DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology.
DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology.
复制标题
DOI：
10.1098/rsif.2015.0580
复制
发表时间：
2015-10-06
期刊：
影响因子：
--
通讯作者：
Yin P
中科院分区：
文献类型：
--
作者：
Grun C;Werfel J;Zhang DY;Yin P
动态DNA纳米技术为在纳米尺度上实现复杂的组装过程、机械行为、传感和计算提供了一条有前途的途径。然而，这些系统的设计是复杂的和容易出错的，因为需要控制系统的动力学路径大大增加了系统的设计约束和可能的故障模式的数量。以前的工具已经自动化了设计工作流程的某些部分，但缺乏集成的解决方案。在这里，我们提出了一个三层的设计过程中实现的软件：一个高层次的可视化编程语言来描述系统，分子编译器建立一个DNA的实现和核苷酸序列的生成和优化。此外，我们的软件还包括用于分析和“调试”硅片设计的工具，以及用于将设计导入/导出到其他常用软件系统的工具。我们介绍的软件是建立在许多现有的软件，但被集成到一个单一的包，使用基于Web的界面在http://molecular-systems.net/workbench访问。我们希望工具之间的深度整合和这种设计过程的灵活性将带来更好的实验结果，更少的实验设计迭代和更复杂的DNA纳米系统的开发。
Dynamic DNA nanotechnology provides a promising avenue for implementing sophisticated assembly processes, mechanical behaviours, sensing and computation at the nanoscale. However, design of these systems is complex and error-prone, because the need to control the kinetic pathway of a system greatly increases the number of design constraints and possible failure modes for the system. Previous tools have automated some parts of the design workflow, but an integrated solution is lacking. Here, we present software implementing a three ‘tier’ design process: a high-level visual programming language is used to describe systems, a molecular compiler builds a DNA implementation and nucleotide sequences are generated and optimized. Additionally, our software includes tools for analysing and ‘debugging’ the designs in silico, and for importing/exporting designs to other commonly used software systems. The software we present is built on many existing pieces of software, but is integrated into a single package—accessible using a Web-based interface at http://molecular-systems.net/workbench. We hope that the deep integration between tools and the flexibility of this design process will lead to better experimental results, fewer experimental design iterations and the development of more complex DNA nanosystems.