Nonequilibrium replication and selection from reactive nucleotides using hyperexponential RNA polymerization in a thermal trap

在热阱中使用超指数 RNA 聚合进行非平衡复制和反应性核苷酸选择

• 批准号: 265469975
• 负责人: Professor Dr. Dieter Braun
• 金额: --
• 依托单位: Lehrstuhl für Theorie komplexer Biosysteme
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2014
• 资助国家: 德国
• 起止时间: 2013-12-31 至 2019-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/265469975?language=en
• 关键词: Nonequilibrium; replication; selection; reactive; nucleotides

Can we use the disequilibrium setting of a thermal gradient to generate a replication-selection process, based only on reactive nucleotides such as cGMP and cCMP? We have recently established an experimental platform that promises to make this ambitious goal attainable. In particular, we have already demonstrated crucial properties required to kickstart a spontaneous process that mimics the transition from a chemical to a biological world, which must have occurred during the Origin of Life. A central issue is the question of how to create such a process while starting from prebiotically plausible conditions, i.e. low concentrations of simple building blocks and in the absence of protein enzymes. We have found that thermal trapping (convection and thermophoresis in a cleft) can be a natural solution to this problem, which in essence uses a global physical non-equilibrium to strongly accumulate molecules and to drive chemical reactions. For instance, we demonstrated recently [C.B. Mast, S. Schink, U. Gerland and D. Braun, PNAS 110, 8030-8035 (2013)], using double-stranded DNA blocks, that a thermal trap can lead to a hyperexponential enhancement of polymerization. We now strive to take this to the single-nucleotide level, exploiting the recently shown fast polymerization of 20mers of RNA from cGMP found by the di Mauro group, which we already confirmed in our lab, albeit in dry conditions. This reaction perfectly matches the conditions for strong thermal trapping and promises a rich structure of replication and selection under the simple non-equilibrium setting of a thermal gradient. We will pursue three major goals:1. Hyperexponential Polymerization. Creation of long RNA molecules in a Thermal Trap. The polymers will be created from a steady inflow of cGMP molecules at low concentrations.2. Codon-Replicator based on tRNA. Replicate long codon sequences using hairpin ligation of cGMP. Starting from poly-C templates, replication will be enhanced by convection and trapping.3. Theoretical description and exploration of the interplay between the non-equilibrium physics of the thermal trap and the stochastic chemical reactions. The approaches will range from simplified analytical treatments to full finite element simulations of detailed models. All approaches are tightly integrated with the experiments.

我们能否利用热梯度的不平衡设置来产生仅基于活性核苷酸（如cGMP和cCMP）的复制选择过程？我们最近建立了一个实验平台，有望实现这一雄心勃勃的目标。特别是，我们已经证明了启动一个自发过程所需的关键特性，这个过程模拟了从化学世界到生物世界的过渡，这一定发生在生命起源期间。一个核心问题是如何在益生前合理的条件下，即在低浓度的简单构建块和缺乏蛋白质酶的情况下，创建这样一个过程。我们发现热捕获（缝隙中的对流和热电泳）可以是解决这个问题的自然方法，它本质上是利用全局物理不平衡来强烈积累分子并驱动化学反应。例如，我们最近证明了[C.B.]Mast， S. Schink， U. Gerland和D. Braun, PNAS 110, 8030-8035(2013)]，使用双链DNA块，热陷阱可以导致聚合的超指数增强。我们现在努力将其提升到单核苷酸水平，利用di Mauro团队最近发现的cGMP快速聚合20米RNA的技术，我们已经在实验室中证实了这一点，尽管是在干燥条件下。该反应完全符合强热捕获的条件，并在简单的热梯度非平衡设置下保证了丰富的复制和选择结构。我们将努力实现三大目标。Hyperexponential聚合。在热阱中产生长RNA分子。这种聚合物将由稳定流入的低浓度cGMP分子产生。基于tRNA的密码子复制子。使用cGMP发夹连接复制长密码子序列。从poly-C模板开始，通过对流和捕获来增强复制。热阱的非平衡物理与随机化学反应之间相互作用的理论描述和探索。方法将从简化的分析处理到详细模型的完整有限元模拟。所有的方法都与实验紧密结合在一起。