Pathway Diversity in the Self-Assembly of DNA-Derived Bioconjugates

Abstract

The pathway diversity of the self-assembly of amphiphilic DNA-pyrene conjugates is described.The hydrophobic pyrene units drive the self-assembly of the anionic oligomers in an aqueous environment into ribbon-shaped, DNA-grafted supramolecular polymers. Isothermal mixing of two types of sorted ribbons, each of which contains only one kind of two complementary oligonucleotides, results in the formation of tight networks. Thermal disassembly of these kinetically trapped networks and subsequent re-assembly of the liberated components leads to mixed supramolecular polymers, which now contain both types of oligonucleotides. The scrambling of the oligonucleotides prevents the interaction between ribbons and, thus, network formation. The results show that a high local density of DNA strands in linear arrays favors hybridization among sorted polymers, whereas hybridization among mixed arrays is prevented. The lack of DNA hybridization among mixed ribbons is ascribed to the electrostatic repulsion between identical, hence non-complementary, oligonucleotides. The findings highlight the importance of kinetically trapped states on the structural and functional properties of supramolecular polymers containing orthogonal self-assembly motifs.

Dual‐Input Regulation and Positional Control in Hybrid Oligonucleotide/Discotic Supramolecular Wires

“…The addition of lipids into DNA scaffolds has led to the development of supramolecular systems with novel functions, as highlighted in recent reviews . DNA hybrid‐grafted supramolecular polymers based on the self‐assembly properties of oligopyrenes have been reported, with the structure of the oligopyrenes dictating the morphology of the final assembly into helical 1D supramolecular polymers and requiring a high temperature to incorporate additional monomers …”

Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

“…These rod-shaped nanoassemblies are quite stable and are decomposed to the monomers only after heating. The interaction of such nanoassemblies containing complementary oligonucleotides leads to the pairing-driven formation of nanorod networks ( Figure 38 ), as confirmed by AFM [ 249 , 250 ]. The oligonucleotide nanorods were also decorated with gold nanoparticles.…”

“…It should be noted that the stacking interactions of oligopyrene fragments can define the formation of oligonucleotide nanoconstructions entirely. When introduced at the oligonucleotide termini, oligopyrene fragments of different molecules interact in solution to form polypyrene [ 249 , 250 ] or mixed polypyrene-perylenediimide [ 251 , 252 ] stacks retaining oligonucleotide parts anchored. These rod-shaped nanoassemblies are quite stable and are decomposed to the monomers only after heating.…”

DNA-inspired oligomers: from oligophosphates to functional materials

“…Applying thermal stimuli is a suitable approach to avoid kinetically trapped states and obtain the desired set of properties. 43 Isothermal mixing of two kinds of 1D DNA-grafted supramolecular polymer containing complementary oligonucleotide strands leads to the formation of cross-linked networks. Despite the dynamic nature of self-assembled materials, these networks remain unchanged for days.…”