北京生物医学工程

一种面向芯片合成技术的寡核苷酸设计方法

Oligonucleotide design for biochip synthesis technology

作者：吴世军郑浩然

单位：                                 中国科学技术大学计算机科学与技术学院(合肥230027)            

关键词：芯片合成技术；寡核苷酸设计；交叉匹配；酶切位点

分类号：

出版年·卷·期（页码）：2015·34·5（495-498）

摘要：

目的研发适用于芯片合成技术的寡核苷酸设计方法。方法面对芯片合成技术的需求，提出新方法，对需要处理的核苷酸序列，通过交叉匹配及酶切位点消除算法对序列中的交叉匹配片段及酶切位点进行密码子替换，尽可能减少交叉匹配及酶切位点序列的出现，对处理后的序列采用近似Tm值优化方法进行切割。结果比对相同序列在该方法和Tmprime两种方法中的结果，从寡核苷酸长度、Tm值范围、错配片段数等因素进行比较，验证了新方法在处理交叉匹配上有很好的效果。结论该方法符合适用于芯片合成技术的寡核苷酸设计的需求，大大减少了交叉匹配及酶切位点的出现情况，为芯片合成技术的寡核苷酸设计提供了一种有效方法。

Objective To develop a new method for designing oligonucleotides for biochip synthesis technology. Methods Facing the needs of biochip synthesis technology, we use mismatch and restrictions’ revision algorithm to do with fragment sequences to reduce the mismatches and restriction sites with synonymous codon, and then cut the sequences into oligonucleotides by using a method approximate to Equi-Tm method. Results The lengths, Tm range, mismatches of oligonucleotides are compared between this method and TmPrime. The new method does well in avoiding mismatches. Conclusions This method satisfies the need of oligonucleotide design for biochip synthesis technology and avoids mismatches and restriction sites as much as possible.

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