title: Insights into templated supramolecular polymerization: binding of naphthalene derivatives to ssDNA templates of different lengths.
abstract: We report on two diaminotriazine-equipped naphthalene derivatives that bind reversibly to a single-stranded DNA template or "tape-measure molecule" via hydrogen bonding, yielding monodisperse double-stranded DNA hybrids with one strand consisting of a supramolecular naphthalene backbone. These assemblies have been investigated extensively, both experimentally and theoretically. The structure and the templated self-assembly process of the complex have been characterized with UV-vis spectroscopy, circular dichroism spectroscopy, molecular dynamics simulations, cryo-transmission electron microscopy, liquid atomic force microscopy, electrospray ionization mass spectrometry, light scattering, and 1H NMR and infrared spectroscopy. We have found that the DNA hybrid complexes have a right-handed helical arrangement stabilized by pi-pi interactions and hydrogen bonds. The hydrophilic hydroxyl group at the end of the ethylene glycol of the guest molecule suppressed both the nontemplated self-assembly of the naphthalene guest molecules and the further aggregation of the entire DNA hybrid complex. Through the use of a theoretical mass-action model for the templated self-assembly, the host-guest and guest-guest interaction energies were estimated by fitting to the spectroscopic data. The differently estimated values of the interaction energies and thermodynamic parameters vary within experimental error, showing the self-consistency of the model. From the obtained correlation between the positions of the guest molecules bound on the template, we have obtained a qualitative theoretical picture of the way in which the guests are physically distributed on the templates. For short templates, the templates are filled one-by-one, even at moderate fractions of bound sites. For larger templates, the templates first have alternating sequences of filled and empty sections, after which, at large fractions of bound sites, virtually all of the binding sites for all template lengths are filled.
authors.affiliation: Laboratory for Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
authors.forename: Pim G A
authors.initials: PG
authors.lastname: Janssen
authors.forename: Sara
authors.initials: S
authors.lastname: Jabbari-Farouji
authors.forename: Mathieu
authors.initials: M
authors.lastname: Surin
authors.forename: Xavier
authors.initials: X
authors.lastname: Vila
authors.forename: Jeroen C
authors.initials: JC
authors.lastname: Gielen
authors.forename: Tom F A
authors.initials: TF
authors.lastname: de Greef
authors.forename: Matthijn R J
authors.initials: MR
authors.lastname: Vos
authors.forename: Paul H H
authors.initials: PH
authors.lastname: Bomans
authors.forename: Nico A J M
authors.initials: NA
authors.lastname: Sommerdijk
authors.forename: Peter C M
authors.initials: PC
authors.lastname: Christianen
authors.forename: Philippe
authors.initials: P
authors.lastname: Leclère
authors.forename: Roberto
authors.initials: R
authors.lastname: Lazzaroni
authors.forename: Paul
authors.initials: P
authors.lastname: van der Schoot
authors.forename: E W
authors.initials: EW
authors.lastname: Meijer
authors.forename: Albertus P H J
authors.initials: AP
authors.lastname: Schenning
mesh_terms: D002942:Circular Dichroism; D020285:Cryoelectron Microscopy; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000648:ultrastructure; D009682:Magnetic Resonance Spectroscopy; D046529:Microscopy, Electron, Transmission; D008958:Models, Molecular; D008968:Molecular Conformation; D009281:Naphthalenes / Q000737:chemistry*; D017186:Titrimetry
chemical_list: D004277:DNA, Single-Stranded; D009281:Naphthalenes; C031721:naphthalene