Jacobson A B, Zuker M
Department of Microbiology, State University of New York at Stony Brook 11794-5222.
J Mol Biol. 1993 Sep 20;233(2):261-9. doi: 10.1006/jmbi.1993.1504.
We have predicted the secondary structure of the entire 4217 nucleotide sequence of the genomic RNA of coliphage Q beta in one computer run using the computer program MFOLD that computes RNA structures within any prescribed increment of the computed minimum free energy. The results are presented in the form of an "energy dot plot" that shows both an optimal folding as well as the superposition of all base-pairs that can form in slightly suboptimal foldings. The plot reveals five large, well-determined, independent structural domains that cover approximately 50% of the viral genome. The predicted structural domains are consistent with and provide support for five large structural domains identified previously by quantitative electron microscopy in Q beta RNA. The dot plot also contains cluttered regions that indicate large numbers of alternative foldings within or between segments of an RNA molecule. These reflect the impossibility of accurate structure prediction and/or the biological reality of more than one folding. Weaker, long range structures, that are observed by electron microscopy in two alternate competing conformations, are located in the regions of the Q beta sequence that correspond to cluttered regions of the dot plot. The potential biological significance of these secondary structures is discussed.
我们使用计算机程序MFOLD在一次计算机运行中预测了噬菌体Qβ基因组RNA的整个4217个核苷酸序列的二级结构，该程序可在计算出的最小自由能的任何规定增量范围内计算RNA结构。结果以“能量点图”的形式呈现，该图显示了最佳折叠以及在略次优折叠中可以形成的所有碱基对的叠加。该图揭示了五个大的、确定良好的独立结构域，它们覆盖了约50%的病毒基因组。预测的结构域与先前通过定量电子显微镜在Qβ RNA中鉴定的五个大结构域一致并提供了支持。点图还包含杂乱区域，表明RNA分子片段内或片段之间存在大量替代折叠。这些反映了准确结构预测的不可能性和/或多种折叠的生物学现实。在电子显微镜下观察到的两种交替竞争构象中的较弱的长程结构，位于Qβ序列中与点图杂乱区域相对应的区域。讨论了这些二级结构的潜在生物学意义。
