An Artificial Ribosome

我们计划创造一种人造核糖体。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，它通过连接从一小部分天然氨基酸中挑选出来的分子构件，‘读取’存储在基因中的信息，并‘写入’相应的蛋白质。能够将遗传密码转化为完全合成的序列定义聚合物的人造机械的创造将具有深远的影响。在比目前可能的反应和时间尺度小几个数量级的反应和时间尺度上进行分子机制的定向进化，将允许探索广阔的化学空间新区域，并导致与多肽和蛋白质的功能匹配和扩展的非天然聚合物的开发。能够在原位合成程序化产品的纳米机器可以实现纳米技术提供“智能”疗法的长期承诺。在更根本的层面上，我们可以重建复杂的生物行为，如基因调控，使人工生命系统的创造--合成生物学的重大挑战--又近了一步。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转换为序列定义的非天然聚合物的人造核糖体。包括我们自己在内的几个团体在实现这一目标方面取得了进展。核糖体已经被“改造”为接受非自然的积木，但这项技术非常耗时，而且积木的池仍然有限。完全从零开始合成的分子机器已经开发出来，可以执行顺序的化学合成，但合成很费力，而且没有容易阅读和重写的人工遗传密码。这两种方法之间的一个中间立场是利用自然的遗传密码-DNA-并将其与以模块化方式由简单组件构建的人工机器相结合。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。我们和其他人已经使用这种方法创建了可以执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，使用的积木是高度反应性的，因此随着时间的推移会降解为无用的。其次，机器无法识别反应是否成功发生，因此经常跳过中间构建块。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，这些DNA机器将激活构建块，使其仅在需要时才变得被动，并且能够在进行下一步之前感知到反应发生的时间。将这两项进展结合起来，将使我们能够创造一种能够自主、多步合成顺序控制聚合物的“人造核糖体”。我们将通过合成一种功能产物，在同一反应容器中并行执行多个合成，以及根据不同的环境信号触发特定产物的合成，展示这一革命性分子技术的一些潜在未来应用。这项工作将导致分子机械、合成生物学和聚合物化学领域的重大进展，并可能有许多实际应用，例如在核酸传感的护理点诊断。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.