Encoding hierarchical assembly pathways of proteins with DNA – pnas.org

Significance

Structural sophistication in nature would not be possible without hierarchical assembly: the concept that an initial building block (e.g., polypeptide) contains all necessary structural and chemical information to determine its assembly along a multistep pathway to generate a complex architecture (e.g., viral capsid). Translating this concept to synthetic systems is an outstanding challenge. Here, we use DNAthe blueprint of lifeto direct the hierarchical assembly of proteins. Through DNA design, we can change the directionality of protein assembly and pathway by which proteinDNA conjugates will assemble as well as realize distinct structures by directing assembly along different pathways. These findings will facilitate the assembly of proteinDNA materials with structural complexity more closely approaching that observed in nature.

The structural and functional diversity of materials in nature depends on the controlled assembly of discrete building blocks into complex architectures via specific, multistep, hierarchical assembly pathways. Achieving similar complexity in synthetic materials through hierarchical assembly is challenging due to difficulties with defining multiple recognition areas on synthetic building blocks and controlling the sequence through which those 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 proteinDNA materials. Through DNA sequence design, we introduce orthogonal DNA interactions with disparate interaction strengths (strong and weak) onto specific geometric regions of a model protein, stable protein 1 (Sp1). We show that the spatial encoding of DNA ligands leads to highly directional assembly via strong interactions and that, by design, the first stage of assembly increases the multivalency of weak DNADNA interactions that give rise to an emergent second stage of assembly. Furthermore, we demonstrate that judicious DNA design not only directs assembly along a given pathway but can also direct distinct structural outcomes from a single pathway. This combination of protein surface and DNA sequence design allows us to encode the structural and chemical information necessary into building blocks to program their multistep hierarchical assembly. Our findings represent a strategy for controlling the hierarchical assembly of proteins to realize a diverse set of proteinDNA materials by design.

Author contributions: O.G.H., B.E.P., and C.A.M. designed research; O.G.H. and B.E.P. performed research; O.G.H. and B.E.P. contributed new reagents/analytic tools; O.G.H. and B.E.P. analyzed data; and O.G.H., B.E.P., and C.A.M. wrote the paper.

The authors declare no competing interest.

This article is a PNAS Direct Submission.

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

All study data are included in the article and/or SI Appendix.

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Encoding hierarchical assembly pathways of proteins with DNA - pnas.org