Supramolecular Recognition of Phosphodiester-Based Donor and Acceptor Oligomers Forming Gels in Water

Abstract

Inspired by automated DNA synthesis, electron-rich dialkoxynaphthalene (DAN) donor and electron-deficient naphthalene-tetracarboxylic diimide (NDI) acceptor phosphodiester-linked homohexamers were synthesized by the phosphoramidite method. Two types of hexamers were prepared, one with only one phosphodiester between the aromatics (i.e., DAN or NDI) and a second with two phosphodiesters around a propanediol between the aromatics, leading to the latter more flexible and more hydrophilic hexamers. The folding properties of these homohexamers alone or mixed together, in water only, were studied by UV–visible absorption spectroscopy and atomic force microscopy (AFM). AFM imaging revealed that a 1:1 mixture of hexaDAN and hexaNDI formed fibers by charge transfer donor–acceptor recognition leading to a hydrogel after drying. The organization of the resulting structures is strongly dependent on the nature of the complementary partner, leading to the formation of mono- or multilayer hydrogel networks with different compactness.

Stabilization of DNA Duplexes and Hairpins by Charge-Transfer Interactions Using DAN:NDI Pairs

“…In another study, we showed that in crystals of the aptamer:thrombin complex, NDI and DAN form an alternate stacking starting from an NDI close to the DNA . These data confirmed molecular modeling studies that predicted alternate stacking. , …”

“…Along with our previous works devoted to the synthesis of DAN-NDI-based supramolecular structures as an alternated sequence, or as a duplex formed by recognition of a hexaDAN and a hexaNDI, these results prompted us to investigate in depth the influence of DAN:NDI pairs as surrogate base pairs in DNA duplexes. We present here a comprehensive study, performed by thermal denaturation, of the effect of charge-transfer interactions induced by the incorporation of multiple DAN (D) and NDI (N) units into DNA duplexes and hairpins at different positions.…”

“…45 These data confirmed molecular modeling studies that predicted alternate stacking. 42,46 Along with our previous works devoted to the synthesis of DAN-NDI-based supramolecular structures as an alternated sequence, 42 or as a duplex formed by recognition of a hexaDAN and a hexaNDI, 46 ■ RESULTS AND DISCUSSION Oligomers Synthesis. Starting from the previously reported phosphoramidite derivatives 1 and 2 42 and Q-linker solid supports 3 and 4 32 (Figure 1), DAN and NDI motifs were introduced into oligonucleotides at different positions using standard automated oligonucleotide synthesis on solid support according to phosphoramidite chemistry 47 (Table 1).…”

A single monomer difference can impact the nanostructure output of precision oligo(phosphodiesters)

“…42 Similar acceptor-donor recognition in phosphodiester oligomers has been shown to assemble hydrogel networks. 43 The Häner group reported multiple studies on the self-assembly of DNA amphiphiles based on pyrene, 44 phenanthrene 45 or tetraphenylethylene moieties 46 with minimal variation of the monomer sequences. A systematic investigation of the influence of the sequence of block oligo ( phosphodiester)s, therefore, remains lacking.…”