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利用微阵列促进RNA结构预测

Facilitating RNA structure prediction with microarrays.

作者信息

Kierzek Elzbieta, Kierzek Ryszard, Turner Douglas H, Catrina Irina E

机构信息

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.

出版信息

Biochemistry. 2006 Jan 17;45(2):581-93. doi: 10.1021/bi051409+.

DOI:10.1021/bi051409+
PMID:16401087
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4070881/
Abstract

Determining RNA secondary structure is important for understanding structure-function relationships and identifying potential drug targets. This paper reports the use of microarrays with heptamer 2'-O-methyl oligoribonucleotides to probe the secondary structure of an RNA and thereby improve the prediction of that secondary structure. When experimental constraints from hybridization results are added to a free-energy minimization algorithm, the prediction of the secondary structure of Escherichia coli 5S rRNA improves from 27 to 92% of the known canonical base pairs. Optimization of buffer conditions for hybridization and application of 2'-O-methyl-2-thiouridine to enhance binding and improve discrimination between AU and GU pairs are also described. The results suggest that probing RNA with oligonucleotide microarrays can facilitate determination of secondary structure.

摘要

确定RNA二级结构对于理解结构-功能关系以及识别潜在的药物靶点至关重要。本文报道了使用含有七聚体2'-O-甲基寡核糖核苷酸的微阵列来探测RNA的二级结构，从而改进对该二级结构的预测。当将杂交结果的实验约束添加到自由能最小化算法中时，大肠杆菌5S rRNA二级结构的预测从已知标准碱基对的27%提高到了92%。还描述了杂交缓冲条件的优化以及应用2'-O-甲基-2-硫代尿苷来增强结合并改善AU和GU对之间的区分。结果表明，用寡核苷酸微阵列探测RNA有助于确定二级结构。

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