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Side chain determinants of biopolymer function during selection and replication

Nature Chemical Biology volume 15, pages 419–426 (2019)Cite this article

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A Publisher Correction to this article was published on 11 March 2019

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Abstract

The chemical functionalities within biopolymers determine their physical properties and biological activities. The relationship between the side chains available to a biopolymer population and the potential functions of the resulting polymers, however, has proven difficult to study experimentally. Using seven sets of chemically diverse charged, polar, and nonpolar side chains, we performed cycles of artificial translation, in vitro selections for binding to either PCSK9 or IL-6 protein, and replication on libraries of random side chain-functionalized nucleic acid polymers. Polymer sequence convergence, bulk population target binding, affinity of individual polymers, and head-to-head competition among post-selection libraries collectively indicate that polymer libraries with nonpolar side chains outperformed libraries lacking these side chains. The presence of nonpolar groups, resembling functionality existing in proteins but missing from natural nucleic acids, thus may be strong determinants of binding activity. This factor may contribute to the apparent evolutionary advantage of proteins over their nucleic acid precursors for some molecular recognition tasks.

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Fig. 1: HFNAP translation, selection, and library design.
Fig. 2: Protein target binding activity, sequence convergence, and sequence distribution of HFNAPs selected for PCSK9 or IL-6 affinity.
Fig. 3: Head-to-head competition of seven pools following iterated selections for binding to PCSK9 or IL-6.
Fig. 4: Target-binding activity of individual HFNAPs by SPR.

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Code availability

The scripts used to analyze data from the head-to-head competition experiments are described and included in Supplementary Notes 2–4.

Data availability

High-throughput sequencing data will be available from the NCBI Sequence Read Archive under accession code SRP153119.

Change history

  • 11 March 2019

    In the version of this article originally published, several data points in Fig. 4c were shifted out of place during production. The corrected version of Fig. 4c is shown below. This error has been corrected in the PDF and HTML versions of the article.

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Acknowledgements

This work was supported by DARPA N66001-14-2-4053, NIH 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 A. Chan, J.P. Maianti, M. Packer, D.L. Usanov, B. Thuronyi, and C. Wilson for helpful comments and discussions. We also thank K. Arnett and R. Stoller for guidance with SPR experiments and analysis.

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Authors and Affiliations

  1. Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA

    Phillip A. Lichtor, Zhen Chen, Jonathan C. Chen & David R. Liu

  2. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA

    Phillip A. Lichtor, Zhen Chen, Nadine H. Elowe, Jonathan C. Chen & David R. Liu

  3. Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA

    David R. Liu

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Contributions

P.A.L., Z.C., J.C.C. performed experiments; P.A.L. and N.H.E. developed the SPR methodology; P.A.L., Z.C., and D.R.L. designed the research and wrote the manuscript; all authors reviewed and edited the manuscript.

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Correspondence to David R. Liu.

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

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Lichtor, P.A., Chen, Z., Elowe, N.H. et al. Side chain determinants of biopolymer function during selection and replication. Nat Chem Biol 15, 419–426 (2019). https://doi.org/10.1038/s41589-019-0229-2

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