Word Design for Biomolecular Information Processing
Word Design for Biomolecular Information Processing
复制标题
生物分子信息处理的文字设计
DOI：
10.1515/zna-2003-2-313
复制
发表时间：
2003
期刊：
影响因子：
--
通讯作者：
F. Gast
中科院分区：
文献类型：
--
作者：
J. Ackermann;F. Gast
DNA序列的设计在许多生物分子应用中起着重要的作用，是探索分子信息处理潜力的最重要的理论任务之一。优化策略是基于刚性“数字”聚合物的模型，通过计算碱基不匹配的数量（汉明距离和相关距离）。在这项工作中，我们展示了这种组合方法的局限性，因为DNA有能力构建更复杂的结构。我们开发了一个模型平台，根据相关词-词交互中出现的所有可能的二级结构来优化词集。结果表明，最优组合具有独特的物理性质，如结合能、熔融温度和G+C含量等。
The design of DNA sequences plays a fundamental role for many biomolecular applications and is one of the most important theoretical tasks to fathom the potential of molecular information processing. Optimization strategies have been based on the model of stiff “digital” polymers by counting the number of base mismatches (Hamming distance and related distances). In this work we show the limitation of such a combinatorial approach because of the ability of DNA to build more complex structures. We develop a model platform to optimize word sets according to all possible secondary structures occurring for the relevant word-word interactions. The fidelity of the hybridization reactions can be improved significantly and as an example of a set of 24 words of 16-mers we show that the optimal set has unique physical properties, such as binding energy, melting temperature, and G+C content.