Interaction between Room Temperature Ionic Liquid [bmim]BF4 and DNA Investigated by Electrochemical Micromethod

Imidazolium-based ionic liquids binding to DNA: Mechanical effects and thermodynamics of the interactions

We performed a robust characterization of the molecular interactions between the DNA molecule and two imidazolium-based ionic liquids (ILs): 1-Butyl-3-methylimidazolium chloride ([bmim]Cl) and 1-Octyl-3-methylimidazolium chloride ([omim]Cl), using single molecule approaches (optical and magnetic tweezers) and bulk techniques (isothermal titration calorimetry and conductivity measurements). Optical and magnetic tweezers allowed us to obtain the changes on the mechanical properties of the DNA complexes formed with both ILs, as well as the relevant physicochemical (binding) parameters of the interaction. Despite the weak binding measured between DNA and the two ILs, we identify a transition on the regime of polymer elasticity of the complexes formed, which results in a relevant DNA compaction for high IL concentrations. In addition, isothermal titration calorimetry and conductivity complemented the single molecule investigation, giving a complete thermodynamic characterization of the interactions and allowing the identification of the most relevant driving forces at various different concentration ranges of the ILs. Based on the results obtained with all the employed techniques, we propose a model for the binding schemes involving DNA and both [bmim]Cl and [omim]Cl.

Electrochemical impedimetric biosensors, featuring the use of Room Temperature Ionic Liquids (RTILs): Special focus on non-faradaic sensing

Over the last decade, significant advancements have been made in the field of biosensing technology. With the rising demand for personalized healthcare and health management tools, electrochemical sensors are proving to be reliable solutions; specifically, impedimetric sensors are gaining considerable attention primarily due to their ability to perform label-free sensing. The novel approach of using Room Temperature Ionic Liquids (RTILs) to improve the sensitivity and stability of these detection systems makes long-term continuous sensing feasible towards a wide range of sensing applications, predominantly biosensing. Through this review, we aim to provide an update on current scientific progress in using impedimetric biosensing combined with RTILs for the development of sensitive biosensing platforms. This review also summarizes the latest trends in the field of biosensing and provides an update on the current challenges that remain unsolved.

Hydrogen bonding of ionic liquids in the groove region of DNA controls the extent of its stabilization: synthesis, spectroscopic and simulation studies

Ionic liquids (ILs) have been extensively used for stabilization and long-term DNA storage. However, molecular level understanding of the role of the hydrogen bond of DNA with ILs in its stabilization is still inadequate. Two ILs, namely, 1,1,3,3-tetramethylguanidinium acetate (TMG) and 2,2-diethyl-1,1,3,3-tetramethylguanidinium acetate (DETMG), have been synthesized, of which TMG has a hydrogen bonding N-H group whereas DETMG does not contain any hydrogen bonding site. It has been found that both TMG and DETMG cations interact in the groove region of DNA; however, their mode of interaction is distinctly different, which causes the stabilization of DNA in the presence of TMG, whereas the effect is opposite in the case of DETMG. It is apparent from the data that only the accommodation of ILs in the groove region is not enough for the stabilization of DNA. MD simulation and spectroscopic studies combinedly indicate that the hydrogen bonding capability of the TMG cation enhances the hydrogen bonding between the Watson-Crick base pairs of DNA, resulting in its stabilization. In contrast, the bigger size as well as the absence of the hydrogen bonding site of the DETMG cation perturbs the minor groove width and base pair step parameters of DNA during its intrusion into the minor groove, which decreases the hydrogen bond between the Watson-Crick base pairs of DNA, leading to destabilization.

Aqueous ionic liquids in comparison with standard co-solutes : Differences and common principles in their interaction with protein and DNA structures

Ionic liquids (ILs) are versatile solvents for a broad range of biotechnological applications. Recent experimental and simulation results highlight the potential benefits of dilute ILs in aqueous solution (aqueous ILs) in order to modify protein and DNA structures systematically. In contrast to a limited number of standard co-solutes like urea, ectoine, trimethylamine-N-oxide (TMAO), or guanidinium chloride, the large amount of possible cation and anion combinations in aqueous ILs can be used to develop tailor-made stabilizers or destabilizers for specific purposes. In this review article, we highlight common principles and differences between aqueous ILs and standard co-solutes with a specific focus on their underlying macromolecular stabilization or destabilization behavior. In combination with statistical thermodynamics theories, we present an efficient framework, which is used to classify structure modification effects consistently. The crucial importance of enthalpic and entropic contributions to the free energy change upon IL-assisted macromolecular unfolding in combination with a complex destabilization mechanism is described in detail. A special focus is also set on aqueous IL-DNA interactions, for which experimental and simulation outcomes are summarized and discussed in the context of previous findings.

