Self‐Assembly of Perylenediimide–Single‐Strand‐DNA Conjugates: Employing Hydrophobic Interactions and DNA Base‐Pairing To Create a Diverse Structural Space

Abstract

The self-assembly behavior of DNA conjugates possessing a perylenediimide (PDI) head group and an N-oligonucleotide tail has been investigated using a combination of optical spectroscopy and cryogenic transmission electron microscopy (cryo-TEM) imaging. To obtain insight into the interplay between PDI hydrophobic interactions and DNA base-pairing we employed systematic variation in the length and composition of the oligo tails. Conjugates with short (TA) or (CG) oligo tails (n≤3) form helical or nonhelical fibers constructed from π-stacked PDI head groups with pendent oligo tails in aqueous solution. Conjugates with longer (TA) oligo tails also form stacks of PDI head groups, which are further aggregated by base-pairing between their oligo tails, leading to fiber bundling and formation of bilayers. The longer (CG) conjugates form PDI end-capped duplexes, which further assemble into PDI-stacked arrays of duplexes leading to large scale ordered assemblies. Cryo-TEM imaging reveals that (CG) gives rise to both fibers and large assemblies, whereas (CG) assembles preferentially into large ordered structures.

Fluorescent Nucleobase Analogues with Extended Pi Surfaces Stabilize DNA Duplexes Containing O6‐Alkylguanine Adducts

“…This result is consistent with previous observations for Per and may be rationalized on the basis of hydrophobic interactions favouring probe pairing with the more hydrophobic O 6 ‐alkylG adducts than with polar canonical nucleobases. This hydrophobic pairing phenomenon has been previously observed with other non‐natural nucleosides . The highest DNA duplex stabilities were observed for ExBenzi paired with either of the O 6 ‐alkylG adducts, while similar stabilization of O 6 ‐alkylG was observed for both ExBIM and Per ( Figure , Table ).…”

DNA-inspired oligomers: from oligophosphates to functional materials

“…An alternative design approach to arrive at 1D supramolecular polymers in sequence-specific oligomers is based on end-to-end stacking of chromophores. 44 Thus, Lewis and Rybtchinski reported a double-stranded DNA capped at both sides with a perylenediimide 15. The strong stacking of the chromophores accounts for the formation of 1D fibers.…”

Amphiphilic DNA Organic Hybrids: Functional Materials in Nanoscience and Potential Application in Biomedicine

“…In 2017, Lewis introduced in detail the self-assembly of PDI-single strand DNA conjugates with different DNA lengths and different DNA sequences. These PDI–DNA conjugates in aqueous solution were assembled into a diverse structural space that includes fibers and more complex aggregates, depending on the hydrophobic π-π-stacking interaction of PDI molecules and base-pairing recognition of oligonucleotide [47]. These results provided a possible research approach to control over self-assembly and realizing novel structural motifs.…”