Combining steady state and temperature jump IR spectroscopy to investigate the allosteric effects of ligand binding to dsDNA.

Changes in the structural dynamics of double stranded (ds)DNA upon ligand binding have been linked to the mechanism of allostery without conformational change, but direct experimental evidence remains elusive. To address this, a combination of steady state infrared (IR) absorption spectroscopy and ultrafast temperature jump IR absorption measurements has been used to quantify the extent of fast (∼100 ns) fluctuations in (ds)DNA·Hoechst 33258 complexes at a range of temperatures. Exploiting the direct link between vibrational band intensities and base stacking shows that the absolute magnitude of the change in absorbance caused by fast structural fluctuations following the temperature jump is only weakly dependent on the starting temperature of the sample. The observed fast dynamics are some two orders of magnitude faster than strand separation and associated with all points along the 10-base pair duplex d(GCATATATCC). Binding the Hoechst 33258 ligand causes a small but consistent reduction in the extent of these fast fluctuations of base pairs located outside of the ligand binding region. These observations point to a ligand-induced reduction in the flexibility of the dsDNA near the binding site, consistent with an estimated allosteric propagation length of 15 Å, about 5 base pairs, which agrees well with both molecular simulation and coarse-grained statistical mechanics models of allostery leading to cooperative ligand binding.

Association and relaxation of supra-macromolecular polymers.

This paper describes the structures created by assembling functionalised entangled polymers and the effect these have on the rheology of the material. A polybutadiene (PBd) linear polymer precursor of sufficient molecular weight to be entangled is used. This is end functionalised with the self-associating group 2-ureido-4pyrimidinone (UPy). Interestingly, despite the relatively high molecular weight of the precursor diluting the UPy concentration, the effect on the material's properties is significant. To characterise the assembled microstructure we present linear rheology, extensional non-linear rheology and small angle X-ray scattering (SAXS). The linear rheology shows that the functionalised PBd assembles into large macro-structures where the terminal relaxation time is up to seven orders of magnitude larger than the precursor. The non-linear rheology shows strain-hardening over a broad range of strain-rates. We then show by both SAXS and modelling of the extensional data that there must exist clusters of UPy associations and hence assembled polymers with branched architecture. By modelling the supra-molecular structure as an effective linear polymer, we show that this would be insufficient in predicting the strain-hardening behaviour at lower extension-rates. Therefore, in this flow regime the strain-hardening is likely to be caused by branching. This is backed up by SAXS measurements which show that UPy clusters larger than pair-pair groups exist.

In Silico Molecular Design, Synthesis, Characterization, and Rheology of Dendritically Branched Polymers: Closing the Design Loop.

It has been a long held ambition of both industry and academia to understand the relationship between the often complex molecular architecture of polymer chains and their melt flow properties, with the goal of building robust theoretical models to predict their rheology. The established key to this is the use of well-defined, model polymers, homogeneous in chain length and architecture. We describe here for the first time, the in silico design, synthesis, and characterization of an architecturally complex, branched polymer with the optimal rheological properties for such structure-property correlation studies. Moreover, we demonstrate unequivocally the need for accurate characterization using temperature gradient interaction chromatography (TGIC), which reveals the presence of heterogeneities in the molecular structure that are undetectable by size exclusion chromatography (SEC). Experimental rheology exposes the rich pattern of relaxation dynamics associated with branched polymers, but the ultimate test is, of course, did the theoretical (design) model accurately predict the rheological properties of the synthesized model branched polymer? Rarely, if ever before, has such a combination of theory, synthesis, characterization, and analysis resulted in a "yes", expressed without doubt or qualification.