DNA and RNA in Anhydrous Media: Duplex, Triplex, and G-Quadruplex Secondary Structures in a Deep Eutectic Solvent

DNA G-quadruplexes are uniquely stable in the presence of denaturants and monovalent cations

Ions in the Hofmeister series exhibit varied effects on biopolymers. Those classed as kosmotropes generally stabilize secondary structure, and those classed as chaotropes generally destabilize secondary structure. Here, we report that several anionic chaotropes exhibit unique effects on one DNA secondary structure - a G quadruplex. These chaotropes exhibit the expected behaviour (destabilization of secondary structure) in two other structural contexts: a DNA duplex and i-Motifs. Uniquely among secondary structures, we observe that G quadruplexes are comparatively insensitive to the presence of anionic chaotropes, but not other denaturants. Further, the presence of equimolar NaCl provided greater mitigation of the destabilization caused by other non-anionic denaturants. These results are consistent with the presence of monovalent cations providing an especially pronounced stabilizing effect to G quadruplexes when studied in denaturing solution conditions.

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G-quadruplexes exhibit the lowest sensitivity to denaturation by anionic chaotropes among several DNA secondary structures.

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In G-quadruplexes, the destabilizing effect of other denaturants is uniquely well-mitigated by the presence of sodium ions.

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This phenomenon affords a structure-specific means of modulating nucleic acid folding.

Urea and Acetamide Rich Solutions Circumvent the Strand Inhibition Problem to Allow Multiple Rounds of DNA and RNA Copying

For decades prebiotic chemists have attempted to achieve replication of RNA under prebiotic conditions with only limited success. One of the long-recognized impediments to achieving true replication of a duplex (copying of both strands) is the so-called strand inhibition problem. Specifically, while the two strands of an RNA (or DNA) duplex can be separated by heating, upon cooling the strands of a duplex will reanneal before mononucleotide or oligonucleotide substrates can bind to the individual strands. Here we demonstrate that a class of plausible prebiotic solvents, when coupled with thermal cycling and varying levels of hydration, circumvents the strand inhibition problem, and allows multiple rounds of information transfer from both strands of a duplex (replication). Replication was achieved by simultaneous ligation of oligomers that bind to their templates with the aid of the solvents. The solvents used consisted of concentrated solutions of urea and acetamide in water (UAcW), components that were likely abundant on the early Earth. The UAcW solvent system favors the annealing of shorter strands over the re-annealing of long strands, thereby circumventing strand inhibition. We observed an improvement of DNA and RNA replication yields by a factor of 100× over aqueous buffer. Information transfer in the UAcW solvent system is robust, being achieved for a range of solvent component ratios, various drying conditions, and in the absence or presence of added salts.

Experimental and Theoretical Study on Theobromine Solubility Enhancement in Binary Aqueous Solutions and Ternary Designed Solvents

The solubility of theobromine was studied both experimentally and theoretically. The solubility was determined spectrophotometrically at 25 °C in neat organic solvents, aqueous binary mixtures, Natural Deep Eutectic Solvents (NADES) and ternary NADES mixtures with water. It was found that addition of water in unimolar proportions with some organic solvents increases theobromine solubility compared to neat solvents. Additionally, using NADES results in a solubility increase of the studied compound not only in relation to water but also DMSO. The addition of water (0.2 molar fraction) to NADES is responsible for an even larger increase of solubility. The measured solubilities were interpreted in terms of three theoretical frameworks. The first one-belonging to the set of data reduction techniques-proved to be very efficient in quantitative back-computations of excess solubility of theobromine in all studied systems. The default approach utilizing the well-recognized COSMO-RS (Conductor-like Screening Model for Real Solvents) framework offered at most a qualitative solubility description. The extended search for possible contacts provided evidence for the existence of many intermolecular complexes that alter the electron density of the solute molecule, thus influencing solubility computations. Taking into account such intermolecular contacts by using the COSMO-RS-DARE (Conductor-like Screening Model for Realistic Solvation-Dimerization, Aggregation, and Reaction Extension) framework seriously increased the accuracy of solubility computations.

