The potential for biopolymers to evolve new structures has important consequences for their ability to optimize function and our attempts to reconstruct their evolutionary histories. Prior work with in vitro systems suggests that structural remodeling of RNA is difficult to achieve through the accumulation of point mutations or through recombination events. Sequence duplication may represent an alternative mechanism that can more readily lead to the evolution of new structures. Structural and sequence elements in many RNAs and proteins appear to be the products of duplication events, indicating that this mechanism plays a major role in molecular evolution. Despite the potential significance of this mechanism, little experimental data is available concerning the structural and evolutionary consequences of duplicating biopolymer sequences. To assess the structural consequences of sequence duplication on the evolution of RNA, we mutagenized an RNA sequence containing two copies of an ATP aptamer and subjected the resulting population to multiple in vitro evolution experiments. We identified multiple routes by which duplication, followed by the accumulation of functional point mutations, allowed our populations to sample two entirely different secondary structures. The two structures have no base pairs in common, but both structures contain two copies of the same ATP-binding motif. We do not observe the emergence of any other functional secondary structures beyond these two. Although this result suggests a limited capacity for duplication to support short-term functional innovation, major changes in secondary structure, like the one observed here, should be given careful consideration as they are likely to frustrate attempts to infer deep evolutionary histories of functional RNAs.

中文翻译：

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大变化，小创新：RNA序列重复的进化结果。

生物聚合物发展新结构的潜力对它们优化功能的能力以及我们重建其进化历史的尝试具有重要意义。体外系统的先前工作表明，通过点突变的积累或重组事件很难实现RNA的结构重塑。序列重复可能代表了一种替代机制，可以更容易地导致新结构的进化。许多RNA和蛋白质中的结构和序列元件似乎是重复事件的产物，表明该机制在分子进化中起主要作用。尽管该机制具有潜在的重要性，但几乎没有关于复制生物聚合物序列的结构和进化后果的实验数据。为了评估序列重复对RNA进化的结构影响，我们诱变了包含两个拷贝的ATP适体的RNA序列，并对所得群体进行了多次体外进化实验。我们确定了多种途径，通过这些途径重复进行，随后积累了功能点突变，使我们的种群能够采样两个完全不同的二级结构。这两个结构没有共同的碱基对，但是两个结构都包含相同ATP结合基序的两个副本。除了这两个功能，我们没有观察到任何其他功能性二级结构的出现。尽管此结果表明支持短期功能创新的复制能力有限，但二级结构的重大变化（如此处观察到的那样）