Centre for DNA Nanotechnology, Interdisciplinary Nanoscience Center, Department of Molecular Biology, Aarhus University, C. F. Møllers Allé 3, Aarhus C, Denmark.
N Biotechnol. 2010 Jul 31;27(3):184-93. doi: 10.1016/j.nbt.2010.02.012. Epub 2010 Mar 1.
Computational tools for prediction and design of DNA and RNA structures are used for different approaches in nucleic acid research. The prediction tools are used for the identification and modeling of biologically important nucleic acid structures, whereas the design tools aim at constructing novel molecular architectures and devices for nanotechnology and synthetic biology. The recent successes in predicting RNA three-dimensional structure directly from sequence and in designing sequences that self-assemble into predefined DNA and RNA nanostructures show that nucleic acid structure is predictable and controllable. The prediction and design approaches deal with reverse problems of relating sequence and structure, but share the main computational principles, visual representations and modeling approaches. The prediction and design tools are introduced together here to provide an overview of their current capabilities and deficiencies. The tools are listed by input and output to provide a user perspective and an extended tool table is made available at http://www.cdna.dk/tools/.
用于预测和设计 DNA 和 RNA 结构的计算工具被用于核酸研究的不同方法。预测工具用于识别和建模具有生物学重要性的核酸结构，而设计工具旨在构建用于纳米技术和合成生物学的新型分子架构和设备。最近在直接从序列预测 RNA 三维结构和设计自组装成预定 DNA 和 RNA 纳米结构的序列方面的成功表明，核酸结构是可预测和可控制的。预测和设计方法处理与序列和结构相关的反问题，但共享主要的计算原理、可视化表示和建模方法。这里一起介绍预测和设计工具，以提供对它们当前能力和缺陷的概述。这些工具按输入和输出进行分类，以提供用户视角，并在 http://www.cdna.dk/tools/ 上提供扩展的工具表。