Functional Nucleic Acids Under Unusual Conditions

Functional nucleic acids (FNAs), including naturally occurring ribozymes and riboswitches as well as artificially created DNAzymes and aptamers, have been popular molecular toolboxes for diverse applications. Given the high chemical stability of nucleic acids and their ability to fold into diverse sequence-dependent structures, FNAs are suggested to be highly functional under unusual reaction conditions. This review will examine the progress of research on FNAs under conditions of low pH, high temperature, freezing conditions, and the inclusion of organic solvents and denaturants that are known to disrupt nucleic acid structures. The FNA species to be discussed include ribozymes, riboswitches, G-quadruplex-based peroxidase mimicking DNAzymes, RNA-cleaving DNAzymes, and aptamers. Research within this space has not only revealed the hidden talents of FNAs but has also laid important groundwork for pursuing these intriguing functional macromolecules for unique applications.

Solvent Screening for Solubility Enhancement of Theophylline in Neat, Binary and Ternary NADES Solvents: New Measurements and Ensemble Machine Learning

Theophylline, a typical representative of active pharmaceutical ingredients, was selected to study the characteristics of experimental and theoretical solubility measured at 25 °C in a broad range of solvents, including neat, binary mixtures and ternary natural deep eutectics (NADES) prepared with choline chloride, polyols and water. There was a strong synergistic effect of organic solvents mixed with water, and among the experimentally studied binary systems, the one containing DMSO with water in unimolar proportions was found to be the most effective in theophylline dissolution. Likewise, for NADES, the addition of water (0.2 molar fraction) resulted in increased solubility compared to pure eutectics, with the highest solubilisation potential offered by the composition of choline chloride with glycerol. The ensemble of Statistica Automated Neural Networks (SANNs) developed using intermolecular interactions in pure systems has been found to be a very accurate model for solubility computations. This machine learning protocol was also applied as an extensive screening for potential solvents with higher solubility of theophylline. Such solvents were identified in all three subgroups, including neat solvents, binary mixtures and ternary NADES systems. Some methodological considerations of SANNs applications for future modelling were also provided. Although the developed protocol is focused exclusively on theophylline solubility, it also has general importance and can be used for the development of predictive models adequate for solvent screening of other compounds in a variety of systems. Formulation of such a model offers rational guidance for the selection of proper candidates as solubilisers in the designed solvents screening.

Understanding The Role of Reline, a Natural DES, on Temperature-Induced Conformational Changes of C-Kit G-Quadruplex DNA: A Molecular Dynamics Study

The noncanonical guanine-rich DNAs have drawn particular attention to the scientific world due to their controllable diverse and polymorphic structures. Apart from biological and medical significance, G-quadruplex DNAs are widely used in various fields such as nanotechnology, nanomachine, biosensors, and biocatalyst. So far, the applications of the G-quadruplex DNA are mainly limited in the water medium. Recently, a new generation of solvent named deep eutectic solvent (DES) has become very popular and has been widely used as a reaction medium of biocatalytic reactions and long-term storage medium for nucleic acids, even at high temperature. Hence, it is essential to understand the role of DES on temperature-induced conformational changes of a G-quadruplex DNA. In this research work, we have explored the temperature-mediated conformational dynamics of c-kit oncogene promoter G-quadruplex DNA in reline medium in the temperature range of 300-500 K, using a total of 10 μs unbiased all-atom molecular dynamics simulation. Here, from RMSD, RMSF, R_g and principal component analyses, we notice that the c-kit G-quadruplex DNA is stable up to 450 K in reline medium. However, it unfolds in water medium at 450 K. It is found that the hydrogen bonding interactions between c-kit G-quadruplex DNA and reline play a key role in the stabilization of the G-quadruplex DNA even at high temperature. Furthermore, in this work we have observed a very interesting and distinctive phenomenon of the central cation of the G-quadruplex DNA. Its position was seen to fluctuate between the two tetrad cores, that is, the region between tetrad-1 and tetrad-2 and that between tetrad-2 and tetrad-3 and vice versa at 450 and 500 K in reline medium which is absent in water medium at 450 K. Moreover, the rate of its oscillation is increased when temperature is increased.

