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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Predicting The Sizes Of Large Rna Molecules
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Predicting The Sizes Of Large Rna Molecules

机译：预测大RNA分子的大小

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We present a theory of the dependence on sequence of the three-dimensional size of large single-stranded (ss) RNA molecules. The work is motivated by the fact that the genomes of many viruses are large ssRNA molecules-often several thousand nucle-otides long-and that these RNAs are spontaneously packaged into small rigid protein shells. We argue that there has been evolutionary pressure for the genome to have overall spatial properties-including an appropriate radius of gyration, R_g-that facilitate this assembly process. For an arbitrary RNA sequence, we introduce the (thermal) average maximum ladder distance () and use it as a measure of the "extendedness" of the RNA secondary structure. The values of viral ssRNAs that package into capsids of fixed size are shown to be consistently smaller than those for randomly permuted sequences of the same length and base composition, and also smaller than those of natural ssRNAs that are not under evolutionary pressure to have a compact native form. By mapping these secondary structures onto a linear polymer model and by using (MLD) as a measure of effective contour length, we predict the R_g values of viral ssRNAs are smaller than those of nonviral sequences. More generally, we predict the average (MLD) values of large nonviral ssRNAs scale as N~(0.67±010), where N is the number of nucleotides, and that their R_g values vary as ~(0.5) in an ideal solvent, and hence as N~(0.34). An alternative analysis, which explicitly includes all branches, is introduced and shown to yield consistent results.
机译：我们提出了一种依赖于大单链（ss）RNA分子三维尺寸序列的理论。许多病毒的基因组都是较大的ssRNA分子-通常长数千个核苷酸-并且将这些RNA自发包装在小的硬质蛋白质壳中，这是这项工作的动力。我们认为基因组具有整体空间特性（包括适当的回转半径R_g）存在进化压力，这有利于该组装过程。对于任意的RNA序列，我们引入（热）平均最大阶梯距离（），并将其用作RNA二级结构“扩展性”的量度。包裹在固定大小的衣壳中的病毒ssRNA的值始终小于相同长度和碱基组成的随机排列序列的值，也小于不受进化压力限制的天然ssRNA的值。具有紧凑的本机形式。通过将这些二级结构映射到线性聚合物模型上，并使用（MLD）作为有效轮廓长度的量度，我们预测病毒ssRNA的R_g值小于非病毒序列的R_g。更一般地说，我们预测大型非病毒ssRNA的平均（MLD）值为N〜（0.67±010），其中N为核苷酸数，理想情况下，它们的R_g值随〜（0.5）变化。溶剂，因此为N〜（0.34）。引入了替代分析，该分析明确包括所有分支，并显示出一致的结果。

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