Hydrophobic organic linkers in the self-assembly of small molecule-DNA hybrid dimers

A computational-experimental study of the role of linkage direction in product distributions and stabilities

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

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Detailed computational and experimental studies reveal the crucial role that hydrophobic interactions play in the self-assembly of small molecule-DNA hybrids (SMDHs) into cyclic nanostructures. In aqueous environments, the distribution of the cyclic structures (dimers or higher-order structures) greatly depends on how well the hydrophobic surfaces of the organic cores in these nanostructures are minimized. Specifically, when the cores are attached to the 3′-ends of the DNA component strands, they can insert into the minor groove of the duplex that forms upon self-assembly, favoring the formation of cyclic dimers. However, when the cores are attached to the 5′-ends of the DNA component strands, such insertion is hindered, leading to the formation of higher-order cyclic structures. These computational insights are supported by experimental results that show clear differences in product distributions and stabilities for a broad range of organic core-linked DNA hybrids with different linkage directions and flexibilities.

Original languageEnglish
Pages (from-to)2366-2376
Number of pages11
JournalJournal of Physical Chemistry B
Volume118
Issue number9
DOIs
Publication statusPublished - Mar 6 2014

Fingerprint

linkages
Dimers
Self assembly
self assembly
DNA
deoxyribonucleic acid
dimers
Molecules
products
strands
molecules
Nanostructures
inserts
grooves
insertion
flexibility
Direction compound
interactions

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Materials Chemistry
  • Surfaces, Coatings and Films

Cite this

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abstract = "Detailed computational and experimental studies reveal the crucial role that hydrophobic interactions play in the self-assembly of small molecule-DNA hybrids (SMDHs) into cyclic nanostructures. In aqueous environments, the distribution of the cyclic structures (dimers or higher-order structures) greatly depends on how well the hydrophobic surfaces of the organic cores in these nanostructures are minimized. Specifically, when the cores are attached to the 3′-ends of the DNA component strands, they can insert into the minor groove of the duplex that forms upon self-assembly, favoring the formation of cyclic dimers. However, when the cores are attached to the 5′-ends of the DNA component strands, such insertion is hindered, leading to the formation of higher-order cyclic structures. These computational insights are supported by experimental results that show clear differences in product distributions and stabilities for a broad range of organic core-linked DNA hybrids with different linkage directions and flexibilities.",
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