OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach
OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach
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DOI：
10.1093/nar/gkg426
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发表时间：
2003-06-15
影响因子：
14.9
通讯作者：
Gulari, E
中科院分区：
文献类型：
--
作者：
Rouillard, JM;Zuker, M;Gulari, E
有一个很大的兴趣，在实施生物信息学技术，允许寡核苷酸的设计，以支持从短的合成DNA片段斑点或原位合成的载玻片上的微阵列的发展。理想地，这样的寡核苷酸应当对其各自的靶完全特异性，以避免任何交叉杂交，并且不应当形成可能在杂交期间干扰标记的探针的稳定的二级结构。我们开发了OligoArray 2.0，这是一个在基因组规模上设计特定寡核苷酸的程序。它使用热力学方法来预测二级结构，并计算芯片上标记探针混合物中独特探针的靶点特异性。此外，OligoArray 2.0可以根据用户输入调整寡核苷酸长度，以适应与杂交要求兼容的窄T-m范围。结合芯片上的寡核苷酸合成，该程序使得在基因组规模上对任何已知基因组序列的生物体进行表达分析成为可能。这不依赖于cDNA或寡核苷酸文库。利用OligoArray 2.0设计了75764个寡核苷酸，代表了26140个拟南芥转录本。其中，我们提供了至少一个特定的寡核苷酸为93%的这些转录本。
There is a substantial interest in implementing bioinformatics technologies that allow the design of oligonucleotides to support the development of microarrays made from short synthetic DNA fragments spotted or in situ synthesized on slides. Ideally, such oligonucleotides should be totally specific to their respective targets to avoid any cross-hybridization and should not form stable secondary structures that may interfere with the labeled probes during hybridization. We have developed OligoArray 2.0, a program that designs specific oligonucleotides at the genomic scale. It uses a thermodynamic approach to predict secondary structures and to calculate the specificity of targets on chips for a unique probe in a mixture of labeled probes. Furthermore, OligoArray 2.0 can adjust the oligonucleotide length, according to user input, to fit a narrow T-m range compatible with hybridization requirements. Combined with on chip oligonucleotide synthesis, this program makes it feasible to perform expression analysis on a genomic scale for any organism for which the genome sequence is known. This is without relying on cDNA or oligonucleotide libraries. OligoArray 2.0 was used to design 75 764 oligonucleotides representing 26 140 transcripts from Arabidopsis thaliana. Among this set, we provide at least one specific oligonucleotide for 93% of these transcripts.