Steger G, Hofmann H, Förtsch J, Gross H J, Randles J W, Sänger H L, Riesner D
Institut für Physikalische Biologie, Universität Düsseldorf, FRG.
J Biomol Struct Dyn. 1984 Dec;2(3):543-71. doi: 10.1080/07391102.1984.10507591.
Viroids are single-stranded circular RNA molecules of 240 to 400 nucleotides which are pathogens of certain higher plants and replicate autonomously in the host cell. Virusoids are similar to viroids in respect to size and circularity but replicate only as genomic part of a plant virus. Their structure and structural transitions have been investigated by thermo-dynamic, kinetic and hydrodynamic methods. The special features of the sequences of these RNAs, which are the basis for their secondary structures and structural flexibility, are investigated with theoretical methods. A set of thermodynamic parameters for helix growth and loop formation is selected from the literature to calculate secondary structures and structural transitions of single-stranded RNAs. Appropriate modifications of the chosen parameter set are discussed. For calculations we used either Tinoco-plots and the model of "cooperative helices" or the Zuker-program based on the exact algorithm of Nussinov et al, or both. Calculations were done for viroids and virusoids. As both are single-stranded, circular RNAs we had to modify the Zuker-program as described in the appendix. Calculations are done for different viroids, i.e. potato spindle tuber, citrus exocortis, chrysanthemum stunt, coconut cadang-cadang, and avocado sunblotch, and for two virusoids, i.e. the circular RNAs of Solanum nodiflorum mottle virus, and velvet tobacco mottle virus. For viroids the calculations confirm our earlier theoretical and experimental results about the extended native structure and the highly cooperative transition into a branched structure. Virusoids show less base pairing, branching in the native secondary structure, and only low cooperativity during denaturation. They resemble more closely the properties of random sequences with length, G:C content, and circularity as in viroids but statistical sequences. The comparison of viroids, virusoids, and circular RNA or random sequences confirms the uniqueness of viroid structure.
类病毒是由240至400个核苷酸组成的单链环状RNA分子，是某些高等植物的病原体，并在宿主细胞中自主复制。拟病毒在大小和环状结构方面与类病毒相似，但仅作为植物病毒基因组的一部分进行复制。它们的结构和结构转变已通过热力学、动力学和流体动力学方法进行了研究。这些RNA序列的特殊特征是其二级结构和结构灵活性的基础，已用理论方法进行了研究。从文献中选择了一组用于螺旋生长和环形成的热力学参数，以计算单链RNA的二级结构和结构转变。讨论了所选参数集的适当修改。对于计算，我们使用了Tinoco图和“协同螺旋”模型，或基于Nussinov等人精确算法的Zuker程序，或两者兼用。对类病毒和拟病毒进行了计算。由于两者都是单链环状RNA，我们必须按照附录中所述对Zuker程序进行修改。对不同的类病毒进行了计算，即马铃薯纺锤块茎类病毒、柑橘裂皮类病毒、菊花矮化类病毒、椰子死亡类病毒和鳄梨日斑类病毒，以及两种拟病毒，即茄无柄斑驳病毒和绒毛烟草斑驳病毒的环状RNA。对于类病毒，计算结果证实了我们早期关于扩展的天然结构以及向分支结构的高度协同转变的理论和实验结果。拟病毒显示出较少的碱基配对、天然二级结构中的分支，以及变性过程中仅较低的协同性。它们在长度、G:C含量和环状结构方面更类似于随机序列的性质，但类病毒是统计序列。类病毒、拟病毒与环状RNA或随机序列的比较证实了类病毒结构的独特性。