A new paradigm in sweat based wearable diagnostics biosensors using Room Temperature Ionic Liquids (RTILs)

Successful commercialization of wearable diagnostic sensors necessitates stability in detection of analytes over prolonged and continuous exposure to sweat. Challenges are primarily in ensuring target disease specific small analytes (i.e. metabolites, proteins, etc.) stability in complex sweat buffer with varying pH levels and composition over time. We present a facile approach to address these challenges using RTILs with antibody functionalized sensors on nanoporous, flexible polymer membranes. Temporal studies were performed using both infrared spectroscopic, dynamic light scattering, and impedimetric spectroscopy to demonstrate stability in detection of analytes, Interleukin-6 (IL-6) and Cortisol, from human sweat in RTILs. Temporal stability in sensor performance was performed as follows: (a) detection of target analytes after 0, 24, 48, 96, and 168 hours post-antibody sensor functionalization; and (b) continuous detection of target analytes post-antibody sensor functionalization. Limit of detection of IL-6 in human sweat was 0.2 pg/mL for 0-24 hours and 2 pg/mL for 24-48 hours post-antibody sensor functionalization. Continuous detection of IL-6 over 0.2-200 pg/mL in human sweat was demonstrated for a period of 10 hours post-antibody sensor functionalization. Furthermore, combinatorial detection of IL-6 and Cortisol in human sweat was established with minimal cross-talk for 0-48 hours post-antibody sensor functionalization.

Spectroscopic and Molecular Docking Study of the Interaction of DNA with a Morpholinium Ionic Liquid

The structural integrity of a nucleic acid under various conditions determines its utility in biocatalysis and biotechnology. Exploration of the ionic liquids (ILs) for extraction of DNA and other nucleic acid based applications requires an understanding of the nature of interaction between the IL and DNA. Considering these aspects, we have studied the interaction between calf-thymus DNA and a less toxic morpholinium IL, [Mor1,2][Br], employing fluorescence correlation spectroscopy (FCS), conventional steady state and time-resolved fluorescence, circular dichroism (CD) and molecular docking techniques. While the CD spectra indicate the stability of DNA and retention of its B-form in the presence of the morpholinium IL, the docking study reveals that [Mor1,2](+) binds to the minor groove of DNA with a binding energy of -4.57 kcal mol(-1). The groove binding of the cationic component of the IL is corroborated by the steady state fluorescence data, which indicated displacement of a known minor groove binder, DAPI, from its DNA-bound state on addition of [Mor1,2][Br]. The FCS measurements show that the hydrodynamic radius of DNA remains more or less constant in the presence of [Mor1,2][Br], thus suggesting that the structure of DNA is retained in the presence of the IL. DNA melting experiments show that the thermal stability of DNA is enhanced in the presence of morpholinium IL.

Biophysical characterization and molecular docking studies of imidazolium based polyelectrolytes-DNA complexes: role of hydrophobicity

Nonviral gene delivery vectors are acquiring greater attention in the field of gene therapy by replacing the biological viral vectors. DNA-cationic polymer complexes are one of the most promising systems to find application in gene therapy. Hence, a complete insight of their biophysical characterization and binding energy profile is important in understanding the mechanism involved in nonviral gene therapy. In this investigation, the interaction between calf thymus DNA (ctDNA) and imidazolium-based poly(ionic liquids) (PILs) also known as polyelectrolytes with three different alkyl side chains (ethyl, butyl, and hexyl) in physiological conditions using various spectroscopic experiments with constant DNA concentration and varying polyelectrolyte concentrations is reported. UV-visible absorption, fluorescence quenching studies, gel electrophoresis, circular dichroism (CD), and Fourier transform infrared spectroscopy (FTIR) have confirmed the binding of polyelectrolytes with DNA. UV-vis absorption measurements and fluorescence quenching revealed that the binding between DNA and the polyelectrolyte is dominated by electrostatic interactions. Additionally, CD and FTIR results indicated that the DNA retained its B-form with minor perturbation in the phosphate backbone without significant change in the conformation of its base pairs. Preference for alkyl side chains (K(PIL-Ethyl Br) < K(PIL-Butyl Br) < K(PIL-Hexyl Br)) toward efficient binding between the polyelectrolyte and DNA was inferred from the binding and quenching constants calculated from the absorption and emission spectra, respectively. Further, in silico molecular docking studies not only validated the observed binding trend but also provided insight into the binding mode of the polyelectrolyte-DNA complex.

Ionic liquids as solvents of polar and non-polar solutes: affinity and coordination

Evolution of H₂O and CO₂ interactions with an ionic liquid (IL) from gas phase to IL phase is described. Affinity is lost and coordination patterns vary in the process, favouring H₂O–anion and CO₂–cation interactions.

DNA Stability in Ionic Liquids and Deep Eutectic Solvents

DNA molecules are known as the genetic information carriers. Recently, they are being explored as a new generation of biocatalysts or chiral scaffolds for metal catalysts. There is also a growing interest of finding alternative solvents for DNA preservation and stabilization, including two unique types of solvents: ionic liquids (ILs) and deep eutectic solvents (DES). Therefore, it is important to understand how DNA molecules interact with these novel ionic solvent systems (i.e. ILs and DES). It is well known that inorganic di- and monovalent ions preferentially bind with major and minor grooves of DNA structures. However, in the case of ILs and DES, organic cation may intrude into the DNA minor grooves; more importantly, electrostatic attraction between organic cations and the DNA phosphate backbone becomes a predominant interaction, accompanying by hydrophobic and polar interactions between ILs and DNA major and minor grooves. In addition, anions may form hydrogen-bonds with cytosine, adenine and guanine bases. Despites these strong interactions, DNA molecules maintain double helical structure in most ionic solvent systems, especially in aqueous IL solutions. Furthermore, the exciting advances of G-quadruplexe DNA structures in ILs and DES are discussed.

