Hydrophobic self-assembly of a perylenediimide-linked DNA dumbbell into supramolecular polymers.
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 × 10(7) M(-1)s(-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.
Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.
Prakash P
PP
Neelakandan
Zhengzheng
Z
Pan
Mahesh
M
Hariharan
Yan
Y
Zheng
Haim
H
Weissman
Boris
B
Rybtchinski
Frederick D
FD
Lewis
D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D007094:Imides / Q000737:chemistry*; D046911:Macromolecular Substances; D046529:Microscopy, Electron, Transmission; D015394:Molecular Structure; D010569:Perylene / Q000031:analogs & derivatives* / Q000737:chemistry; D011108:Polymers / Q000737:chemistry*
D007094:Imides; D046911:Macromolecular Substances; D011108:Polymers; C521332:perylenediimide; D010569:Perylene; D004247:DNA