Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.
Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
Biochim Biophys Acta Gen Subj. 2018 Mar;1862(3):705-725. doi: 10.1016/j.bbagen.2017.10.019. Epub 2017 Oct 31.
While the RNA world hypothesis is widely accepted, it is still far from complete: the existence of self-replicating ribozyme, consisting of potentially hundreds of nucleotides, is a core assumption for the majority of RNA world models. The appearance of such long RNA molecules under prebiotic conditions is not self-evident. Recombination seems to be a plausible way of creating RNA diversity, resulting in the appearance of functional RNAs, capable of self-replicating.
We report here on the study of recombination process modelled with two 96 nts RNA fragments. Detection of recombination products was performed with RT-PCR followed by TA-cloning and Sanger sequencing.
A wide range of recombinant products was detected. We found that (i) the most efficient ligation was observed for RNA species forming bulges or internal loops, with ligation partners located within the loop; (ii) a strong preference was observed for formation of a few types of major products with a large variety of minor products; (iii) ligation could occur with participation of either 2',3'-cyclophosphate or 5'-ppp; (iv) the presence of key reaction components, i.e. 5'ppp-RNAs, enabled the formation of additional types of product; (v) molecular dynamics simulations of one of the most abundant products suggests that the ligation results in a preferable formation of 2'-5'- rather than 3'-5'-linkages.
The study demonstrates regularities of new RNA molecules formation with non-enzymatic recombination process.
Our findings provide new data supporting the RNA World hypothesis and show the way of new RNA sequences emergence under prebiotic conditions.
尽管 RNA 世界假说被广泛接受，但它仍然远未完成：具有潜在数百个核苷酸的自我复制核酶的存在是大多数 RNA 世界模型的核心假设。在原始条件下出现如此长的 RNA 分子并不是显而易见的。重组似乎是产生 RNA 多样性的一种合理方式，导致具有自我复制能力的功能性 RNA 的出现。
我们在这里报告了使用两个 96 个核苷酸的 RNA 片段模拟重组过程的研究。使用 RT-PCR 进行重组产物的检测，然后进行 TA 克隆和 Sanger 测序。
检测到广泛的重组产物。我们发现：（i）形成凸起或内部环的 RNA 种类观察到最有效的连接，连接伙伴位于环内；（ii）观察到形成少数几种主要产物的强烈偏好，而次要产物种类繁多；（iii）可以通过参与 2',3'-环磷酸或 5'-ppp 进行连接；（iv）存在关键反应成分，即 5'ppp-RNAs，能够形成其他类型的产物；（v）对最丰富产物之一的分子动力学模拟表明，连接导致形成优选的 2'-5'-而不是 3'-5'-键。
该研究证明了非酶促重组过程中新 RNA 分子形成的规律。
我们的发现提供了支持 RNA 世界假说的新数据，并展示了在原始条件下新 RNA 序列出现的途径。
