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

我们尝试使用磷酸二氢胆碱（choline dhp）的水合离子液体（IL）来控制沃森-克里克碱基对的稳定性，因为水合离子液体是适合于广泛的化学反应的绿色溶剂，并且可以确保生物分子的长期稳定性。我们的定量分析表明，在4 M胆碱dhp中，A-T碱基对比G-C碱基对更稳定。我们还发现，DNA三链体结构通过形成Hoogsteen碱基对显着稳定的胆碱dhp溶液相比，NaCl溶液。热力学分析和分子动力学计算表明，胆碱离子与DNA沟的特异性结合是A-T碱基对和Hoogsteen碱基对稳定化的原因。为了利用三链体形成的稳定性来开发双链DNA的传感系统，我们设计了一种DNA分子信标，并发现该分子信标可以特异性地检测目标双链体。

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.