Enhancing the melting properties of small molecule-DNA hybrids through designed hydrophobic interactions: An experimental-computational study

Ibrahim Eryazici, Ilyas Yildirim, George C Schatz, Sonbinh T. Nguyen

Research output: Contribution to journalArticle

23 Citations (Scopus)


Detailed experimental and computational studies revealed the important role that hydrophobic interactions play in the aqueous assembly of rigid small molecule-DNA hybrid (rSMDH) building blocks into nanoscale cage and face-to-face (ff) dimeric structures. In aqueous environments, the hydrophobic surfaces of the organic cores in these nanostructures are minimized by interactions with the core in another rSMDHs, with the bases in the attached DNA strands, and/or with the base pairs in the final assembled structures. In the case that the hydrophobic surfaces of the cores could not be properly isolated in the assembly process, an ill-defined network results instead of dimers, even at low concentration of DNA. In contrast, if ff dimers can be formed with good minimization of the exposed hydrophobic surfaces of the cores, they are highly stable structures with enhanced melting temperatures and cooperative melting behavior.

Original languageEnglish
Pages (from-to)7450-7458
Number of pages9
JournalJournal of the American Chemical Society
Issue number17
Publication statusPublished - May 2 2012


ASJC Scopus subject areas

  • Chemistry(all)
  • Catalysis
  • Biochemistry
  • Colloid and Surface Chemistry

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