Seiffert Jan, Huhle Alexander
Dresden University of Technology, Institute for Materials Sceience, D-01062 Dresden, Germany.
J Biomol Struct Dyn. 2008 Apr;25(5):453-66. doi: 10.1080/07391102.2008.10507193.
Production of various structures by self-assembling single stranded DNA molecules is a widely used technology in the filed of DNA nanotechnology. Base sequences of single strands do predict the shape of the resulting nanostructure. Therefore, sequence design is crucial for the successful structure fabrication. This paper presents a sequence design algorithm based on mismatch minimization that can be applied to every desired DNA structure. With this algorithm, junctions, loops, single as well as double stranded regions, and very large structures up to several thousand base pairs can be handled. Thereby, the algorithm is fast for the most structures. Algorithm is Java-implemented. Its implementation is called Seed and is available publicly. As an example for a successful sequence generation, this paper presents the fabrication of DNA chain molecules consisting of double-crossover (DX) tiles as well.
通过自组装单链DNA分子来生成各种结构是DNA纳米技术领域中广泛使用的一项技术。单链的碱基序列确实能够预测最终纳米结构的形状。因此，序列设计对于成功构建结构至关重要。本文提出了一种基于错配最小化的序列设计算法，该算法可应用于任何所需的DNA结构。利用此算法，可以处理连接点、环、单链和双链区域，以及长达数千个碱基对的非常大的结构。因此，对于大多数结构而言，该算法速度很快。该算法是用Java实现的。其实现版本名为Seed，可公开获取。作为成功生成序列的一个例子，本文还介绍了由双交叉（DX）瓦片组成的DNA链分子的构建。
