RNA Chemistry and the RNA World

核糖体的核心存在RNA，核苷酸辅因子的广泛使用，以及从RNA前体合成DNA和一些氨基酸，表明RNA曾经是生命进化早期的主要催化和遗传聚合物。 这种“RNA世界”假说假设RNA能够进行维持和进化“核糖体”所需的所有反应。 我的实验室的长期目标之一是选择和进化一种RNA复制酶核酶，能够在实验室中维持基于RNA的进化。 这样的系统可以被称为“活的”，并将化学的简单性与生物学的复杂性结合起来。 确定产生RNA复制所需的最小复杂性将前所未有地了解早期地球从非生物世界过渡到生物世界所面临的困难。 目标一和二：走向RNA复制酶核酶：我们将使用传统的和乳液为基础的体外选择方法来分离上级RNA聚合酶核酶，是高度加工。 现有技术的聚合酶核酶能够快速形成磷酸二酯键，但几乎不能适当地保持其延伸的引物-模板底物。 克服这个中心问题有可能将聚合速率提高十倍或更多倍，并提供在以小时测量的时间尺度内将模板延伸数百个核苷酸的前景-如果实现的话，这是一个令人兴奋的前景！ 目标二：易位机制和均聚物聚合酶：我们将选择将poly（A）尾逐步掺入RNA引物末端的聚合酶核酶。 这样的聚合酶是令人感兴趣的，因为长均聚物的进行性合成需要易位机制，在掺入核苷酸之后，易位机制必须重置聚合酶复合物以看起来完全像初始状态，以便允许迭代聚合。 这种机制最终可以证明在RNA复制过程中取代非模板链非常有用，因此在开发复制酶核酶中发挥重要作用。

The presence of RNA at the core of the ribosome, the extensive use of nucleotide cofactors, and the synthesis of DNA and some amino acids from RNA precursors suggests that RNA was once the dominant catalytic and genetic polymer early in the evolution of life. This 'RNA World' hypothesis assumes that RNA is capable of all the reactions required to maintain and evolve a 'ribo-organism'. One of my laboratories long term objectives is to select and evolve an RNA replicase ribozyme capable of sustaining RNA based evolution in the laboratory. Such a system could be called 'alive' and would marry the underlying simplicity of chemistry to the complexity of biology. Identifying the minimal complexity required to produce an RNA replicace would inform as never before about the difficulties faced on the early Earth in transitioning from an abiotic to biotic world. Aims I&II: Towards an RNA replicase ribozyme: We will use conventional and emulsion based in vitro selection methodologies to isolate superior RNA polymerase ribozymes that are highly processive. The current state of the art polymerase ribozyme is capable of rapid phosphodiester bond formation, but is nearly unable to appropriately hold the primer-template substrate it extends. Overcoming this central problem has the potential to increase polymerization rates by factors of ten or more and offers the prospect of extending a template by hundreds of nucleotides in a time scale measured in hours - an exciting prospect if realized! Aim II: Translocation mechanism & homopolymer polymerases: We will select for polymerase ribozymes that processively incorporate poly(A) tails onto the end of an RNA primer. Such polymerases are interesting as the processive synthesis of a long homopolymer requires a translocation mechanism that, after the incorporation of a nucleotide, must reset the polymerase complex to look exactly like the initial state so as to allow iterative polymerization. Such a mechanism ultimately could prove very useful in displacing a non-template strand during RNA replication and thus play an important role in developing a replicase ribozyme.