Coding of hierarchical protein assembly pathways with DNA

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Importance

Structural sophistication in nature would not be possible without hierarchical assembly: the concept that an initial building block (e.g., a polypeptide) contains all of the structural and chemical information necessary to determine its assembly along a multi-pathway steps to generate a complex architecture (eg, the viral capsid). Translating this concept into synthetic systems is a big challenge. Here we use DNA – the model of life – to direct the hierarchical assembly of proteins. Through DNA design, we can change the direction of protein assembly and the pathway by which protein-DNA conjugates will assemble as well as make distinct structures by directing assembly along different pathways. . These findings will facilitate the assembly of protein-DNA materials with a structural complexity closer to that seen in nature.

Abstract

The structural and functional diversity of materials in nature depends on the controlled assembly of discrete building blocks into complex architectures via specific, multi-stage, hierarchical assembly paths. Achieving similar complexity in synthetic materials through hierarchical assembly is difficult due to the difficulties in defining multiple recognition zones on synthetic building blocks and controlling the sequence through which these recognition sites direct assembly. Here, we show that we can exploit the chemical anisotropy of proteins and the programmability of DNA ligands to deliberately control the hierarchical assembly of protein-DNA materials. Through the design of DNA sequences, we introduce orthogonal DNA interactions with disparate interaction forces (“strong” and “weak”) on specific geometric regions of a model protein, stable protein 1 ( Sp1). We show that the spatial coding of DNA ligands leads to highly directional assembly via strong interactions and that, by design, the first assembly step increases the multivalence of weak DNA-DNA interactions which give rise to an emerging second step. assembly. Furthermore, we demonstrate that judicious DNA design not only directs assembly along a given pathway, but can also drive distinct structural results from a single pathway. This combination of protein surface and DNA sequence design allows us to encode the necessary structural and chemical information into building blocks to program their hierarchical multi-step assembly. Our results represent a strategy to control the hierarchical assembly of proteins in order to achieve a diverse set of protein-DNA materials by design.

Footnotes

    • Accepted August 25, 2021.
  • Author contributions: research designed by OGH, BEP and CAM; OGH and BEP have done research; OGH and BEP provided new reagents / analytical tools; OGH and BEP analyzed the data; and OGH, BEP and CAM wrote the article.

  • The authors declare no competing interests.

  • This article is a direct PNAS submission.

  • This article contains additional information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2106808118/-/DCSupplemental.

Data availability

All study data is included in the article and / or SI Annex.


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