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.

Figure 1.

(a) Types of base pairs in nucleic acids. The triplet is drawn based on the assumption of acidic conditions; N3 of cytosine is protonated. (b) Structures of nucleic acids for duplex, triplex and G-quadruplex.

Figure 2.

The chemical structure of (a) choline dhp and (b) the DES for a mixture of choline chloride (2-hydroxyethyl-trimethylammonium chloride) and urea in a 1:2 molar ratio.

Figure 3.

Normalized UV melting curves for ODN1 (open circles), ODN2 (closed squares), ODN3 (open triangles), ODN4 (closed circles), ODN5 (open squares) and ODN6 (closed triangles) in solution containing 50 mM MES (pH 6.0), 1 mM Na2EDTA and (a) 4 M NaCl or (b) 4 M choline dhp. DNA strand concentration was 5 μM. (Permission for use was received (48)).

Figure 4.

Sequences and schematic structures of (a) triplexes (Ts1, Ts2, Ts3 and iTs1) and (b) duplexes (Ds1, Ds2, Ds3 and iDs1). Filled and open circles indicate Watson–Crick and Hoogsteen base pairs, respectively.

Figure 5.

Thermal stability of DNA triplexes. Normalized UV melting curves at 260 nm for Ts1 (blue), Ts2 (green) and Ts3 (red) in (a) 4 M NaCl solution and (b) 4 M choline dhp solution. Solutions also contained 50 mM Tris (pH 7.0) and 1 mM Na₂EDTA. Total DNA strand concentration was 30 μM .

Figure 6.

Choline ions buried in the minor groove of ODN1. DNA atoms are shown as grey spheres. Carbon atoms of choline ions are shown in yellow, oxygen atoms of choline ions are shown in red and hydrogen atoms are shown in white (68).

Figure 7.

(a) The bases of the triplet of T–A*T. (b) The structure of Ts1 as depicted by the van der Waals model. First (5′-TTTTTTTCTTCT-3′), second (5′-AGAAGAAAAAAA-3′) and third (5′-TCTTCTTTTTTT-3′) strands are indicated by light blue, light green and pink, respectively.

Figure 8.

Choline ion binding to the triplex estimated by MD simulations. A snapshot of Ts1 after 20-ns MD simulations in the (a) absence or (b) presence of choline ions. First (5′-TTTTTTTCTTCT-3′), second (5′-AGAAGAAAAAAA-3′) and third (5′-TCTTCTTTTTTT-3′) strands in Ts1 are indicated by light blue, light green and pink, respectively. Ts1 and choline ions (yellow) are depicted as van der Waals models. The choline ions bound to the minor grove and major part of the major groove in Ts1 are highlighted in (c) and (d), respectively. The choline ions surrounding the third strand in Ts1 are highlighted in (e) .

Figure 9.

G-quadruplex folding depends on a solution with (a) low viscosity and (b) high viscosity (85).