Nowak Robert M, Wojtowicz-Krawiec Anna, Plucienniczak Andrzej
Institute of Electronic Systems, Warsaw University of Technology, Nowowiejska 15/19, 00-665 Warsaw, Poland.
Institute of Biotechnology and Antibiotics, Staroscinska 5, 02-512 Warsaw, Poland.
Biomed Res Int. 2015;2015:413262. doi: 10.1155/2015/413262. Epub 2015 Jan 6.
Artificial gene synthesis requires consideration of nucleotide sequence development as well as long DNA molecule assembly protocols. The nucleotide sequence of the molecule must meet many conditions including particular preferences of the host organism for certain codons, avoidance of specific regulatory subsequences, and a lack of secondary structures that inhibit expression. The chemical synthesis of DNA molecule has limitations in terms of strand length; thus, the creation of artificial genes requires the assembly of long DNA molecules from shorter fragments. In the approach presented, the algorithm and the computer program address both tasks: developing the optimal nucleotide sequence to encode a given peptide for a given host organism and determining the long DNA assembly protocol. These tasks are closely connected; a change in codon usage may lead to changes in the optimal assembly protocol, and the lack of a simple assembly protocol may be addressed by changing the nucleotide sequence. The computer program presented in this study was tested with real data from an experiment in a wet biological laboratory to synthesize a peptide. The benefit of the presented algorithm and its application is the shorter time, compared to polymerase cycling assembly, needed to produce a ready synthetic gene.
人工基因合成需要考虑核苷酸序列的设计以及长DNA分子的组装方案。分子的核苷酸序列必须满足许多条件，包括宿主生物体对某些密码子的特定偏好、避免特定的调控子序列以及不存在抑制表达的二级结构。DNA分子的化学合成在链长方面存在局限性；因此，人工基因的创建需要将较短的片段组装成长DNA分子。在本文提出的方法中，算法和计算机程序解决了这两个任务：为给定的宿主生物体设计编码给定肽的最佳核苷酸序列，并确定长DNA组装方案。这些任务紧密相连；密码子使用的变化可能导致最佳组装方案的改变，而简单组装方案的缺乏可以通过改变核苷酸序列来解决。本研究中提出的计算机程序用来自湿实验室合成肽实验的真实数据进行了测试。与聚合酶循环组装相比，所提出算法及其应用的优势在于合成一个可用的合成基因所需的时间更短。
