Stable G-quadruplex structure in a hydrated ion pair: cholinium cation and dihydrogen phosphate anion

DNA nanotechnology in ionic liquids and deep eutectic solvents

Nucleic acids have the ability to generate advanced nanostructures in a controlled manner and can interact with target sequences or molecules with high affinity and selectivity. For this reason, they have applications in a variety of nanotechnology applications, from highly specific sensors to smart nanomachines and even in other applications such as enantioselective catalysis or drug delivery systems. However, a common disadvantage is the use of water as the ubiquitous solvent. The use of nucleic acids in non-aqueous solvents offers the opportunity to create a completely new toolbox with unprecedented degrees of freedom. Ionic liquids (ILs) and deep eutectic solvents (DESs) are the most promising alternative solvents due to their unique electrolyte and solvent roles, as well as their ability to maintain the stability and functionality of nucleic acids. This review aims to be a comprehensive, critical, and accessible evaluation of how much this goal has been achieved and what are the most critical parameters for accomplishing a breakthrough.

Low-Frequency Spectra of Hydrated Ionic Liquids with Kosmotropic and Chaotropic Anions

In this study, we investigated the water concentration dependence of the intermolecular vibrations of two hydrated ionic liquids (ILs), cholinium dihydrogen phosphate ([ch][dhp]) and cholinium bromide ([ch]Br), using femtosecond Raman-induced Kerr effect spectroscopy (fs-RIKES). The anions of the former and latter hydrated ILs are kosmotropic and chaotropic, respectively. We found that the spectral peak of ∼50 cm-1 shifted to the low-frequency side in hydrated [ch][dhp], indicating the weakening of its intermolecular interactions. In contrast, no change in the peak frequency of the low-frequency band at ∼50 cm-1 was observed with increasing water concentration in hydrated [ch]Br. The vibrational density of states (VDOS) spectra generated from molecular dynamics (MD) simulations were in qualitative agreement with the experimental results. Decomposition analysis of the VDOS spectra for each component revealed that the red shift of the low-frequency band in the hydrated [ch][dhp] upon water addition was essentially due to the contributions of anions and water rather than that of the cholinium cation. We also found from the low-frequency spectra of the two hydrated ILs that they differed in the concentration dependence of the 180 cm-1 band, which is assigned as a hindered translational motion of water molecules combined to form O···O stretching motions. From the relationship between the peak frequency of the low-frequency band and the bulk parameter, which is the square root of the surface tension divided by the density, we found that the peak frequency in the hydrated IL with kosmotropic [dhp]- depends on the bulk parameter, similar to the case for an aqueous solution of the typical deep eutectic solvent reline. However, the peak frequency of the hydrated IL with chaotropic Br- is constant with the bulk parameter.

Mechanisms of Biological Effects of Ionic Liquids: From Single Cells to Multicellular Organisms

The review presents a detailed discussion of the evolving field studying interactions between ionic liquids (ILs) and biological systems. Originating from molten salt electrolytes to present multiapplication substances, ILs have found usage across various fields due to their exceptional physicochemical properties, including excellent tunability. However, their interactions with biological systems and potential influence on living organisms remain largely unexplored. This review examines the cytotoxic effects of ILs on cell cultures, biomolecules, and vertebrate and invertebrate organisms. Our understanding of IL toxicity, while growing in recent years, is yet nascent. The established findings include correlations between harmful effects of ILs and their ability to disturb cellular membranes, their potential to trigger oxidative stress in cells, and their ability to cause cell death via apoptosis. Future research directions proposed in the review include studying the distribution of various ILs within cellular compartments and organelles, investigating metabolic transformations of ILs in cells and organisms, detailed analysis of IL effects on proteins involved in oxidative stress and apoptosis, correlation studies between IL doses, exposure times and resulting adverse effects, and examination of effects of subtoxic concentrations of ILs on various biological objects. This review aims to serve as a critical analysis of the current body of knowledge on IL-related toxicity mechanisms. Furthermore, it can guide researchers toward the design of less toxic ILs and the informed use of ILs in drug development and medicine.

