Local and cooperative structural transitions of double-stranded DNA in choline-based deep eutectic solvents

The possibility of using deep eutectic solvents (DESs) as co-solvents for stabilizing and preserving the native structure of DNA provides an attractive opportunity in the field of DNA biotechnology. The rationale of this work is a systematic investigation of the effect of hydrated choline-based DES on the structural stability of a 30-base-pair double-stranded DNA model via a combination of spectroscopic experiments and MD simulations. UV absorption and CD experiments provide evidence of a significant contribution of DESs to the stabilization of the double-stranded canonical (B-form) DNA structure. Multi-wavelength synchrotron UV Resonance Raman (UVRR) measurements indicate that the hydration shell of adenine-thymine pairs is strongly perturbed in the presence of DESs and that the preferential interaction between H-bond sites of guanine residues and DESs is significantly involved in the stabilization of the dsDNA. Finally, MD calculations show that the minor groove of DNA is significantly selective for the choline part of the investigated DESs compared to the major groove. This finding is likely to have a significant impact not only in terms of thermal stability but also in the modulation of ligand-DNA interactions.

Constituent- and Composition-Dependent Surfactant Aggregation in (Lanthanide Salt + Urea) Deep Eutectic Solvents

Due to the ease of tailoring the physicochemical properties by simply changing a constituent or composition, deep eutectic solvents (DESs) possess widely varying capabilities for surfactant self-assembly that could depend on the surfactant headgroup charge. The self-aggregation process of three surfactants, sodium dodecylsulfate (SDS), cetyltrimethylammonium bromide (CTAB), and Triton X-100 (TX-100), dissolved in DESs composed of a lanthanide salt (Ln) and urea (U) is investigated. The role of the identity of the metal salt is assessed by using [La(NO₃)₃·6H₂O] (La) and [Ce(NO₃)₃·6H₂O] (Ce) and that of the composition is deciphered by systematically changing the mole ratio of the metal salt and urea in (La/U) DESs. The response to a fluorescence probe pyrene-1-carboxaldehyde along with electrical conductance and surface tension measurements is used to obtain the critical aggregation concentration (CAC). While the CACs in 1:3.5 (Ln/U) for SDS are significantly lower than that in water, the values are marginally higher for CTAB and TX-100. The CACs for all three surfactants are similar in 1:3.5 (La/U) and (Ce/U) DESs, implying that the identity of the metal in the salt is not so important. Increasing the urea composition in (La/U) DESs results in increased CAC for SDS and CTAB; however, a minimal decrease in CAC is observed for TX-100. From the temperature dependence of CAC, thermodynamic parameters, ΔG_agg⁰, ΔH_agg⁰, and ΔS_agg⁰, of the surfactant self-aggregation process are estimated. These parameters reveal that while at a lower urea content, the SDS/CTAB self-assembly process is enthalpically driven, it becomes entropically favored at higher urea concentrations. The TX-100 self-aggregation in these DESs is found to be strongly enthalpically favored and entropically un-favored. These parameters are explained as a combination of passage of the solvophobic surfactant chain from the bulk DES to the aggregate pseudo-phase and differential orientation/organization of DES constituents around surfactant monomers and/or aggregates.

Time-Dependent Hydrogen Bond Network Formation in Glycerol-Based Deep Eutectic Solvents

Over the last few years, Deep Eutectic Solvents have gained popularity as a novel class of green solvents, due to their feasible synthesis and overall low production costs. The properties of glycerol (Gly)-based Deep Eutectic Solvents are frequently associated with the formation of an extended hydrogen bond network. In this study, two-dimensional Nuclear Magnetic Resonance (NMR) spectroscopy is employed to analyse the effect of glycerol oversaturation of the hydrogen bond acceptor, choline chloride (ChCl) on the structural arrangement of glyceline (molar ratio 1 : 2 ChCl:Gly), selected to represent Gly-based Deep Eutectic Solvents. The rearrangement of glycerol molecules, additionally trapping water molecules inside of isolated clusters, is revealed during a time-resolved analysis, performed in the presence of various fractions of water added to solvent. 200 % oversaturated Deep Eutectic Solvent (1 : 4 ChCl:Gly) is found to be a suitable cryoprotectant candidate, based on the revealed glycerol-water interactions.

Green approaches in synthesising nanomaterials for environmental nanobioremediation: Technological advancements, applications, benefits and challenges

Green synthesis approaches of nanomaterials (NMs) have received considerable attention in recent years as it addresses the sustainability issues posed by conventional synthesis methods. However, recent works of literature do not present the complete picture of biogenic NMs. This paper addresses the previous gaps by providing insights into the stability and toxicity of NMs, critically reviewing the various biological agents and solvents required for synthesis, sheds light on the factors that affect biosynthesis, and outlines the applications of NMs across various sectors. Despite the advantages of green synthesis, current methods face challenges with safe and appropriate solvent selection, process parameters that affect the synthesis process, nanomaterial cytotoxicity, bulk production and NM morphology control, tedious maintenance, and knowledge deficiencies. Consequently, the green synthesis of NMs is largely trapped in the laboratory phase. Nevertheless, the environmental friendliness, biocompatibility, and sensitivities of the resulting NMs have wider applications in biomedical science, environmental remediation, and consumer industries. To the scale-up application of biogenic NMs, future research should be focused on understanding the mechanisms of the synthesis processes, identifying more biological and chemical agents that can be used in synthesis, and developing the practicality of green synthesis at the industrial scale, and optimizing the factors affecting the synthesis process.

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.

Self-Assembled Porphyrazine Nucleosides on DNA Templates: Highly Fluorescent Chromophore Arrays and Sizing Forensic Tandem Repeat Sequences

The formation of chromophore arrays using a DNA templating approach leads to the creation of supramolecular assemblies, where the optical properties of the overall system can be fine-tuned to a large extent. In particular, porphyrin derivatives have been shown to be versatile building blocks; mostly covalent chemistry was used for embedding the units into DNA strands. Self-assembly of porphyrin modified nucleosides, on the other hand, has not been investigated as a simplified approach. We report on the synthesis of a magnesium(II) tetraaza porphine (MgTAP) coupled to deoxyuridine, and array formation on DNA templates which contain well-defined oligo(dA) segments showing strong fluorescence enhancement which is significantly larger than that with a Zn-porphyrin. The use of the deep-eutectic solvent glycholine is essential for successful assembly formation. The system allows for sizing of short tandem repeat markers with multiple adenosines, thus the concept could be adaptable to in vitro forensic DNA profiling with a suitable set of different chromophores on all nucleosides.

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.