Development of new DNA nano-switches based on the stabilization of A-T base pairs relative to G-C base pairs

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We attempted the control of stabilities of Watson-Crick base pairs using a hydrated ionic liquid (IL) of choline dihydrogen phosphate (choline dhp), because hydrated ILs are green solvents suitable for a wide range of chemical reactions and may ensure long-term stability of biomolecules. Our quantitative analysis demonstrated that A-T base pairs are more stable than G-C base pairs in 4 M choline dhp. We also found that DNA triplex structures via the formation of Hoogsteen base pairs were significantly stabilized in the choline dhp solution compared to NaCl solutions. Thermodynamic analyses and molecular dynamics calculations revealed that the stabilization of A-T base pairs and Hoogsteen base pairs was due to specific binding of choline ions to DNA grooves. To take advantage of the stabilization of triplex formations to develop the sensing systems of double-stranded DNAs, we designed a DNA molecular beacon and found that the molecular beacon can specifically detect the target duplex.