An Artificial Ribosome
Lead Research Organisation:
University of Oxford
Department Name: Oxford Physics
Abstract
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.
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.
Planned Impact
The impact of our creation of an artificial ribosome will be scientific, technological, and societal.
Several scientific research fields will benefit from this research. Our systems are modelled on biological molecular machinery and on biological principles of programmed assembly, replication and evolution - contributing to research in *synthetic biology*. We aim to enable *sequence-controlled polymer synthesis*, a scientific challenge and an important research field in its own right. Natural proteins, made by linking the same amino acid building blocks in different sequences, are extraordinarily diverse, including sensors, exquisitely precise catalysts and structural elements: these natural examples demonstrate that control of sequence is the key to control of function. Our machinery will allow similar control over molecular assembly while allowing the use of a much wider palette of building blocks and chemistries and thus give access to new functionalities, including the possibility of unnatural polymers that emulate the ability of proteins to adopt well-defined functional folds. This will be an important advance in the field of *nanoscience* in general and *synthetic molecular machinery* in particular. It will help to lay the foundations of a completely new field of *molecular robotics*.
Our programme will provide excellent interdisciplinary training, for post-doctoral researchers directly employed and graduate students working on associated projects, enabling them to face challenges at the interfaces between chemistry, physics and biology. It will thus contribute to the creation of a workforce with the skills required to translate 21st Century science into technologies, products and industries.
We will bring together the UK's diverse community of researchers working in fields related to the development of artificial life through a focused workshop designed to generate a follow-on Programme Grant application.
We will use this project as an opportunity to open up public discussion of nanotechnology. Applications envisaged for our research are hugely positive and run counter to stereotypical 'grey goo' horror stories around nanoscience. Through the innovative use of outreach activities bridging the arts and sciences we will promote a more nuanced understanding and debate of the subject. Activities planned include: a Meet the Expert event in collaboration with the Thinktank Birmingham Science Museum; a schools' workshop in which students learn about recent advances in artificial life before exploring its social and ethical implications through science fiction; and participation in a national science event, e.g. Big Bang Festival, RS Summer Exhibition or British Science Festival. The results of consultations performed as part of our public engagement programme will be channelled through the learned societies to provide advice to government on future policy developments.
Several scientific research fields will benefit from this research. Our systems are modelled on biological molecular machinery and on biological principles of programmed assembly, replication and evolution - contributing to research in *synthetic biology*. We aim to enable *sequence-controlled polymer synthesis*, a scientific challenge and an important research field in its own right. Natural proteins, made by linking the same amino acid building blocks in different sequences, are extraordinarily diverse, including sensors, exquisitely precise catalysts and structural elements: these natural examples demonstrate that control of sequence is the key to control of function. Our machinery will allow similar control over molecular assembly while allowing the use of a much wider palette of building blocks and chemistries and thus give access to new functionalities, including the possibility of unnatural polymers that emulate the ability of proteins to adopt well-defined functional folds. This will be an important advance in the field of *nanoscience* in general and *synthetic molecular machinery* in particular. It will help to lay the foundations of a completely new field of *molecular robotics*.
Our programme will provide excellent interdisciplinary training, for post-doctoral researchers directly employed and graduate students working on associated projects, enabling them to face challenges at the interfaces between chemistry, physics and biology. It will thus contribute to the creation of a workforce with the skills required to translate 21st Century science into technologies, products and industries.
We will bring together the UK's diverse community of researchers working in fields related to the development of artificial life through a focused workshop designed to generate a follow-on Programme Grant application.
We will use this project as an opportunity to open up public discussion of nanotechnology. Applications envisaged for our research are hugely positive and run counter to stereotypical 'grey goo' horror stories around nanoscience. Through the innovative use of outreach activities bridging the arts and sciences we will promote a more nuanced understanding and debate of the subject. Activities planned include: a Meet the Expert event in collaboration with the Thinktank Birmingham Science Museum; a schools' workshop in which students learn about recent advances in artificial life before exploring its social and ethical implications through science fiction; and participation in a national science event, e.g. Big Bang Festival, RS Summer Exhibition or British Science Festival. The results of consultations performed as part of our public engagement programme will be channelled through the learned societies to provide advice to government on future policy developments.