Hydrated Ionic Liquids: Perspective for Bioscience

Hydrated ionic liquid (IL) is a simple mixture of IL and water. Unique aqueous electrolyte solution can be designed by mixing IL with limited amount of water. In most hydrated ILs, there are no free water and all are strongly interacted with ions. The properties of hydrated ILs, such as polarity, viscosity, ion mobility, and hydrogen bonding ability, can therefore be controlled simply by water content. This mixture is expected to provide similar environment to that of living cell, and is desired to be effective solvents for biomolecules. In this account, we would like to survey the basic properties, recent results, and future aspects of the hydrated ILs.

Enzymatic Reactions using Ionic Liquids for Green Sustainable Chemical Process; Stabilization and Activation of Lipases

The enzymatic reaction is highly respected from an environmentally-friendly point-of-view. Optimization of the reaction media and supporting materials of enzymes must be investigated in parallel with the effort to develop new enzymes. Lipases are frequently used for organic syntheses as synthetic tools even industry because of their acceptance of having a broad range of substrates, stability, and availability. We have investigated the possibility of ILs as both a solvent and activating or stabilization agent of enzymes, in particular, lipase as a model enzyme. ILs allowed recyclable use of a lipase and significant acceleration of transesterification, and also enhanced the stability and reaction activity of a lipase by immobilization through a lyophilization process. We discuss how we enhanced the enzyme capability using the IL engineering focusing on lipase-catalyzed reactions, i. e., realization of the recyclable use of an enzyme, how ILs mediated the enhanced reaction rate, and improved the stability of the enzyme.

A universal approach for synthesis of copper nanoclusters templated by G-rich oligonucleotide sequences and their applications in sensing

Herein, five common G4 sequences have been selected, including three different length of telomere DNA, hemin aptamer, and thrombin aptamer, to synthesize Cu nanoclusters (Cu NCs) in-situ. All G4s are proper templates for Cu NCs with low temperature treatment. The particles (G4-Cu NCs) smaller than 3 nm in diameter were obtained and showed light green fluorescence. This is the first report of metal clusters templated by G4s in-situ. As proof of the concept, hemin and alkaline phosphatase (ALP) were used as the targets to test whether the system can monitor the interaction between G4s and its substrate. The results suggest that G4-Cu NCs can indicate the behavior of G4 and its interaction with hemin, and sensing ALP is achieved with the aid of ATP. The linear ranges of hemin and ALP are 300-4000 nM and 10-500 U/L, respectively, and the corresponding limits of detection as low as 97 nM for hemin and 2.8 U/L for ALP. Moreover, this present system has been successfully applied for the detection of ALP in human serum samples with satisfactory recoveries. This synthesis approach is universal, and it can be easily extended to evaluating the formation of G4, or monitoring the interaction between G4 and its substrate, or selective targeting individual G4, or sensitive detection of other important biomarkers by changing template G4 sequence.

The combined action of cations and anions of ionic liquids modulates the formation and stability of G-quadruplex DNA

G-Quadruplex (Gq) formation and stabilization by any molecule is an essential requirement for its application in therapy, especially in oncology. Metal cations have shown higher propensity of the formation of the Gq structure and its stabilization. In this study, the role of both cations and anions of ionic liquids (ILs) on the Gq formation of human telomere (hTeloG) and its stability was investigated using spectroscopic and molecular dynamics simulation techniques. Irrespective of the nature of anions of ILs, tetramethylguanidinium (TMG) cations associated with different anions can form an antiparallel Gq structure in hTeloG. However, the propensity of the formation of an antiparallel Gq structure and its stability depend on the chain length of anions of ILs. Gq is significantly less stable in ILs having longer hydrocarbon chain anions compared to the short chain anions suggesting that the hydrophobicity of the anion plays a critical role in the stability and formation of the Gq structure by ILs. The data indicate that longer hydrocarbon chain anions of ILs preferably interact in the loop region of Gq through hydrophobic interaction which enhances the overall binding of the cation of ILs with Gq causing a decrease in the stacking energy between the G-quartets as well as Hoogsteen hydrogen bonds between the guanine bases leading to the destabilization of the antiparallel Gq structure.

