A unique secondary folding pattern for 5S RNA corresponds to the lowest energy homologous secondary structure in 17 different prokaryotes.
A unique secondary folding pattern for 5S RNA corresponds to the lowest energy homologous secondary structure in 17 different prokaryotes.
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DOI：
10.1093/nar/9.8.1885
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发表时间：
1981-04
影响因子：
14.9
通讯作者：
G. Studnicka;F. Eiserling;J. Lake
中科院分区：
文献类型：
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作者：
G. Studnicka;F. Eiserling;J. Lake
基于螺旋能量过滤计算，提出了原核生物核糖体5S RNA的一般二级结构。我们已经考虑了17种不同的原核5S RNA共有的所有二级结构，并为每个5S序列计算了（全局）最小能量二级结构（每个序列可能有300，000个共同结构）。17种不同的最小能量二级结构都对应于一个单一的二级结构模型，只有微小的差异。这是强有力的证据，表明这种一般的5S折叠模式对应于功能性5S rRNA的二级结构。一般的5S二级结构是分叉的，与tRNA的三叶草类似，被命名为“叉骨”模型。它恒定的8个双螺旋区域;一个在茎，四个在第一，或恒定的臂，和三个在第二arm. Four这些双螺旋区域中存在于一个模型早先提出的（1）和四个额外的区域没有提出他们在这里。在最小能量一般结构中，恒定臂中的四个螺旋正好是15个核苷酸对长。这些螺旋堆积在革兰氏阳性菌的序列中，也可能堆积在革兰氏阴性菌的序列中。在来自革兰氏阳性细菌的序列中，恒定臂的长度通过不寻常的最小能量相互作用维持在15个堆叠对，所述最小能量相互作用涉及插入在两个相邻螺旋区域之间的C26-G57碱基对。
A general secondary structure is proposed for the 5S RNA of prokaryotic ribosomes, based on helical energy filtering calculations. We have considered all secondary structures that are common to 17 different prokaryotic 5S RNAs and for each 5S sequence calculated the (global) minimum energy secondary structure (300,000 common structures are possible for each sequence). The 17 different minimum energy secondary structures all correspond, with minor differences, to a single, secondary structure model. This is strong evidence that this general 5S folding pattern corresponds to the secondary structure of the functional 5S rRNA. The general 5S secondary structure is forked and in analogy with the cloverleaf of tRNA is named the "wishbone" model. It constant 8 double helical regions; one in the stem, four in the first, or constant arm, and three in the second arm. Four of these double helical regions are present in a model earlier proposed (1) and four additional regions not proposed by them are presented here. In the minimum energy general structure, the four helices in the constant arm are exactly 15 nucleotide pairs long. These helices are stacked in the sequences from gram-positive bacteria and probably stacked in gram-negative sequences as well. In sequences from gram-positive bacteria the length of the constant arm is maintained at 15 stacked pairs by an unusual minimum energy interaction involving a C26-G57 base pair intercalated between two adjacent helical regions.