An Artificial Ribosome

我们建议制造一种人造核糖体。生命依赖于精确的、顺序控制的聚合物合成。核糖体是一种天然的分子机器，它“读取”存储在基因中的信息，并通过连接从一小部分天然氨基酸中选择的分子构建块来“写入”相应的蛋白质。能够将遗传密码翻译成完全由合成序列定义的聚合物的人工机器的创造将具有深远的意义。通过分子机械在反应和时间尺度上的定向进化，比目前可能的要小几个数量级，这将允许探索广阔的化学空间新区域，并导致非天然聚合物的发展，这些聚合物与肽和蛋白质的功能相匹配并扩展。能够就地编程合成产品的纳米机器可以实现纳米技术提供“智能”治疗的长期承诺。在更基本的层面上，我们可以重建复杂的生物行为，如基因调控，使人造生命系统的创造——合成生物学的巨大挑战——更接近一步。我们将结合我们在DNA纳米技术和聚合物化学方面的专业知识，构建能够将核酸遗传密码翻译成序列定义的非天然聚合物的人工核糖体。包括我们在内的几个团体已经朝着这一目标取得了进展。核糖体已经被“改造”成可以接受非自然的构建块，但这项技术非常耗时，而且构建块的数量仍然有限。完全从零开始合成的分子机器已经被开发出来，可以进行连续的化学合成，但这种合成非常费力，而且没有易于读取和重写的人工遗传密码。这两种方法之间的中间地带是利用自然的遗传密码——DNA——并将其与由简单组件以模块化方式构建的人工机器集成在一起。我们使用DNA纳米技术，利用DNA双螺旋的可预测碱基配对，来构建这些机器。我们和其他人已经用这种方法创造了可以进行顺序化学合成的自主分子机器。然而，这些早期的尝试受到两个问题的严重限制。首先，所使用的构建模块是高度反应性的，因此随着时间的推移会降解而变得无用。其次，机器无法识别反应是否成功发生，因此经常跳过中间的构建模块。在这个雄心勃勃的计划中，我们将通过开发DNA机器来解决这些问题，这种机器只在需要时激活构建块，使其产生反应，并且能够在进行下一步之前感知反应的发生。整合这两项进展将使我们能够创造一种“人工核糖体”，能够自主地、多步骤地合成序列控制的聚合物。我们将通过合成功能性产品，在同一反应容器中并行进行多种合成，以及根据不同的环境信号触发特定产品的合成，来展示这种变革性分子技术的一些潜在的未来应用。这项工作将在分子机器、合成生物学和聚合物化学领域取得重大进展，并可能有许多实际应用，例如在即时诊断的核酸传感方面。通过一项传播、讲习班和知识交流方案，我们将确保我们的新技术惠及能够实际使用这些技术的受益者。

We propose to create an artificial ribosome.Life depends on precise, sequence-controlled polymer synthesis. The ribosome is the natural molecular machine that 'reads' information stored in genes and 'writes' the corresponding proteins by concatenating molecular building blocks chosen from a small set of natural amino acids. The creation of artificial machinery capable of translating a genetic code into a completely synthetic sequence-defined polymer would have profound implications. Directed evolution by molecular machinery working on reaction- and time-scales orders of magnitude smaller than currently possible would allow exploration of vast new regions of chemical space and lead to the development of non-natural polymers that match and extend the functionalities of peptides and proteins. Nanomachines capable of programmed product synthesis in situ could realize the longstanding promise of nanotechnology to deliver 'smart' therapeutics. On a more fundamental level, we could recreate complex biological behaviours such as gene regulation, bringing the creation of artificial living systems -the grand challenge of synthetic biology- a step closer. We will combine our expertise in DNA nanotechnology and polymer chemistry to build artificial ribosomes capable of translating a nucleic acid genetic code into sequence-defined, non-natural polymers. Several groups, including our own, have made progress towards this goal. The ribosome has been 'engineered' to accept unnatural building blocks, but this technique is extremely time-consuming and the pool of building blocks remains limited. Molecular machines synthesised entirely from scratch have been developed that perform sequential chemical synthesis, but the syntheses are laborious and there is no readily readable and rewritable artificial genetic code. A middle ground between these two approaches is to make use of nature's genetic code - DNA - and integrate it with an artificial machine constructed in a modular fashion from simple components. We use DNA nanotechnology, which makes use of the predictable base-pairing of the DNA double helix, to construct these machines. We and others have used this approach to create autonomous molecular machines that can perform sequential chemical synthesis. However, these early attempts have been severely limited by two problems. First, the building blocks used are highly reactive and so degrade to become useless over time. Second, the machines have no way of recognising if a reaction has occurred successfully or not, so often skip intermediate building blocks.In this ambitious programme we will address these issues by developing DNA machines that activate building blocks to become reactive only when they are needed and that are capable of sensing when a reaction has occurred before progressing to the next step. Integrating these two advances will allow us to create an 'artificial ribosome' capable of autonomous, multistep synthesis of sequence-controlled polymers. We will demonstrate some of the potential future applications of this transformative molecular technology by synthesising a functional product, performing multiple syntheses in parallel in the same reaction vessel, and triggering synthesis of particular products in response to different environmental signals.This work will result in significant advances in the areas of molecular machines, synthetic biology and polymer chemistry, and could have numerous practical applications, for example in nucleic acid sensing for point-of-care diagnostics. Through a programme of dissemination, workshops and knowledge exchange we will ensure that our new technologies reach beneficiaries who can make practical use of them.