Ionic liquids: prospects for nucleic acid handling and delivery

Operations with nucleic acids are among the main means of studying the mechanisms of gene function and developing novel methods of molecular medicine and gene therapy. These endeavours usually imply the necessity of nucleic acid storage and delivery into eukaryotic cells. In spite of diversity of the existing dedicated techniques, all of them have their limitations. Thus, a recent notion of using ionic liquids in manipulations of nucleic acids has been attracting significant attention lately. Due to their unique physicochemical properties, in particular, their micro-structuring impact and tunability, ionic liquids are currently applied as solvents and stabilizing media in chemical synthesis, electrochemistry, biotechnology, and other areas. Here, we review the current knowledge on interactions between nucleic acids and ionic liquids and discuss potential advantages of applying the latter in delivery of the former into eukaryotic cells.

Use of Ionic Liquids in Protein and DNA Chemistry

Ionic liquids (ILs) have been receiving much attention as solvents in various areas of biochemistry because of their various beneficial properties over the volatile solvents and ILs availability in myriad variants (perhaps as many as 108) owing to the possibility of paring one cation with several anions and vice-versa as well as formulations as zwitterions. Their potential as solvents lies in their tendency to offer both directional and non-directional forces toward a solute molecule. Because of these forces, ionic liquids easily undergo intermolecular interactions with a range of polar/non-polar solutes, including biomolecules such as proteins and DNA. The interaction of genomic species in aqueous/non-aqueous states assists in unraveling their structure and functioning, which have implications in various biomedical applications. The charge density of ionic liquids renders them hydrophilic and hydrophobic, which retain intact over long-range of temperatures. Their ability in stabilizing or destabilizing the 3D-structure of a protein or the double-helical structure of DNA has been assessed superior to the water and volatile organic solvents. The aptitude of an ion in influencing the structure and stability of a native protein depends on their ranking in the Hofmeister series. However, at several instances, a reverse Hofmeister ordering of ions and specific ion-solute interaction has been observed. The capability of an ionic liquid in terms of the tendency to promote the coiling/uncoiling of DNA structure is noted to rely on the basicity, electrostatic interaction, and hydrophobicity of the ionic liquid in question. Any change in the DNA's double-helical structure reflects a change in its melting temperature (T m), compared to a standard buffer solution. These changes in DNA structure have implications in biosensor design and targeted drug-delivery in biomedical applications. In the current review, we have attempted to highlight various aspects of ionic liquids that influence the structure and properties of proteins and DNA. In short, the review will address the issues related to the origin and strength of intermolecular interactions, the effect of structural components, their nature, and the influence of temperature, pH, and additives on them.

Predicting Entropic Effects of Water Mixing with Ionic Liquids Containing Anions of Strong Hydrogen Bonding Ability: Role of the Cation

Ionic liquids (ILs) such as choline dihydrogen phosphate exhibit an extraordinary solubilizing ability for proteins such as cytochrome C when mixed with 20 wt % water. Most widely used imidazolium-based ionic liquids coupled with dihydrogen phosphate do not exhibit the same solubilizing properties, suggesting that a multifunctional cation such as choline might play a key role in enhancing these properties of ionic liquid mixtures with water. In this theoretical work, we compare intermolecular interactions between the water molecule and ionic liquid ions in two ion-paired clusters of choline- and 1-butyl-3-methyl-imidazolium-based ionic liquids coupled with acetate, dihydrogen phosphate, and mesylate. Gibbs free energy (GFE) of solvation of water in these ionic liquids was calculated. Incorporation of a water molecule into ionic liquid clusters was accompanied by negative GFEs of solvation in both types of cations. These results were in good agreement with previously reported experimental GFEs of solvation of water in ILs. Compared to imidazolium-based clusters, strong interionic interactions of choline ionic liquids resulted in more negative GFEs due to their smaller deformation upon the addition of a water molecule, with dihydrogen phosphate and mesylate predicting the lowest GFEs of -30.1 and -43.5 kJ/mol^-1, respectively. Lower GFEs of solvation of water in choline-based clusters were also accompanied with smaller entropic penalties, suggesting that water easily incorporates itself into the existing ionic network. Analysis of the intramolecular bonds within the water molecule showed that the choline hydroxyl group donates electron density to the neighboring water molecule, leading to additional polarization. The predicted infrared spectra of clusters of ionic liquids with water showed a pronounced red shift due to strongly polarized O-H bonds, in excellent agreement with the experimentally measured infrared spectra of ionic liquid mixtures with water. Increased polarization of water in choline-based ionic liquids undoubtedly creates more effective solvents for stabilizing biological molecules such as proteins.

