Abstract：
Organic molecule-mediated noncanonical DNA self-assembly expands the standard DNA base-pairing alphabets. However, only a very limited number of small molecules have been recognized as mediators because of the tedious and complicated experiments like crystallization and microscopy imaging. Here we present an integrative screening protocol incorporating molecular dynamics (MD) for fast theoretical simulation and native polyacrylamide gel electrophoresis for convenient experimental validation. Melamine, the molecule that was confirmed mediating noncanonical DNA base-pairing, and 38 other candidate molecules were applied to demonstrate the feasibility of this protocol. We successfully identified seven stable noncanonical DNA duplex structures, and another eight novel structures with sub-stability. In addition, we discovered that hairpins at both ends can significantly stabilize the noncanonical DNA structures, providing a guideline to design small organic molecule-incorporated DNA structures. Such an efficient screening protocol will accelerate the design of alternative DNA-molecule architectures beyond Watson-Crick pairs. Considering the wide range of potential mediators, it will also facilitate applications such as noncovalent, highly dense loading of drug molecules in DNA-based delivery system and probe design for sensitive detection of certain molecules.
摘要：
有机分子介导的非规范DNA自组装扩展了标准DNA碱基配对字母。然而,只有非常有限数量的小分子已被认为是介质，因为繁琐和复杂的实验，如结晶和显微镜成像。在这里，我们提出了一种整合分子动力学（MD）的筛选方案，用于快速理论模拟和天然聚丙烯酰胺凝胶电泳，以方便实验验证。三聚氰胺,被证实介导非规范DNA碱基配对的分子，和38个其他候选分子被用来证明这个方案的可行性。我们成功鉴定出7个稳定的非规范DNA双链体结构,和另外八个具有亚稳定性的新颖结构。此外,我们发现两端的发夹可以显著稳定非规范DNA结构，为设计有机小分子掺入的DNA结构提供指导。这种有效的筛选方案将加速超越Watson-Crick对的替代DNA-分子架构的设计。考虑到广泛的潜在中介，它还将促进应用，如非共价，基于DNA的递送系统和探针设计中的药物分子的高密度负载，用于灵敏检测某些分子。