Rapid dissolution of DNA in a novel bio-based ionic liquid with long-term structural and chemical stability: successful recycling of the ionic liquid for reuse in the process

DNA from salmon testes was solubilised in two bio-based ionic liquids up to 3.5% w/w in 6 h. No structural degradation of the molecule was observed for the sample solubilised in choline-indole-3-acetate (chol-IAA). However, the molecule was found to be denatured in choline-indole-3-butyrate (chol-IBA). The structural and chemical stability of the DNA molecules after six months of storage in the former was established. Further recyclability of the ionic liquid with very high yield (90-95%) for consecutive reuse in the redissolution of DNA was demonstrated.

Groove binding mechanism of ionic liquids: a key factor in long-term stability of DNA in hydrated ionic liquids?

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.

Interactions between ionic liquid surfactant [C12mim]Br and DNA in dilute brine

Interactions between ionic liquid surfactant [C(12)mim]Br and DNA in dilute brine were investigated in terms of various experimental methods and molecular dynamics (MD) simulation. It was shown that the aggregation of [C(12)mim]Br on DNA chains is motivated not only by electrostatic attractions between DNA phosphate groups and [C(12)mim]Br headgroups but also by hydrophobic interactions among [C(12)mim]Br alkyl chains. Isothermal titration calorimetry analysis indicated that the [C(12)mim]Br aggregation in the presence and absence of DNA are both thermodynamically favored driven by enthalpy and entropy. DNA undergoes size transition and conformational change induced by [C(12)mim]Br, and the charges of DNA are neutralized by the added [C(12)mim]Br. Various microstructures were observed such as DNA with loose coil conformation in nature state, necklace-like structures, and compact spherical aggregates. MD simulation showed that the polyelectrolyte collapses upon the addition of oppositely charged surfactants and the aggregation of surfactants around the polyelectrolyte was reaffirmed. The simulation predicted the gradual neutralization of the negatively charged polyelectrolyte by the surfactant, consistent with the experimental results.

Binding characteristics and molecular mechanism of interaction between ionic liquid and DNA

The binding characteristics and molecular mechanism of the interaction between a typical ionic liquid (IL), 1-butyl-3-methylimidazolium chloride ([bmim]Cl), as a green solvent and DNA were investigated for the first time by conductivity measurements, fluorescence spectroscopy, dynamic light scattering (DLS), cryogenic transmission electron microscopy (cryo-TEM), circular dichroism spectroscopy, (31)P nuclear magnetic resonance (NMR) spectroscopy, Fourier transform infrared spectroscopy, isothermal titration calorimetry (ITC), and quantum chemical calculations. It was found that the critical aggregation concentration of [bmim]Cl is decreased in the presence of DNA, and the addition of [bmim]Cl induced a continuous fluorescence quenching of the intercalated probe ethidium bromide (EtBr), indicating that the interaction between the ionic liquid and DNA is sufficiently strong to exclude EtBr from DNA. DLS results show that [bmim]Cl can induce a coil-to-globule transition of DNA at a low IL concentration, which was confirmed by the cryo-TEM images of DNA-IL complexes. With [bmim]Cl added, the resulting globular DNA structures and the extended DNA coils are first compacted, and then grow in size. During the binding process, DNA maintains the B-form, but the base packing and helical structure of DNA are altered to a certain extent. The (31)P NMR and IR spectra indicate that the cationic headgroups of bmim(+) groups interact with the phosphate groups of DNA through electrostatic attraction, and the hydrocarbon chains of bmim(+) groups interact with the bases through strong hydrophobic association. ITC results reveal the interaction enthalpy between [bmim]Cl and DNA and show that the hydrophobic interaction between the hydrocarbon chains of [bmim]Cl and the bases of DNA provides the dominant driving force in the binding. On the basis of quantum chemical calculations, it can be inferred that at a low IL concentration, the cationic headgroups of [bmim]Cl would be localized within several angstroms of the DNA phosphates, whereas the hydrophobic chains would be arranged parallel to the DNA surface. When the IL concentration is above 0.06 mol/L, the cationic headgroups are near DNA phosphates, and the hydrocarbon chains are perpendicularly attached to the DNA surface.

Slowing DNA translocation through nanopores using a solution containing organic salts

One of the key challenges to nanopore DNA sequencing is to slow down DNA translocation. Here, we report that the translocation velocities of various DNA homo- and copolymers through protein pores could be significantly decreased by using electrolyte solutions containing organic salts. Using a butylmethylimidazolium chloride (BMIM-Cl) solution instead of the commonly used KCl solution, DNA translocation rates on the order of hundreds of microseconds per nucleotide base were achieved. The much enhanced resolution of the nanopore coupled with different event blockage amplitudes produced by different nucleotides permits the convenient differentiation between various DNA molecules.