Hydration States of Cholinium Phosphate-Type Ionic Liquids as a Function of Water Content

We investigated the hydration states of cholinium phosphate-type ionic liquids (ILs) in relation to ion structure, focusing on the influence of the hydroxyl group of the cation and the alkyl chain length of the anion. Water activity measurements provided information on the macroscopic hydration states of the hydrated ILs, while NMR measurements and molecular dynamics simulations clearly showed the microscopic interactions and coordination of the water molecules. The hydrogen bonding networks in these ILs were influenced by the anion structure and water content, and the mobility of water molecules was influenced by the number of hydroxyl groups in the cation and anion.

Ionic Liquids as Stabilization and Refolding Additives and Solvents for Proteins

This chapter focuses on recent advances in the use of ionic liquids as additives and solvents in protein applications. The solvent properties of ionic liquids can be tuned by the appropriate selection of cation and anion. The effects of different kinds of ionic liquids on protein stability and refolding behavior have been investigated and reported. The ionic liquid properties affect the intermolecular interactions of proteins, inducing different formations and folding behavior. These effects also vary with the concentration of ionic liquids. Although many of the associated mechanisms are not completely clear, some of this behavior may be attributed to the kosmotropicity of the ions and their Hofmeister effects. Graphical Abstract.

Hydrated ionic liquids enable both solubilisation and refolding of aggregated concanavalin A

Dissolution and refolding of aggregated concanavalin A were demonstrated in hydrated ionic liquids.

Biological and nanotechnological applications using interactions between ionic liquids and nucleic acids

Nucleic acids have emerged as powerful biological and nanotechnological tools. In biological and nanotechnological experiments, methods of extracting and purifying nucleic acids from various types of cells and their storage are critical for obtaining reproducible experimental results. In nanotechnological experiments, methods for regulating the conformational polymorphism of nucleic acids and increasing sequence selectivity for base pairing of nucleic acids are important for developing nucleic acid-based nanomaterials. However, dearth of media that foster favourable behaviour of nucleic acids has been a bottleneck for promoting the biology and nanotechnology using the nucleic acids. Ionic liquids (ILs) are solvents that may be potentially used for controlling the properties of the nucleic acids. Here, we review researches regarding the behaviour of nucleic acids in ILs. The efficiency of extraction and purification of nucleic acids from biological samples is increased by IL addition. Moreover, nucleic acids in ILs show long-term stability, which maintains their structures and enhances nuclease resistance. Nucleic acids in ILs can be used directly in polymerase chain reaction and gene expression analysis with high efficiency. Moreover, the stabilities of the nucleic acids for duplex, triplex, and quadruplex (G-quadruplex and i-motif) structures change drastically with IL cation-nucleic acid interactions. Highly sensitive DNA sensors have been developed based on the unique changes in the stability of nucleic acids in ILs. The behaviours of nucleic acids in ILs detailed here should be useful in the design of nucleic acids to use as biological and nanotechnological tools.

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.

