Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function.
Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function.
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DOI：
10.1093/nar/gkm1085
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发表时间：
2008-04
影响因子：
14.9
通讯作者：
Turner DH
中科院分区：
文献类型：
--
作者：
Kierzek E;Kierzek R;Moss WN;Christensen SM;Eickbush TH;Turner DH
将LNA（锁核酸，即在核糖的2′氧和4′碳之间具有甲基桥的寡核苷酸）和2，6-二氨基嘌呤掺入到2′-O-甲基RNA五聚体和六聚体探针中，以制备大致等能结合未配对RNA的微阵列。也就是说，如果靶是解折叠的，则结合大致不依赖于靶序列。等能结合和短探针长度简化了与结构化RNA结合的解释，以提供对靶RNA二级结构的了解。利用基因芯片结合技术和化学作图技术对家蚕反转录转座子R2 5′端编码区（R2 Bm 5′ RNA）的二级结构进行了分析。这种R2 Bm 5′ RNA协调R2蛋白的功能，负责在将R2序列插入基因组期间切割DNA的第二条链。实验结果被用作自由能最小化算法的约束条件，以提供R2 Bm 5′ RNA二级结构的初始模型。
LNA (locked nucleic acids, i.e. oligonucleotides with a methyl bridge between the 2′ oxygen and 4′ carbon of ribose) and 2,6-diaminopurine were incorporated into 2′-O-methyl RNA pentamer and hexamer probes to make a microarray that binds unpaired RNA approximately isoenergetically. That is, binding is roughly independent of target sequence if target is unfolded. The isoenergetic binding and short probe length simplify interpretation of binding to a structured RNA to provide insight into target RNA secondary structure. Microarray binding and chemical mapping were used to probe the secondary structure of a 323 nt segment of the 5′ coding region of the R2 retrotransposon from Bombyx mori (R2Bm 5′ RNA). This R2Bm 5′ RNA orchestrates functioning of the R2 protein responsible for cleaving the second strand of DNA during insertion of the R2 sequence into the genome. The experimental results were used as constraints in a free energy minimization algorithm to provide an initial model for the secondary structure of the R2Bm 5′ RNA.
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影响因子：
14.9
作者：
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通讯作者：
Maizel, JV
影响因子：
14.9
作者：
Adamiak, DA;Rypniewski, WR;Adamiak, RW
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Adamiak, RW
影响因子：
14.9
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TINOCO, I
影响因子：
14.9
作者：
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通讯作者：
Becker, MM
影响因子：
14.9
作者：
Kierzek, Elzbieta;Mathews, David H.;Ciesielska, Anna;Turner, Douglas H.;Kierzek, Ryszard
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Kierzek, Ryszard