[en] 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 p-p 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.
Disciplines :
Chemistry Physics
Author, co-author :
Janssen, P.G.A.
Jabbari-Farouji, S.
Surin, Mathieu ; Université de Mons > Faculté des Sciences > Chimie des matériaux nouveaux
Vila, X.
Gielen, J.C.
de Greef, T.F.A.
Vos, M.R.J.
Bomans, P.H.H.
Sommerdijk, N.A.J.M.
Christianen, P.C.M.
Leclère, Philippe ; Université de Mons > Faculté des Sciences > Chimie des matériaux nouveaux
Lazzaroni, Roberto ; Université de Mons > Faculté des Sciences > Service de Chimie des matériaux nouveaux
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In principle, ΔHe can be determined by fitting the temperature dependent data with the model for cooperative self-assembly. However, we found that because of a second process, the calculated enthalpy of the temperature-dependent measurements increases with the concentration and deviates from the enthalpy found via the concentration- dependent T e measurement. Possibly the lateral interactions present between strands of G (see the cryo-TEM image) give rise to an additional decrease in absorption intensity and therefore a higher enthalpy.
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In this experiment, a nonstoichiometric ratio was used in order to determine Tp more accurately. It should be noted that Tte does not change with the ratio between the guest and the thymine while Tp shows a linear trend with the logarithm of this ratio. Tte depends on the guest concentration, while Tp also depends on the template concentration. See the Supporting Information.
The G1-dT40 mixture at this concentration was not suitable for detecting hydrogen bonds because the mixture precipitated during the measurements and thus gave only very broad signals at temperatures where aggregates are formed.
Previously, we have shown with ESI-MS that G1 binds to oligothymines via hydrogen bonding (see ref 12b). We obtained similar results for G2; see the Supporting Information.
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The correlation length ξ0 here is defined exactly at the polymerization transition for the idealized case of an infinitely long chain. For template sizes q > ξ0, ξ0 ≈ξ is reasonably accurate. For template sizes q < ξ0, ξ decreases with q.
For these long template lengths, a predominance of completely filled templates is present only at high template coverages of, say, > 0.9, where the actual correlation length £ approaches infinity.
The theoretical model provides us with much more information about the details of the system than only gross averages, which can be of great value for the practical applications of templated self-assemblies. In principle, our course-grained model can be used to calculate the way that the guest monomers are distributed over the templates quantitatively as a function of q and 6 via an implicit set of equations (see the Supporting Information). For ease of calculation and clarity, we chose to directly construct a qualitative picture of the dominant configurations of the occupation of the templates by relating the binding energies ε and g with q and 6, similar to what was done by Zimm and Bragg14 for the helix- coil transition in polypeptides.
