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

Ashutosh Kumar Mishra, Haim Weissman, Elisha Krieg, Kevin A. Votaw, Martin McCullagh, Boris Rybtchinski, Frederick D. Lewis

Research output: Contribution to journalArticle

7 Citations (Scopus)


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)n or (CG)n 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)n 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)n 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)3 gives rise to both fibers and large assemblies, whereas (CG)5 assembles preferentially into large ordered structures.

Original languageEnglish
Pages (from-to)10328-10337
Number of pages10
JournalChemistry - A European Journal
Issue number43
Publication statusPublished - Aug 1 2017



  • aggregation
  • dna base-pairing
  • hydrophobic effect
  • imaging
  • pi-interaction

ASJC Scopus subject areas

  • Chemistry(all)

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