Possibilities and limits of DNA-enabled programmable 2D self-assembly

27 May 2024, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Programmable self-assembly provides a promising avenue to improve upon traditional synthesis and create multi-component materials with emergent properties and arbitrary nanoscale complexity. However, its most successful realizations utilizing DNA often use complicated arduous procedures that result in low yields. Here, we employ coarse-grained molecular dynamics to uncover the ranges of temperatures and misbinding strengths needed for successful one-pot self-assembly of generic, two-dimensional (2D), and distinguishable blocks. Analysis of the energies associated with a single-stranded DNA interacting with all other sequences within a mixture revealed that the success of DNA-based assembly is primarily determined by the strongest misbinding a given sequence can encounter with a sequence highly similar to its reverse complement. This enabled us to design optimized sequence ensembles with acceptably weak and consequently rare misbinding. An estimate is provided for the maximum size of, and complexity of sequences needed to synthesize self-assembled structures with high accuracy and yield, with potential relevance for DNA-functionalized low-dimensional materials for electronics and energy storage.

Keywords

programmable self-assembly
misbinding
error-free DNA-mediated assembly
DNA sequence design
coarse-grained molecular dynamics
DNA-functionalized 2D materials
aperiodic nanostructures

Supplementary materials

Title
Description
Actions
Title
Programmable Self-Assembly SI
Description
Supplementary MD simulations, methods section, and examples of optimal DNA sequence collections with low misbinding.
Actions

Comments

Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.