Robust nucleation control via crisscross polymerization of highly coordinated DNA slats

Dionis Minev,William M Shih,Christopher M Wintersinger,Anastasia Ershova

doi:10.1038/s41467-021-21755-7

Dionis Minev, William M Shih + Show 2 more

Open Access

https://doi.org/10.1038/s41467-021-21755-7

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Abstract

Natural biomolecular assemblies such as actin filaments or microtubules can exhibit all-or-nothing polymerization in a kinetically controlled fashion. The kinetic barrier to spontaneous nucleation arises in part from positive cooperativity deriving from joint-neighbor capture, where stable capture of incoming monomers requires straddling multiple subunits on a filament end. For programmable DNA self-assembly, it is likewise desirable to suppress spontaneous nucleation to enable powerful capabilities such as all-or-nothing assembly of nanostructures larger than a single DNA origami, ultrasensitive detection, and more robust algorithmic assembly. However, existing DNA assemblies use monomers with low coordination numbers that present an effective kinetic barrier only for slow, near-reversible growth conditions. Here we introduce crisscross polymerization of elongated slat monomers that engage beyond nearest neighbors which sustains the kinetic barrier under conditions that promote fast, irreversible growth. By implementing crisscross slats as single-stranded DNA, we attain strictly seed-initiated nucleation of crisscross ribbons with distinct widths and twists.

Highlights

Natural biomolecular assemblies such as actin filaments or microtubules can exhibit all-ornothing polymerization in a kinetically controlled fashion
To explore how a monomer’s coordination number can be incremented to maintain the kinetic barrier to spontaneous nucleation while using irreversible growth conditions, we modeled the free energies of assemblies using different monomer designs with the kinetic Tile Assembly Model[6,8,11]
The half coordination number n for a given monomer is defined as the number of bonds it must make to be attached to an assembly using near-reversible reaction conditions (ε → 0)

Summary

Introduction

Natural biomolecular assemblies such as actin filaments or microtubules can exhibit all-ornothing polymerization in a kinetically controlled fashion. Barriers can be constructed by kinetic trapping of monomers into inactive states (see Supplementary Discussion 1 for more discussion), and/or by making stable capture of incoming monomers contingent on the cooperative binding of two or more previously acquired neighbors (i.e., half the monomer coordination number)1–38 In the latter case—which we refer to here as joint-neighbor capture of monomers—a large coordination number would allow two prized characteristics of selfassembly that otherwise would be mutually exclusive for such systems: near-complete suppression of spontaneous nucleation[39,40] along with rapid, irreversible growth from introduced seeds. We establish a theoretical comparison showing that crisscross assembly sustains kinetic barriers under fast, irreversible reaction conditions far better than existing DNA tile systems We implement this architecture with singlestranded DNA (ssDNA) slats that polymerize from introduced DNA-origami or ssDNA seeds into monodisperse ribbons with average lengths in excess of 4 μm. We show the formation of ribbons with programmable twists and coils that can be assembled into tubes of different diameters

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