Optimization, thermodynamic characteristics and solubility predictions of natural deep eutectic solvents used for sulfonamide dissolution

The limited water solubility of sulfonamides provokes a search for new solvents offering not only increased solubility but also environmental and health safety. Therefore, six sulfonamides were studied in a series of natural deep eutectic solvents (NADES) comprising choline chloride with multi-hydroxyl compounds. Experimental screening aimed at finding the optimized NADES composition revealed that unimolar proportion of choline chloride and glycerol offers the highest solubility advantage, equal up to 43 times compared with water at 37 °C. Besides, quantum chemistry computations based on the COSMO-RS protocol were conducted in order to gain an insight into the thermodynamic characteristics of the systems and to explain the origin of the observed solubility increase. It was found that the factor responsible for the solubility gain in NADES are the interactions between choline chloride and sulfonamide drug molecules, having the highest affinities expressed in terms of Gibbs free energy of corresponding reactions. Finally, utilizing the obtained results together with artificial neural networks led to a perfect match between experimental and predicted solubility, documented by the mean absolute percentage error value below 2.5%. The developed protocol seems to be so general and accurate that screening of potential new API-NADES systems can be significantly simplified.

Solubility advantage of sulfanilamide and sulfacetamide in natural deep eutectic systems: experimental and theoretical investigations

Objective: The aim of this study was to explore the possibility of using natural deep eutectic solvents (NADES) as solvation media for enhancement of solubility of sulfonamides, as well as gaining some thermodynamic characteristics of the analyzed systems. Significance: Low solubility of many active pharmaceutical ingredients is a well-recognized difficulty in pharmaceutical industry, hence the need for different strategies addressing this problem. Among such strategies, those that are environmentally and economically beneficial are of particular interest. Methods: The solubility of sulfanilamide and sulfacetamide in 21 different NADES compositions comprising choline chloride with sugars or sugar alcohols was measured spectrophotometrically. Thermodynamic parameters describing the studied systems were determined using the COSMO-RS computational protocol. Results: All of the considered NADES compositions gave an increase in solubility of the studied sulfonamides, with the highest solubilities obtained for the system comprising choline chloride and glycerol in unimolar proportions, which gave a solubility advantage of 83.7 and 73.8 for sulfanilamide and sulfacetamide, respectively. Theoretical studies indicated that the dissolution of both considered sulfonamides has a low endothermic character, with the lowest enthalpy values obtained for the most optimal, i.e. unimolar, proportions. The non-monotonous trend of enthalpy of dissolution was also discussed in terms of intermolecular interactions. Conclusions: The obtained results show the feasibility of using NADES as solubility enhancers for sulfonamides and encourage for further exploration in this field.

Selection of Anti-gluten DNA Aptamers in a Deep Eutectic Solvent

Herein, we show the feasibility of using deep eutectic solvents as a faster way of selecting aptamers targeting poorly water-soluble species. This unexplored concept is illustrated for gluten proteins. In this way, aptamer-based gluten detection can be performed directly in the extraction media with improved detectability. We envision deep implications for applications not only in food safety control but also in biomedicine.

Self-assembly and surface behaviour of pure and mixed zwitterionic amphiphiles in a deep eutectic solvent

Recent investigations have shown that deep eutectic solvents provide a suitable environment for self-organisation of biomolecules, in particular phospholipids and proteins. However, the solvation of complex lyophilic moieties by deep eutectic solvents still remains unclear. Here we explore the behaviour of zwitterionic surfactants in choline chloride:glycerol eutectic mixture. Dodecyl-2-(trimethylammonio)ethylphosphate and N-alkyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (alkyl = dodecyl, tetradecyl) surfactants were investigated by means of surface tension, X-ray reflectivity and small-angle neutron scattering. These surfactants were found to remain surface active and form globular micelles in deep eutectic solvents. Still, the surface behaviour of these species was found to differ depending on the headgroup and tail structure. The morphology of the micelles also slightly varies between surfactants, demonstrating differences in the packing of individual monomers. The characteristics of mixtures of the dodecyl surfactants is also reported, showing a deviation from ideal mixing associated with attractive interactions between sulfobetaine and phosphocholine headgroups. Such non-ideality results in variation of the surface behaviour and self-assembly of these surfactant mixtures. The results presented here will potentially lead to the development of new alternatives for drug-delivery, protein solubilisation and biosensing through a better fundamental understanding of the behaviour of zwitterionic surfactants in deep eutectic solvents.

