Hydrophobic self-assembly of a perylenediimide-linked DNA dumbbell into supramolecular polymers

Prakash P. Neelakandan, Zhengzheng Pan, Mahesh Hariharan, Yan Zheng, Haim Weissman, Boris Rybtchinski, Frederick D. Lewis

Research output: Contribution to journalArticle

67 Citations (Scopus)

Abstract

The self-assembly of DNA dumbbell conjugates possessing hydrophobic perylenediimide (PDI) linkers separated by an eight-base pair A-tract has been investigated. Cryo-TEM images obtained from dilute solutions of the dumbbell in aqueous buffer containing 100 mM NaCl show the presence of structures corresponding to linear end-to-end assemblies of 10-30 dumbbell monomers. The formation of assemblies of this size is consistent with analysis of the UV-vis and fluorescence spectra of these solutions for the content of PDI monomer and dimer chromophores. Assembly size is dependent upon the concentration of dumbbell and salt as well as the temperature. Kinetic analysis of the assembly process by means of salt-jump stopped-flow measurements shows that it occurs by a salt-triggered isodesmic mechanism in which the rate constants for association and dissociation in 100 mM NaCl are 3.2 × 107 M -1s-1 and 1.0 s-1, respectively, faster than the typical rate constants for DNA hybridization. TEM and AFM images of samples deposited from solutions having higher concentrations of dumbbell and NaCl display branched assemblies with linear regions >1 μm in length and diameters indicative of the formation of small bundles of dumbbell end-to-end assemblies. These observations provide the first example of the use of hydrophobic association for the assembly of small DNA duplex conjugates into supramolecular polymers and larger branched aggregates.

Original languageEnglish
Pages (from-to)15808-15813
Number of pages6
JournalJournal of the American Chemical Society
Volume132
Issue number44
DOIs
Publication statusPublished - Nov 10 2010

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Self assembly
Polymers
DNA
Salts
Base Pairing
Buffers
Fluorescence
Rate constants
Monomers
Association reactions
Temperature
Transmission electron microscopy
Flow measurement
Chromophores
perylenediimide
Dimers
Display devices
Kinetics

ASJC Scopus subject areas

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

Cite this

Hydrophobic self-assembly of a perylenediimide-linked DNA dumbbell into supramolecular polymers. / Neelakandan, Prakash P.; Pan, Zhengzheng; Hariharan, Mahesh; Zheng, Yan; Weissman, Haim; Rybtchinski, Boris; Lewis, Frederick D.

In: Journal of the American Chemical Society, Vol. 132, No. 44, 10.11.2010, p. 15808-15813.

Research output: Contribution to journalArticle

Neelakandan, Prakash P. ; Pan, Zhengzheng ; Hariharan, Mahesh ; Zheng, Yan ; Weissman, Haim ; Rybtchinski, Boris ; Lewis, Frederick D. / Hydrophobic self-assembly of a perylenediimide-linked DNA dumbbell into supramolecular polymers. In: Journal of the American Chemical Society. 2010 ; Vol. 132, No. 44. pp. 15808-15813.
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