Recursive construction of perfect DNA molecules from imperfect oligonucleotides
Recursive construction of perfect DNA molecules from imperfect oligonucleotides
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DOI：
10.1038/msb.2008.26
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发表时间：
2008-05-01
影响因子：
9.9
通讯作者：
Shapiro, Ehud
中科院分区：
文献类型：
--
作者：
Linshiz, Gregory;Ben Yehezkel, Tuval;Shapiro, Ehud
从可能有缺陷的积木中制造出无缺陷的复杂物体是计算机工程、纳米技术和合成生物学的一个基本挑战。在这里，我们第一次展示了如何使用递归来解决这一挑战，并展示了一个递归程序，该程序可以从易错寡核苷酸构建无错误的DNA分子及其文库。分而治之（D&C）是一种典型的递归问题解决技术，它通过计算机将靶DNA序列分成重叠的寡核苷酸，这些寡核苷酸足够短，可以直接合成，尽管有错误;易错寡核苷酸在体外递归组合，形成易错DNA分子;然后识别、提取这些分子的无错误片段并将其用作递归构建过程的另一迭代的新的、通常更长且更准确的输入;重复整个过程直到形成无错误的靶分子。我们的递归构建过程超越了现有的从头DNA合成方法的速度，精度，自动化，易于结合合成和天然DNA片段，并能够构建设计师的DNA文库。因此，它为合成生物分子和生物体的设计和构建提供了一个新的和强大的基础。
Making faultless complex objects from potentially faulty building blocks is a fundamental challenge in computer engineering, nanotechnology and synthetic biology. Here, we show for the first time how recursion can be used to address this challenge and demonstrate a recursive procedure that constructs error-free DNA molecules and their libraries from error-prone oligonucleotides. Divide and Conquer (D&C), the quintessential recursive problem-solving technique, is applied in silico to divide the target DNA sequence into overlapping oligonucleotides short enough to be synthesized directly, albeit with errors; error-prone oligonucleotides are recursively combined in vitro, forming error-prone DNA molecules; error-free fragments of these molecules are then identified, extracted and used as new, typically longer and more accurate, inputs to another iteration of the recursive construction procedure; the entire process repeats until an error-free target molecule is formed. Our recursive construction procedure surpasses existing methods for de novo DNA synthesis in speed, precision, amenability to automation, ease of combining synthetic and natural DNA fragments, and ability to construct designer DNA libraries. It thus provides a novel and robust foundation for the design and construction of synthetic biological molecules and organisms.