RNAProbeDesigner:mRNA探针特异性序列搜索方法

RNAProbeDesigner: A Method for the Specific Oligonucleotide Design in mRNA Probe

mRNA不仅是生物体内蛋白质合成的"图纸",还参与生命活动的很多调节过程。随着分子影像技术的发展,mRNA探针在医药领域的应用越来越广泛。探针的特异性是衡量探针效果的重要指标。本文基于BLAST的序列搜索方法,根据目标mRNA中的每个片段与细胞中其他RNA的相似程度,筛选可用于特异性识别mRNA的寡核苷酸片段,并将该方法编写为一套自动化的mRNA探针特异性序列的搜索程序——RNAProbeDesigner。选取4种蛋白的mRNA对该程序进行测试,结果显示,该程序搜索出的片段中,有部分结果在以往的文献中已被报道用于相应探针的设计,从而证明了该方法的可靠性。

Messenger RNA （mRNA） is the blueprint for protein synthesis in living cell and at the same time it is an active regulator in life activities. With the rapid development of molecular imaging techniques, mRNA probe has been widely used in the fields of modern medicine and molecular biology. The specificity of a probe is one of the most important measures to assess its effect, thus in this article an automatic algorithm - RNAProbeDesigner to find the specific oligonucleotides in mRNA based on BLAST results was established. Firstly ,the exon region of a target mRNA was split into several fragments and each fragment contained 18 -23 nucleo- tides ; Secondly, using BLAST each oligonucleotide compared with the NCBI＇ s RNA database ; Thirdly were found the specific ones according to our selection score - Sm. 4 kinds of proteins＇ mRNAs （GAPDH, NK1R, ERBB2, EGFR） were chosen to test the program＇s reliability and accuracy. The results showed that some of the predicted sepecific sequences by RNAProbeDesigner were already used in several reported mRNA probes according to the recent papers, and the best specific oligonucleotides predicted by the program usually obtained a good specificity, namely lower Sm than that of the reported ones. Additionally, a detailed analysis of the relationship between the specificity and length of the oligonueleotide showed that as the length of the oligonucleotide increased, the specificity improved. It is concluded that RNAProbeDesigner can be an effective tool for the specific oligonucleotide design in mRNA probe.