Assessing the Suitability of a Dicationic Ionic Liquid as a Stabilizing Material for the Storage of DNA in Aqueous Medium

Abstract

The present study has been undertaken with an objective to find out a suitable medium for the long-term stability and storage of the ct-DNA structure in aqueous solution. For this purpose, the potential of a pyrrolidinium-based dicationic ionic liquid (DIL) in stabilizing ct-DNA structure has been investigated by following the DNA–DIL interaction. Additionally, in order to understand the fundamental aspects regarding the DNA–DIL interaction in a comprehensive manner, studies are also done by employing structurally similar monocationic ionic liquids (MILs). The investigations have been carried out both at ensemble-average and single molecular level by using various spectroscopic techniques. The molecular docking study has also been performed to throw more light into the experimental observations. The combined steady-state and time-resolved fluorescence, fluorescence correlation spectroscopy, and circular dichroism measurements have demonstrated that DILs can effectively be used as better storage media for ct-DNA as compared to MILs. Investigations have also shown that the extra electrostatic interaction between the cationic head group of DIL and the phosphate backbone of DNA is primarily responsible for providing better stabilization to ct-DNA, retaining its native structure in aqueous medium. The outcomes of the present study are also expected to provide valuable insights in designing new polycationic IL systems that can be used in nucleic acid-based applications.

Deciphering the Role of Anions of Ionic Liquids in Modulating the Structure and Stability of ct-DNA in Aqueous Solutions

“…Consequently, they showcase distinct behaviors when introduced into an aqueous solution, and as a result, their interactions with ct -DNA are not uniform. Additionally, the static or dynamic nature of the quenching mechanism can be distinguished by monitoring the temperature dependence of the K sv . , It is evident from Table S1 that the K sv value increases with the rise in temperatures in the presence of each IL. This observation indicates that the fluorescence quenching of the DAPI-DNA complex by ILs is dynamic in nature.…”

“…To understand the mechanistic pathway involved in the present case, i.e., during the interaction of ILs with the DAPI-DNA complex and the resulting quenching of fluorescence, we have utilized the classical Stern–Volmer equation (SV). The equation is given as eq italicF 0 italicF = 1 + italick sv [ IL ] Here F 0 is the fluorescence intensity of the DAPI-DNA complex in the absence of the quencher (here IL), F is the fluorescence intensity in the presence of [IL] and K sv denotes the Stern–Volmer quenching constant.…”

“…Furthermore, the magnitude of the binding constant confirms that irrespective of the nature of anion to which imidazolium-ion is associated with, it interacts at the minor/major-groove of ct-DNA. 5,7,48 Interestingly, from Table 2, it can be revealed that at lower concentrations the binding strength between investigated ILs and ct-DNA follows an order…”

“…A tris-HCl buffer solution of concentration 5 mM and pH 7.2 was prepared by diluting a 1 M buffer with Milli-Q water. The stock solutions of ct-DNA (100 μM) and DAPI (200 μM) were prepared in a 5 mM buffer following the documented procedures . The concentration of the ct -DNA solution in the buffer was determined by monitoring the molal extinction coefficient of ct -DNA at 260 nm, which was found to be 6600 cm –1 .…”

“…Recently, the utilization of ionic liquids (ILs) has emerged as a potential tool in the realm of nucleic-acid stabilization and preservation in aqueous solutions. − In this context, the cationic components of ILs are always believed to play a fundamental role as they are shown to preferentially interact with the phosphate backbone of DNA, thereby stabilizing the double helical structure. , Indeed, in the majority of research studies focusing on DNA-IL interactions, a significant emphasis has often been placed on understanding the role of the cationic moiety of ILs. The importance of IL anions in the said event has often been overlooked, possibly due to their lower binding affinities for the DNA backbone. − However, ILs are known to display structural transitions from ion pairs to distinct ions based on their hydration characteristics, and these free ions and associated ion-pairs are considered to exhibit different behavior in the interaction event with the biomolecules. − Therefore, IL anions can also contribute to nucleic acid stabilization not only directly through interactions with DNA bases but also indirectly by influencing the solvent structure surrounding DNA or by altering some physio-chemical parameters such as pH, ionic strength, and polarity of the medium. − Hence, understanding these interactions between anions of ILs and DNA, as well as their impact on the surrounding environment, is crucial for optimizing the composition and conditions of ILs for specific nucleic acid–based applications.…”