Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
1] Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan [2] Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
Sci Rep. 2014 Jan 8;4:3593. doi: 10.1038/srep03593.
The instability of Hoogsteen base pairs relative to Watson-Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson-Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson-Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo.
Hoogsteen 碱基对相对于 Watson-Crick 碱基对的不稳定性限制了三链体形成寡核苷酸在生物学上的应用。水合离子液体 (IL) 为广泛的化学反应提供了有利的环境，并且已知会影响 Watson-Crick 碱基对的稳定性。我们发现，与中性 pH 的水性缓冲液相比，水合磷酸二氢胆碱中 DNA 三链体的形成显著稳定。有趣的是，在水合 IL 中，Hoogsteen 碱基对的稳定性被发现与 Watson-Crick 碱基对相当。在存在胆碱离子的情况下，对 DNA 三链体的分子动力学模拟表明，由于第三链在沟中的周围结合了胆碱离子，因此 DNA 三链体得到稳定。我们的发现将有助于开发新的 DNA 材料。我们的数据还表明，在细胞内，当细胞内胆碱离子及其衍生物丰富时，三链体的形成可能会得到稳定。