Effect of water and ionic liquids on biomolecules

The remarkable progress in the field of ionic liquids (ILs) in the last two decades has involved investigations on different aspects of ILs in various conditions. The nontoxic and biocompatible nature of ILs makes them a suitable substance for the storage and application of biomolecules. In this regard, the aqueous IL solutions have attracted a large number of studies to comprehend the role of water in modulating various properties of biomolecules. Here, we review some of the recent studies on aqueous ILs that concern the role of water in altering the behavior of ILs in general and in case of biomolecules solvated in ILs. The different structural and dynamic effects caused by water have been highlighted. We discuss the different modes of IL interaction that are responsible for stabilization and destabilization of proteins and enzymes followed by examples of water effect on this. The role of water in the case of nucleic acid storage in ILs, an area which has mostly been underrated, also has been emphasized. Our discussions highlight the fact that the effects of water on IL behavior are not general and are highly dependent on the nature of the IL under consideration. Overall, we aim to draw attention to the significance of water dynamics in the aqueous IL solutions, a better understanding of which can help in developing superior storage materials for application purposes.

Hydrated ionic liquids as a liquid chaperon for refolding of aggregated recombinant protein expressed in Escherichia coli

We have succeeded in refolding of aggregated recombinant protein from Escherichia coli in hydrated ionic liquids. In cholinium dihydrogen phosphate containing a limited amount of water molecules, aggregated solid cellulase was dissolved and refolding was successfully carried out without further processing.

Ionic liquid induced G-quadruplex formation and stabilization: spectroscopic and simulation studies

Among different polymorphs of DNA, G-quadruplex (GQ) formation in guanine rich sequences has received special attention due to its direct relevance to cellular aging and abnormal cell growths. To date, smaller ions like Na⁺, K⁺, Li⁺, and NH₄⁺ are the best possible selective GQ stabilizing materials. Herein, we report that an ionic liquid (IL), i.e. guanidinium tris(pentafluoroethyl)trifluorophosphate, can not only instigate the GQ formation in the absence of conventional GQ forming ions (like Na⁺, K⁺, NH₄⁺, etc.), but also stabilizes the GQ structure. This conformational transition has been confirmed through different spectroscopic tools and molecular dynamics (MD) simulation studies. MD simulation shows that one of the guanidinium cations resides in the G-tetrad core, while bulky anions prefer to stay near the GQ surface resulting in GQ formation and stabilization. This study thus brings out a special type of ionic liquid that acts as a GQ stabilizer. The origin of GQ stabilization by IL presented here may also help in the future design of IL for GQ formation and stabilization.

Aqueous ionic liquids and their effects on protein structures: an overview on recent theoretical and experimental results

Ionic liquids (ILs) are used in a variety of technological and biological applications. Recent experimental and simulation results reveal the influence of aqueous ionic liquids on the stability of protein and enzyme structures. Depending on different parameters like the concentration and the ion composition, one can observe distinct stabilization or denaturation mechanisms for various ILs. In this review, we summarize the main findings and discuss the implications with regard to molecular theories of solutions and specific ion effects. A preferential binding model is introduced in order to discuss protein-IL effects from a statistical mechanics perspective. The value of the preferential binding coefficient determines the strength of the ion influence and indicates a shift of the chemical equilibrium either to the native or the denatured state of the protein. We highlight the role of water in order to explain the self-association behavior of the IL species and discuss recent experimental and simulation results in the light of the observed binding effects.

Ionic-Liquid-Mediated Extraction and Separation Processes for Bioactive Compounds: Past, Present, and Future Trends

Ionic liquids (ILs) have been proposed as promising media for the extraction and separation of bioactive compounds from the most diverse origins. This critical review offers a compilation on the main results achieved by the use of ionic-liquid-based processes in the extraction and separation/purification of a large range of bioactive compounds (including small organic extractable compounds from biomass, lipids, and other hydrophobic compounds, proteins, amino acids, nucleic acids, and pharmaceuticals). ILs have been studied as solvents, cosolvents, cosurfactants, electrolytes, and adjuvants, as well as used in the creation of IL-supported materials for separation purposes. The IL-based processes hitherto reported, such as IL-based solid-liquid extractions, IL-based liquid-liquid extractions, IL-modified materials, and IL-based crystallization approaches, are here reviewed and compared in terms of extraction and separation performance. The key accomplishments and future challenges to the field are discussed, with particular emphasis on the major lacunas found within the IL community dedicated to separation processes and by suggesting some steps to overcome the current limitations.

