Evolution of aptamers with secondary structures from a new specificity and new an ATP aptamer
Evolution of aptamers with secondary structures from a new specificity and new an ATP aptamer
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DOI：
10.1261/rna.5990203
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发表时间：
2003-12-01
期刊：
影响因子：
4.5
通讯作者：
Szostak, JW
中科院分区：
文献类型：
--
作者：
Huang, Z;Szostak, JW
有时可以通过几个碱基的突变，在不改变适体结构的情况下，实现靶特异性的微小变化。如果目标的几何形状或化学性质发生较大的变化，则可能需要对适体进行更彻底的改变。在后一种情况下，在序列空间靠近原适体的区域是否还能找到结构解和功能解是未知的。为了研究这些问题，我们设计了一个体外选择实验，旨在研究ATP适体的进化特异性。ATP适体与核碱基和糖同时接触。我们使用了一种亲和矩阵，其中GTP通过糖固定，因此需要大量改变或失去糖接触，以及改变对核碱基的识别。经过仅仅五轮的筛选，新的适体被划分为三大类，每一类的二级结构都不同于ATP适体。原适体与新适体的平均序列同源性为76%。大多数突变要么破坏原有的二级结构，要么形成新的二级结构或新的识别环。我们的研究结果表明，在ATP适体附近的序列空间区域存在识别显著不同配体的新结构。这些从具有明确特异性和折叠的RNA分子中出现的新功能和结构的例子为RNA的进化灵活性和适应性提供了新的视角。
Small changes in target specificity can sometimes be achieved, without changing aptamer structure, through mutation of a few bases. Larger changes in target geometry or chemistry may require more radical changes in an aptamer. In the latter case, it is unknown whether structural and functional solutions can still be found in the region of sequence space close to the original aptamer. To investigate these questions, we designed an in vitro selection experiment aimed at evolving specificity of an ATP aptamer. The ATP aptamer makes contacts with both the nucleobase and the sugar. We used an affinity matrix in which GTP was immobilized through the sugar, thus requiring extensive changes in or loss of sugar contact, as well as changes in recognition of the nucleobase. After just five rounds of selection, the pool was dominated by new aptamers failing into three major classes, each with secondary structures distinct from that of the ATP aptamer. The average sequence identity between the original aptamer and new aptamers is 76%. Most of the mutations appear to play roles either in disrupting the original secondary structure or in forming the new secondary structure or the new recognition loops. Our results show that there are novel structures that recognize a significantly different ligand in the region of sequence space close to the ATP aptamer. These examples of the emergence of novel functions and structures from an RNA molecule with a defined specificity and fold provide a new perspective on the evolutionary flexibility and adaptability of RNA.