Ionic Liquid-Driven Modulation of DNA Brush Morphology on Nanoparticle Surfaces

Abstract

The morphology of DNA is strongly influenced by its surrounding environment, including factors such as pH, salt type and valency, and the presence of polymers. Inorganic salts are known to reduce the DNA chain length through mechanisms like electrostatic screening and ion bridging. In contrast, ionic liquids, a new class of organic salts, have previously been found to increase the DNA chain length, indicating a distinct mode of interaction between the ionic liquid and DNA chains. This study utilizes self-assembled DNA-AuNPs as a model system to examine changes in the DNA chain morphology and the nanoscale interaction mechanisms in ionic liquid environment. The DNA chain lengths are measured in solution using X-ray scattering measurements at varying concentrations of two imidazolium ([BMIM] acetate and [EMIM] acetate) based ionic liquids. Additionally, Molecular Dynamics (MD) simulations are performed mimicking the experimental system. Our results suggest an interplay of electrostatic and groove-binding interactions governing the DNA chain morphology, which depends on IL concentration and the composition of the DNA chains. It has been found that for DNA chains with majority ssDNA, electrostatic interaction dominate, however with increasing composition of double strands, the DNA chains exhibits compaction due to non-electrostatic hydrophobic groove-binding mechanism.

Figures (19)

• Figure 1: Schematic illustration of the Small Angle X-ray Scattering setup used to study the self-assembly structures of DNA-grafted gold nanoparticles in Ionic Liquid (IL) environments. The self-assembly behaviour is investigated in the presence of [$EMIM$] acetate and [$BMIM$] acetate. The corresponding structure factor, $S(q)$, as a function of scattering vector, $q$, are shown for a) [$EMIM$] acetate and b) [$BMIM$] acetate. The observed $S(q)$ indicates the formation of randomly ordered self-assembly.
• Figure 2: Dependence of DNA brush length, $H$ on the concentration of Ionic Liquid. a) Comparison of $H$ with increasing concentration of [$EMIM$] acetate and [$BMIM$] acetate. The experimental data is analysed using the power law ($H~\sim~C_{s}^{-\alpha}$) The fitted data shows different regimes with scaling exponent ($\alpha$). b) Effect [$BMIM$] acetate with added $NaCl$ compared to [$BMIM$] acetate and $NaCl$ alone. Insets illustrate the DNA-AuNP system corresponding to ds17.
• Figure 3: (a) Schematic representation of system design indicating the ratio of the dsDNA to ssDNA. The ds 17, ds 32, ds 53, and ds 90 have dsDNA to ssDNA ratio of 15:70, 27:58, 45:40, and 77:8, respectively. Here ds 90 indicates presence of 90% paired dsDNA nuclotides. (b) Dependence of length of DNA chain, $H$ on the concentration of [$BMIM$] acetate, analyzed by varying the dsDNA to ssDNA ratio.
• Figure 4: Representative instantaneous snapshots of DNA-grafted AuNPs at three different ionic liquid (IL) concentrations from the final frames of 200 ns all-atom molecular dynamics (MD) simulations. Based on the percentage of paired dsDNA bases, the two systems are defined as follows: (a) dsDNA-rich (ds 90) system, which exhibits pronounced groove binding of IL cations even at lower ionic strengths, and (b) ssDNA-rich (ds 32) system, where DNA brush length undergoes significant compaction at higher ionic strengths due to dominant electrostatic interactions between IL cations and the flexible single-stranded segments. These distinct behaviors are further illustrated in the schematics shown in - (c) dsDNA-rich (ds 90) and (d) ssDNA-rich (ds 32) systems, respectively.
• Figure 5: End-to-end distance ($L_e$) of the DNA chains, calculated from the 200 ns MD simulation trajectory, shows that with increasing ([$BMIM$] acetate) IL concentration, DNA chain length decreases, strongly modulated by the relative ssDNA and dsDNA compositions. (a) In ssDNA-rich systems (i.e.,ds 32), faster chain compaction is observed over time, with increasing IL concentrations. (b) The dsDNA-rich ds 90 exhibit significantly less reduction in $L_e$ due to the increased chain stiffness arising from DNA groove bindings as compared to ds 32. (c) Comparative variation of $L_e$ across three different ILs concentrations for both ssDNA- and dsDNA-rich systems, highlighting the distinct compaction regimes.