Shabi Uri, Kaplan Shai, Linshiz Gregory, Benyehezkel Tuval, Buaron Hen, Mazor Yair, Shapiro Ehud
Syst Synth Biol. 2010 Sep;4(3):227-36. doi: 10.1007/s11693-010-9059-y. Epub 2010 Jun 15.
Polymerase Chain Reaction (PCR) is the DNA-equivalent of Gutenberg's movable type printing, both allowing large-scale replication of a piece of text. De novo DNA synthesis is the DNA-equivalent of mechanical typesetting, both ease the setting of text for replication. What is the DNA-equivalent of the word processor? Biology labs engage daily in DNA processing-the creation of variations and combinations of existing DNA-using a plethora of manual labor-intensive methods such as site-directed mutagenesis, error-prone PCR, assembly PCR, overlap extension PCR, cleavage and ligation, homologous recombination, and others. So far no universal method for DNA processing has been proposed and, consequently, no engineering discipline that could eliminate this manual labor has emerged. Here we present a novel operation on DNA molecules, called Y, which joins two DNA fragments into one, and show that it provides a foundation for DNA processing as it can implement all basic text processing operations on DNA molecules including insert, delete, replace, cut and paste and copy and paste. In addition, complicated DNA processing tasks such as the creation of libraries of DNA variants, chimeras and extensions can be accomplished with DNA processing plans consisting of multiple Y operations, which can be executed automatically under computer control. The resulting DNA processing system, which incorporates our earlier work on recursive DNA composition and error correction, is the first demonstration of a unified approach to DNA synthesis, editing, and library construction.
The online version of this article (doi:10.1007/s11693-010-9059-y) contains supplementary material, which is available to authorized users.
聚合酶链式反应（PCR）相当于古登堡活字印刷术对DNA的作用，二者都能实现一段文本的大规模复制。从头DNA合成相当于机械排版对DNA的作用，二者都能简化文本排版以便复制。那么文字处理器相当于对DNA的什么呢？生物学实验室每天都在进行DNA处理——利用大量人工密集型方法，如定点诱变、易错PCR、组装PCR、重叠延伸PCR、切割与连接、同源重组等，来创造现有DNA的变异体和组合。到目前为止，还没有提出一种通用的DNA处理方法，因此也没有出现能够消除这种人工操作的工程学科。在此，我们展示了一种对DNA分子的新操作，称为Y操作，它能将两个DNA片段连接成一个，并表明它为DNA处理奠定了基础，因为它可以对DNA分子执行所有基本的文本处理操作，包括插入、删除、替换、剪切粘贴和复制粘贴。此外，复杂的DNA处理任务，如创建DNA变体文库、嵌合体和延伸序列，可以通过由多个Y操作组成的DNA处理方案来完成，这些操作可以在计算机控制下自动执行。由此产生的DNA处理系统，结合了我们早期在递归DNA合成和纠错方面的工作，是DNA合成、编辑和文库构建统一方法的首次证明。
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