Application of a computational model of natural deep eutectic solvents utilizing the COSMO-RS approach for screening of solvents with high solubility of rutin

The screening of natural deep eutectic solvents (NADES) to identify those with the ability to strongly solvate rutin was conducted using the COSMO-RS methodology. A NADES model was constructed that took into account the possible ionic and neutral forms of its constituents. The distributions of all forms were computed based on the equilibrium constants of neutralization reactions between amino and carboxylic acids. The proposed model was validated against the experimental solubilities of 15 NADES. A linear relationship between these data and the estimated activity coefficient values was found. The screening encompassed 126 different NADES. It was found that ten of them outperformed the best reference system. The most effective two-component solvent comprised proline combined with 2,3-diaminosuccinic acid, and the solubility of rutin in this solvent was found to be 130% greater than its solubility in the best reference system. The amino acids associated with the highest rutin solubilities were all cyclic, and the use of carboxylic acids with two carboxyl groups and a main chain consisting of two methylene groups with two amino substituents was observed to yield the best rutin solubilities. Because of the acidic properties of rutin, the presence of basic sites on the components of the NADES generally leads to enhanced solubility.

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 and properties of DNA in apolar solvents

The study of nucleic acids in low-polarity environments paves the way for novel biotechnological applications of DNA. Here, we use a repertoire of atomistic molecular simulation tools to study the nature of DNA when placed in a highly apolar environment and when transferred from aqueous to apolar solvent. Our results show that DNA becomes stiffer in apolar solvents and suggest that highly negatively charged states, which are the most prevalent in water, are strongly disfavored in apolar solvents and neutral states with conformations not far from the aqueous ones are the dominant forms. Transfer from water to an apolar solvent such as CCl₄ is unlikely to occur, but our results suggest that if forced, the DNA would migrate surrounded by a small shell of water (the higher the DNA charge, the larger the number of water molecules in this shell). Even the neutral form (predicted to be the dominant one in apolar solvents) would surround itself by a small number of highly stable water molecules when moved from water to a highly apolar environment. Neutralization of DNA charges seems a crucial requirement for transfer of DNA to apolar media, and the most likely mechanism to achieve good transfer properties.

MD and NMR analyses of choline and TMA binding to duplex DNA: on the origins of aberrant sequence-dependent stability by alkyl cations in aqueous and water-free solvents

It has been known for decades that alkylammonium ions, such as tetramethyl ammonium (TMA), alter the usual correlation between DNA GC-content and duplex stability. In some cases it is even possible for an AT-rich duplex to be more stable than a GC-rich duplex of the same length. There has been much speculation regarding the origin of this aberration in sequence-dependent DNA duplex stability, but no clear resolution. Using a combination of molecular dynamics simulations and NMR spectroscopy we demonstrate that choline (2-hydroxy-N,N,N-trimethylethanaminium) and TMA are preferentially localized in the minor groove of DNA duplexes at A·T base pairs and these same ions show less pronounced localization in the major groove compared to what has been demonstrated for alkali and alkali earth metal ions. Furthermore, free energy calculations show that single-stranded GC-rich sequences exhibit more favorable solvation by choline than single-stranded AT-rich sequences. The sequence-specific nature of choline and TMA binding provides a rationale for the enhanced stability of AT-rich sequences when alkyl-ammonium ions are used as the counterions of DNA. Our combined theoretical and experimental study provides one of the most detailed pictures to date of cations localized along DNA in the solution state, and provides insights that go beyond understanding alkyl-ammonium ion binding to DNA. In particular, because choline and TMA bind to DNA in a manner that is found to be distinct from that previously reported for Na(+), K(+), Mg(2+), and Ca(2+), our results reveal the important but underappreciated role that most other cations play in sequence-specific duplex stability.