Quantitative assessment of kosmotropicity of hydrated ionic liquids by nuclear magnetic resonance

The NMR chemical shift variation of H₂O varied with the component ion and reflected the kosmotropicity quantitatively in hydrated ionic liquids.

G-quadruplex DNA-based asymmetric catalysis of michael addition: Effects of sonication, ligands, and co-solvents

There is an escalating interest of using double stranded DNA molecules as a chiral scaffold to construct metal-biomacromolecule hybrid catalysts for asymmetric synthesis. Several recent studies also evaluated the use of G-quadruplex DNA-based catalysts for asymmetric Diels-Alder and Friedel-Crafts reactions. However, there is still a lack of understanding of how different oligonucleotides, salts (such as NaCl and KCl), metal ligands and co-solvents affect the catalytic performance of quadruplex DNA-based hybrid catalysts. In this study, we aim to systematically evaluate these key factors in asymmetric Michael addition reactions, and to examine the conformational and molecular changes of DNA by circular dichroism (CD) spectroscopy and gel electrophoresis. We achieved up to 95% yield and 50% enantiomeric excess (ee) when the reaction of 2-acylimidazole 1a and dimethylmalonate was catalyzed by 5'-G3 (TTAG3 )3 -3' (G4DNA1) in 20 mM MOPS (pH 6.5) containing 50 mM KCl and 40 µM [Cu(dmbipy)(NO3 )2 ], and G4DNA1 was pre-sonicated in ice bath for 10 min prior to the reaction. G-quadruplex-based hybrid catalysts provide a new tool for asymmetric catalysis, but future mechanistic studies should be sought to further improve the catalytic efficiency. The current work presents a systematic study of asymmetric Michael addition catalyzed by G-quadruplex catalysts constructed via non-covalent complexing, and an intriguing finding of the effect of pre-sonication on catalytic efficiency. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:891-898, 2016.

DNA sensor's selectivity enhancement and protection from contaminating nucleases due to a hydrated ionic liquid

The thermodynamic stability of certain mismatched base pairs has made the development of DNA sequence sensing systems challenging. Thus, the stability of fully matched and mismatched DNA oligonucleotides in the hydrated ionic liquid choline dihydrogen phosphate (choline dhp) was investigated. Mismatched base pairs were significantly destabilized in choline dhp relative to those in aqueous buffer. A molecular beacon that forms a triplex with a conserved HIV-1 sequence was then designed and tested in choline dhp. The molecular beacon specifically detected the target duplex via triplex formation at concentrations as low as 1 pmol per 10 μL with 10,000-fold sequence selectivity. Moreover, the molecular beacon was protected from a contaminating nuclease in choline dhp, and DNAs in aqueous solutions were not sufficiently stable for practical use.

Active biopolymers in green non-conventional media: a sustainable tool for developing clean chemical processes

By understanding structure–function relationships of active biopolymers (e.g. enzymes and nucleic acids) in green non-conventional media, sustainable chemical processes may be developed.

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.

Enhanced enzymatic degradation resistance of plasmid DNA in ionic liquids

Buffered ionic liquids can substantially enhance enzymatic degradation resistance of plasmid DNA, indicating the potential to serve as next-generation biological storage buffer at ambient temperature.

Inhibited fragmentation of mAbs in buffered ionic liquids

Choline-based buffered ionic liquids have been demonstrated to greatly inhibit enzymatic degradation of antibodies, and are promising as next-generation biological buffers.

