showcase the tunability of these behaviours, we design a DNA fluid that exhibits a time-dependent increase, followed by a temporally-gated decrease, of its viscosity. Our results present a class of polymeric fluids that leverage naturally occurring enzymes to drive diverse time-varying rheology by performing architectural alterations to the constituents.

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 fluidiser" for bacterial genomes.Prokaryotic and eukaryotic genomes carry out complex biological tasks which would be impossible if randomly folded [1][2][3][4][5]. In bacteria, nucleoid-associated proteins (NAPs) [3] play an important role in folding the genome [3,[6][7][8]. Single-molecule techniques have shed light into how certain NAPs bind, bend, kink, coat or stiffen short DNA molecules in dilute conditions [7,[9][10][11][12][13][14]. However, we have little to no evidence on what is their impact on entangled and crowded DNA [6]. For instance, while DNA segregation is impaired when NAPs are removed from the cell [5, 8], the NAP-mediated mechanisms through which this segregation is achieved remain to be determined. Here, we focus on the Integration Host Factor (IHF), an abundant NAP, present at about 6,000 and 30,000 dimers per cell in E. coli during growing and stationary phase, respectively [15,16]. IHF binds preferentially to a consensus sequence with high affinity (dissociation constant K d ≃ 2nM) but also non-specifically (K d ≃ 2µM) [17] and creates among the sharpest DNA bends in nature, up to 150 • [13]. It plays a key role in horizontal gene transfer, integration and excision of phage λDNA [18] and DNA looping [19]. Recent evidence suggest that IHF may also mediate DNA bridging through non-specific, weak interactions which transiently stabilise distal DNA segments in 3D proximity [13]. Additionally, IHF appears to strengthen biofilms by interacting with extracellular DNA [20]. In light of this evidence, it remains unclear how IHF affects DNA entanglements in dense conditions, such as those of the bacterial nucleoid.

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.

Understanding and controlling the rheology of polymeric fluids that are out-of-equilibrium is a fundamental problem in biology and industry. For example, to package, repair, and replicate DNA, cells use enzymes to constantly manipulate DNA topology, length, and structure. Inspired by this impressive feat, we combine experiments with theory and simulations to show that complex fluids of entangled DNA display a rich range of non-equilibrium material properties when undergoing enzymatic reactions that alter their topology and size. We reveal that while enzymatically-active fluids of linear DNA display universal viscous thinning, circular DNA fluids - undergoing the same non-equilibrium process - display thickening with a rate and degree that can be tuned by the DNA and enzyme concentrations. Our results open the way for the topological functionalization of DNA-based materials via naturally occurring enzymes to create a new class of "topologically-active" materials that can autonomously alter their rheological properties in a programmable manner.

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