Nucleic acid sample storage is of paramount importance in biotechnology and forensic sciences. Very recently, hydrated ionic liquids (ILs) have been identified as ideal media for long-term DNA storage. Hence, understanding the binding characteristics and molecular mechanism of interactions of ILs with DNA is of both practical and fundamental interest. Here, we employ molecular dynamics simulations and spectroscopic experiments to unravel the key factors that stabilize DNA in hydrated ILs. Both simulation and experimental results show that DNA maintains the native B-conformation in ILs. Simulation results further suggest that, apart from the electrostatic association of IL cations with the DNA backbone, groove binding of IL cations through hydrophobic and polar interactions contributes significantly to DNA stability. Circular dichroism spectral measurements and fluorescent dye displacement assay confirm the intrusion of IL molecules into the DNA minor groove. Very interestingly, the IL ions were seen to disrupt the water cage around DNA, including the spine of hydration in the minor groove. This partial dehydration by ILs likely prevents the hydrolytic reactions that denature DNA and helps stabilize DNA for the long term. The detailed understanding of IL-DNA interactions provided here could guide the future development of novel ILs, specific for nucleic acid solutes.

Spatial and temporal expression of genes is essential for maintaining phenotype integrity. Transcription factors (TFs) modulate expression patterns by binding to specific DNA sequences in the genome. Along with the core binding motif, the flanking sequence context can play a role in DNA–TF recognition. Here, we employ high-throughput in vitro and in silico analyses to understand the influence of sequences flanking the cognate sites in binding of three most prevalent eukaryotic TF families (zinc finger, homeodomain and bZIP). In vitro binding preferences of each TF toward the entire DNA sequence space were correlated with a wide range of DNA structural parameters, including DNA flexibility. Results demonstrate that conformational plasticity of flanking regions modulates binding affinity of certain TF families. DNA duplex stability and minor groove width also play an important role in DNA–TF recognition but differ in how exactly they influence the binding in each specific case. Our analyses further reveal that the structural features of preferred flanking sequences are not universal, as similar DNA-binding folds can employ distinct DNA recognition modes.

Ionic liquids (ILs) are emerging as a novel class of solvents in chemical and biochemical research. Their range of applications further expands when a small quantity of water is added. Thus, the past decade has seen extensive research on IL/water binary mixtures. While the thermophysical properties of most of these mixtures exhibited the expected trend, few others have shown deviations from the general course. One such example is the increase in density of the 1-alkyl-3-methyl imidazolium acetate ([Rn mim][Ac])-based ILs with the addition of low to moderate concentrations of water. Although such a unique trend was observed for imidazolium cations of different tail lengths and also from independent experiments, the molecular basis of this unique behavior remains unknown. In this study, we examine the nanostructural reordering in [Rn mim][Ac] (n = 2-6) ILs due to added water by means of molecular dynamics simulations, and correlate the observed changes to the sui-generis density trend. Results suggest that the initial rise in density in these ILs mainly pertains to the water-induced increased spatial correlation among the polar components, where high basicity of the acetate anion plays a key role. At moderate water concentration, the density can rise further for ILs with longer cation tails due to hydrophobic clustering. Thus, while [emim][Ac]/water mixtures exhibit the density turnover at Xw = 0.5, [bmim][Ac] and [hmim][Ac] show the turnover at Xw = 0.7. The detailed understanding provided here could help the preparation of optimal IL/water binary mixtures for various biochemical applications.

Persistence length of double-stranded DNA (dsDNA) is known to decrease with an increase in ionic concentration of the solution. In contrast to this, here we show that the persistence length of dsDNA increases dramatically as a function of ionic liquid (IL) concentration. Using all atom explicit solvent molecular dynamics simulations and theoretical models, we present, for the first time, a systematic study to determine the mechanical properties of dsDNA in various hydrated ILs at different concentrations. We find that dsDNA in 50 wt % ILs have lower persistence length and stretch modulus in comparison to 80 wt % ILs. We further observe that both the persistence length and stretch modulus of dsDNA increase as we increase the concentration of ILs. The present trend of the stretch modulus and persistence length of dsDNA with IL concentration supports the predictions of the macroscopic elastic theory, in contrast to the behavior exhibited by dsDNA in monovalent salt. Our study further suggests the preferable ILs that can be used for maintaining DNA stability during long-term storage.

Research on nucleobases has always been on the forefront owing to their ever-increasing demand in the pharmaceutical, agricultural, and other industries. The applications, however, became limited due to their poor solubility in water. Recently, ionic liquids (ILs) have emerged as promising solvents for nucleobase dissolution, as they exhibit >100-fold increased solubility compared to water. But the high viscosity of ILs remains as a bottleneck in the field. Here, by solubility and viscosity measurements, we show that addition of low-to-moderate quantity of water preserves the high solubilizing capacity of ILs, while reducing the viscosity of the solution by several folds. To understand the mechanism of nucleobase dissolution, molecular dynamics simulations were carried out, which showed that at low concentrations water incorporates into the IL-nucleobase network without much perturbing of the nucleobase-IL interactions. At higher concentrations, increasing numbers of IL anion-water hydrogen bonds replace IL-nucleobase interactions, which have been confirmed by (1)H- and (13)C NMR chemical shifts of the IL ions.