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Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes
Published on: November 1, 2012
Controlling the thermally-driven crystallization of DNA-coated nanoparticles with formamide
Theodore Hueckel1, Seungyeon Woo1, Robert J Macfarlane1
1Department of Materials Science and Engineering, Massachusetts Institute of Technology (MIT), 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA. rmacfarl@mit.edu.
Abstract:
DNA-coated nanoparticles, also known as programmable atom equivalents (PAEs), facilitate the construction of materials with nanoscopic precision. Thermal annealing plays a pivotal role by controlling DNA hybridization kinetics and thermodynamics, which ensures the formation of intended structures. While various design handles such as particle size, DNA design, and salt concentration influence the stability of the DNA duplexes linking PAEs in a lattice, their influence on the system's melting temperature (Tm) often follows complicated trends that make rational tuning of self-assembly challenging. In this work, the denaturant formamide is used to precisely tune the thermal response of PAEs. Our results reveal a clear and predictable trend in the PAEs' response to formamide, enabling rational control over the Tm of a diverse set of PAE systems. Unlike adjustments made through alterations to PAE design or solution parameters such as ionic strength, formamide achieves its temperature shift without impacting the kinetics of assembly. As a result, PAEs can be rapidly crystallized at ambient temperatures, producing superlattices with similar quality to PAE crystals assembled through standard protocols that use higher temperatures. This study therefore positions formamide as a useful tool for enhancing the synthesis of complex nanostructures under mild conditions.

