Angers-Loustau Alexandre, Rainy Jeffrey, Wartiovaara Kirmo
Institute of Biomedicine, University of Helsinki, Helsinki, Finland.
BMC Mol Biol. 2007 Sep 17;8:77. doi: 10.1186/1471-2199-8-77.
Most molecular biology experiments, and the techniques associated with this field of study, involve a great deal of engineering in the form of molecular cloning. Like all forms of engineering, perfect information about the starting material is crucial for successful completion of design and strategies.
We have generated a program that allows complete in silico simulation of the cloning experiment. Starting with a primary DNA sequence, PlasmaDNA looks for restriction sites, open reading frames, primer annealing sequences, and various common domains. The databases are easily expandable by the user to fit his most common cloning needs. PlasmaDNA can manage and graphically represent multiple sequences at the same time, and keeps in memory the overhangs at the end of the sequences if any. This means that it is possible to virtually digest fragments, to add the digestion products to the project, and to ligate together fragments with compatible ends to generate the new sequences. Polymerase Chain Reaction (PCR) fragments can also be virtually generated using the primer database, automatically adding to the fragments any 5' extra sequences present in the primers.
PlasmaDNA is a program available both on Windows and Apple operating systems, designed to facilitate molecular cloning experiments by building a visual map of the DNA. It then allows the complete planning and simulation of the cloning experiment. It also automatically updates the new sequences generated in the process, which is an important help in practice. The capacity to maintain multiple sequences in the same file can also be used to archive the various steps and strategies involved in the cloning of each construct. The program is freely available for download without charge or restriction.
大多数分子生物学实验以及与此研究领域相关的技术都涉及大量分子克隆形式的工程学内容。与所有工程形式一样，关于起始材料的完整信息对于成功完成设计和策略至关重要。
我们开发了一个程序，可对克隆实验进行完整的计算机模拟。从原始DNA序列开始，PlasmaDNA会查找限制性酶切位点、开放阅读框、引物退火序列以及各种常见结构域。用户可轻松扩展数据库以满足其最常见的克隆需求。PlasmaDNA可同时管理和以图形方式呈现多个序列，并在内存中保留序列末端的突出端（如果有的话）。这意味着可以虚拟消化片段，将消化产物添加到项目中，并将具有兼容末端的片段连接在一起以生成新序列。也可使用引物数据库虚拟生成聚合酶链反应（PCR）片段，并自动将引物中存在的任何5'额外序列添加到片段中。
PlasmaDNA是一款适用于Windows和苹果操作系统的程序，旨在通过构建DNA可视化图谱来促进分子克隆实验。然后它允许对克隆实验进行完整的规划和模拟。它还会自动更新过程中生成的新序列，这在实践中是一项重要帮助。在同一文件中维护多个序列的能力也可用于存档每个构建体克隆过程中涉及的各个步骤和策略。该程序可免费下载且无任何收费或限制。
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