US researchers have developed a purely chemical and enzyme-free system that can build synthetic polymers using DNA as a template. The work offers the opportunity to harness the power of natural selection by creating large libraries of synthetic polymers in a similar way that nature evolves biopolymers such as proteins.
The field of synthetic genetics is relatively new and aims to direct the genetic machinery of life to evolve synthetic polymers. These could have new or improved biological functions not found in nature, which could have biomedical applications.
Previously, directed evolution strategies were limited because they could only evolve molecules similar to biopolymers that occur in nature, namely nucleic acids and proteins. This is because these methods rely on interactions with nature’s polymerase enzymes to undergo transcription and translation processes in order to replicate.
Although one way around this is to develop synthetic polymerases, it is a major undertaking that often requires sophisticated protein engineering. This drawback means that synthetic polymers have primarily served as bulk materials, rather than as precisely folded molecules that can target a specific molecule or catalyse a chemical reaction.Synthetic successNow, David Liu’s lab at Harvard University in US has overcome this limitation by coming up with an enzyme-free approach which, under the guidance of DNA templates, forms genetically-encoded synthetic polymers that are structurally distinct from nucleic acids.‘Unlike those made by traditional chemical polymerisation methods, the synthetic polymers generated in our system are sequence-defined, length-defined and programmed by DNA templates,’ explains co-author Jia Niu. ‘In contrast to many of the current translation strategies that rely upon biological transcription or translation machinery, our method can accommodate a variety of different backbone and side chain structures that cannot otherwise be incorporated, such as beta peptides.’The team’s system works by using macrocyclic substrates that allow DNA-templated couplings with synthetic polymer building blocks that are structurally unrelated to nucleic acids. To prevent the polymer from directly interacting with the template, they introduced peptide nucleic acid (PNA) adapter units which mediate the interaction with the DNA template.A polymer product was then generated after disulfide linkers between the adapters and the building blocks were cleaved. The team showed the system could make several synthetic polymers including polyethylene glycol and beta peptides.Evolving libraries‘Since this process also covalently linked the product with its encoding template, iterated rounds of translation, selection and template amplification, could be performed enabling the opportunity to evolve the synthetic polymer toward novel or improved functions,’ says Niu.‘This is a major new advance that could dramatically expand our understanding of the types of polymers that are capable of undergoing Darwinian evolution,’ comments John Chaput who investigates synthetic genetics at Arizona State University, US.The team are now trying to determine whether their DNA-templated translation system is capable of generating a library of synthetic polymers containing billions of sequences. ’Our hope is that such libraries will be diverse enough to enable the ready discovery of synthetic polymers with a vast array of functions ranging from binding to catalysis,’ says Niu. ‘As these experiments continue, it will be interesting to see what types of structures can be isolated from their libraries,’ says Chaput. ‘Will synthetic polymers isolated by in vitro evolution collapse into structures that resemble folded proteins or will they adopt completely different types of structures whose shapes are governed by a new set of rules? I suspect that it could be a little bit of both, but it remains to be seen.’‘We have long envisioned that synthetic polymers could fold into tertiary structures and function at the single-molecule level if they had defined and heritable sequence information to enable them to be subjected to iterative rounds of directed evolution,’ Niu adds. ‘This work is a step toward this ultimate goal.’
ReferencesJ Niu, R Hili and D R Liu, Nat. Chem., 2013, DOI: 10.1038/NCHEM.1577
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