Self-assembly of perylenediimide-single strand DNA conjugates: Employing hydrophobic interactions and DNA base pairing to create a diverse structural space

The self-assembly behavior of DNA conjugates possessing a perylenediimide (PDI) head group and a single N-oligonucleotide tail has been investigated using a combination of optical spectroscopy and cryogenic transmission electron microscopy (cryo-TEM) imaging. In order to obtain insight into the interplay between DNA base pairing and PDI hydrophobic interactions we employed systematic variation in the length and composition of the oligo tails. Conjugates with short (TA)n or (CG)n oligo tails (n ≤ 3) form fibers (helical or nonhelical) constructed from -stacked PDI head groups with pendent oligo tails at room temperature in aqueous solution. Conjugates with longer (TA)n oligo tails also form stacks of PDI head groups in solution, which are further stabilized by base pairing between their oligo tails, leading to fiber bundling and formation of bilayers. The longer (CG)n conjugates (n  3) 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)3 gives rise to both fibers and large assemblies, while (CG)5 assembles preferentially into large ordered structures. Overall, we show that the PDI-N-oligonucleotide conjugate motif can assemble via hydrophobic -stacking and/or oligo base pairing resulting in a diverse structural space. Our findings provide guidelines for the design of simple and complex structures from molecules containing DNA strands and hydrophobic moieties.