Non-natural G-quadruplex in a non-natural environment

The biocompatibility as well as the sustainability of a deep eutectic solvent makes it a good substitute for aqueous media in studying biomolecules. Understanding the structure and stability of natural and non-natural G-quadruplexes in aqueous and highly viscous media will be useful in biological and nanodevice applications. We report the synthesis and conformational analysis of a model G-rich oligonucleotide G3T3 and non-natural G-rich sequences Pyr1-Pyr3 in aqueous and highly viscous media. Progressive increases in the loop replacement with a non-natural pyrene linker leads to a systematic increase of the thermal denaturation temperature of the modified G-rich oligonucleotides Pyr1-Pyr3 in 10 mM cacodylate buffer (pH 7.2) containing 100 mM KCl, as monitored using UV-Vis spectroscopy. A circular dichroism signal clearly revealed the formation of a predominantly anti-parallel vs. parallel conformation in the natural G-rich oligonucleotide G3T3 as well as the non-natural G-rich oligonucleotides Pyr1-Pyr3 in 10 mM cacodylate buffer (pH 7.2) containing 100 mM KCl. On the other hand, we observed thermodynamic destabilization of G-rich oligonucleotides in a deep eutectic solvent (DES; 1 : 2 choline chloride-urea) containing 100 mm KCl with an increase in loop replacements. Interestingly, we observed an exclusively parallel G-quadruplex conformation in the case of G3T3 in DES containing 100 mm KCl. While pyrene containing G-rich oligonucleotides Pyr1-Pyr3 exhibited a predominantly parallel vs. anti-parallel G-quadruplex conformation in DES containing 100 mM KCl.

Structure, stability and behaviour of nucleic acids in ionic liquids

Nucleic acids have become a powerful tool in nanotechnology because of their conformational polymorphism. However, lack of a medium in which nucleic acid structures exhibit long-term stability has been a bottleneck. Ionic liquids (ILs) are potential solvents in the nanotechnology field. Hydrated ILs, such as choline dihydrogen phosphate (choline dhp) and deep eutectic solvent (DES) prepared from choline chloride and urea, are 'green' solvents that ensure long-term stability of biomolecules. An understanding of the behaviour of nucleic acids in hydrated ILs is necessary for developing DNA materials. We here review current knowledge about the structures and stabilities of nucleic acids in choline dhp and DES. Interestingly, in choline dhp, A-T base pairs are more stable than G-C base pairs, the reverse of the situation in buffered NaCl solution. Moreover, DNA triplex formation is markedly stabilized in hydrated ILs compared with aqueous solution. In choline dhp, the stability of Hoogsteen base pairs is comparable to that of Watson-Crick base pairs. Moreover, the parallel form of the G-quadruplex is stabilized in DES compared with aqueous solution. The behaviours of various DNA molecules in ILs detailed here should be useful for designing oligonucleotides for the development of nanomaterials and nanodevices.

Comparable stability of Hoogsteen and Watson-Crick base pairs in ionic liquid choline dihydrogen phosphate

The instability of Hoogsteen base pairs relative to Watson-Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson-Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson-Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo.

G-quadruplexes form ultrastable parallel structures in deep eutectic solvent

G-quadruplex DNA is highly polymorphic. Its conformation transition is involved in a series of important life events. These controllable diverse structures also make G-quadruplex DNA a promising candidate as catalyst, biosensor, and DNA-based architecture. So far, G-quadruplex DNA-based applications are restricted done in aqueous media. Since many chemical reactions and devices are required to be performed under strictly anhydrous conditions, even at high temperature, it is challenging and meaningful to conduct G-quadruplex DNA in water-free medium. In this report, we systemically studied 10 representative G-quadruplexes in anhydrous room-temperature deep eutectic solvents (DESs). The results indicate that intramolecular, intermolecular, and even higher-order G-quadruplex structures can be formed in DES. Intriguingly, in DES, parallel structure becomes the G-quadruplex DNA preferred conformation. More importantly, compared to aqueous media, G-quadruplex has ultrastability in DES and, surprisingly, some G-quadruplex DNA can survive even beyond 110 °C. Our work would shed light on the applications of G-quadruplex DNA to chemical reactions and DNA-based devices performed in an anhydrous environment, even at high temperature.