Structure, stability and behaviour of nucleic acids in ionic liquids

Abstract

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.

Interaction studies of cholinium-based ionic liquids with calf thymus DNA: Spectrophotometric and computational methods

“…3b and 3c depict the H-bonding and hydrophobic interactions between the DNA and cholinium ion. It has been found that the cholinium ion preferred to enter minor groove region rich in AT base, which is in line with the previous work [26,30]. Notably, the presence of polar groups (hydroxy) and non-polar fragment (methyl) in cholinium ion assist in the interaction with DNA.…”

“…A similar observation has been made by Wand and co-workers [24]. Recently, Sugimoto and co-workers [26,30] studied the interaction of cholinium dihydrogenphosphate ([Ch]DHP) with oligodeoxynucleotides using melting temperatures measurement and MD simulations. Much useful information has been extracted at supramolecular level in this study.…”

“…Combining these two, several articles have been published describing the interaction of DNA with imidazolium, morpholinium, etc. based ILs [21][22][23][24][25][26][27][28][29]. For example, Liu and co-workers studied the impact of alkyl chain length present on imidazolium-based ILs [23] towards ct-DNA through extensive photophysical methods.…”

Solvation Structure of Uracil in Ionic Liquids

“…Consequently, the observation that both the cation and anion of the IL solvent have key contributions to the solvation of nucleobases is both expected and notably different to cases with carbohydrates and sugars and builds an elegant picture of the dissolution mechanism of nucleobases, requiring co-operative solvation by both ions of the ionic liquid. In order to understand, for instance, the structure and solvation of biomolecules in solvated in ionic liquids (a growing area of research owing to the stabilising properties of the IL), [23] a practical starting point is the individual nucleic acid bases, for which the precise solvation details can be more easily extracted.…”

i-Motifs are more stable than G-quadruplexes in a hydrated ionic liquid

“…17 Ionic liquids (ILs) have been used as solvents in the field of nanotechnology and are a good media for development of DNA materials because they provide favourable environments for a wide range of chemical reactions and are environmentally friendly solvents. [26][27][28] We hypothesized that the presence of the hydrated IL could impact the stability of C-C + base pairs in i-motif tetraplexes. 22 A representative IL, choline dihydrogen phosphate (choline dhp), dissolved in a small amount of water (B20 wt%) ensures long-term stability of biomolecules like DNA and proteins.…”