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Evolution of sequence-defined highly functionalized nucleic acid polymers

Abstract

The evolution of sequence-defined synthetic polymers made of building blocks beyond those compatible with polymerase enzymes or the ribosome has the potential to generate new classes of receptors, catalysts and materials. Here we describe a ligase-mediated DNA-templated polymerization and in vitro selection system to evolve highly functionalized nucleic acid polymers (HFNAPs) made from 32 building blocks that contain eight chemically diverse side chains on a DNA backbone. Through iterated cycles of polymer translation, selection and reverse translation, we discovered HFNAPs that bind proprotein convertase subtilisin/kexin type 9 (PCSK9) and interleukin-6, two protein targets implicated in human diseases. Mutation and reselection of an active PCSK9-binding polymer yielded evolved polymers with high affinity (KD = 3 nM). This evolved polymer potently inhibited the binding between PCSK9 and the low-density lipoprotein receptor. Structure–activity relationship studies revealed that specific side chains at defined positions in the polymers are required for binding to their respective targets. Our findings expand the chemical space of evolvable polymers to include densely functionalized nucleic acids with diverse, researcher-defined chemical repertoires.

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Fig. 1: Design and construction of the sequence-defined polymer library.
Fig. 2: Selection of PCSK9-binding polymers from a random HFNAP library.
Fig. 3: Evolution of an improved PCSK9-binding polymer.
Fig. 4: Characterization of IL-6-binding HFNAPs selected from a random library.

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Acknowledgements

This work was supported by the DARPA Fold Fx program (N66001-14-2-4053), the NIH R01 EB022376 (formerly R01 GM065400) and R35 GM118062, and the Howard Hughes Medical Institute. Z.C. was partially supported by the Y. Kishi Graduate Prize in Chemistry and Chemical Biology sponsored by the Eisai Corporation. The authors thank J. Niu, R. Hili, J. P. Maianti, D. L. Usanov and A. Chan for helpful discussions. We thank the Center for Macromolecular Interactions in the Department of Biological Chemistry and Molecular Pharmacology at Harvard Medical School for access to the Biacore T200 SPR instrument, and M. Blome, B. Lang and K. Arnett for technical assistance with the SPR experiments. We thank the Harvard FAS Small Molecule Mass Spectrometry facility for access to ESI-MS instruments and S. A. Trauger for technical assistance.

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Z.C. and D.R.L. conceived and designed the study. Z.C., P.A.L., A.P.B. and J.C.C. performed the experiments. Z.C., P.A.L. and D.R.L. wrote the manuscript.

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Correspondence to David R. Liu.

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Z.C., D.R.L., and Harvard University have filed patent applications on DNA-templated polymerization.

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Chen, Z., Lichtor, P.A., Berliner, A.P. et al. Evolution of sequence-defined highly functionalized nucleic acid polymers. Nature Chem 10, 420–427 (2018). https://doi.org/10.1038/s41557-018-0008-9

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