Persistent, well-defined, monodisperse, pi-conjugated organic nanoparticles via G-quadruplex self-assembly.

Several oligo(p-phenylene-vinylene) oligomers capped with a guanosine or a guanine moiety have been prepared via a palladium-catalyzed cross-coupling reaction. Their self-assembly, in both the absence and presence of alkaline salts, has been studied by means of different techniques in solution (NMR, MS, UV-vis, CD, fluorescence), solid state (X-ray diffraction), and on surfaces (STM, AFM). When no salt is added, these pi-conjugated molecules self-associate in a mixture of hydrogen-bonded oligomers, among which the G-quartet structure may be predominant if the steric hindrance around the guanine base becomes important. In contrast, in the presence of sodium or potassium salts, well-defined assemblies of eight functional molecules (8mers) can be formed selectively and quantitatively. In these assemblies, the pi-conjugated oligomers are maintained in a chirally tilted (J-type) stacking arrangement, which is manifested by negative Cotton effects, small bathochromic absorption and emission shifts, and fluorescence enhancements. Furthermore, these self-assembled organic nanostructures, approximately 1.5-2.0 nm high and 8.5 nm wide, exhibit an extraordinary stability to temperature or concentration changes in apolar media, and they can be transferred and imaged over solid substrates as individual nanoparticles, showing no significant dissociation or further aggregation.

Insights into templated supramolecular polymerization: binding of naphthalene derivatives to ssDNA templates of different lengths.

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.

Electrospray-ionization mass spectrometry for screening the specificity and stability of single-stranded-DNA templated self-assemblies.

Supramolecular complexes consisting of a single-stranded oligothymine (dTn) as the host template and an array of guest molecules equipped with a complementary diaminotriazine hydrogen-bonding unit have been studied with electrospray-ionization mass spectrometry (ESI-MS). In this hybrid construct, a supramolecular stack of guest molecules is hydrogen bonded to dTn. By changing the hydrogen-bonding motif of the DNA host template or the guest molecules, selective hydrogen bonding was proven. We were able to detect single-stranded-DNA (ssDNA)-guest complexes for strands with lengths of up to 20 bases, in which the highest complex mass detected was 15 kDa; these complexes constitute 20-component self-assembled objects. Gas-phase breakdown experiments on single- and multiple-guest-DNA assemblies gave qualitative information on the fragmentation pathways and the relative complex stabilities. We found that the guest molecules are removed from the template one by one in a highly controlled way. The stabilities of the complexes depend mainly on the molecular weight of the guest molecules, a fact suggesting that the complexes collapse in the gas phase. By mixing two different guests with the ssDNA template, a multicomponent dynamic library can be created. Our results demonstrate that ESI-MS is a powerful tool to analyze supramolecular ssDNA complexes in great detail.

Double cation adduction in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of electron deficient anthraquinone derivatives.

Six anthraquinone derivatives were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS). Clear (pseudo) molecular ions were observed for all the compounds. Interestingly, for some derivatives, strong ions with double cation adduction were also recorded in the positive mode. It is remarkable that all these ions are singly charged. In this work, possible mechanisms for the double cation adduction were investigated and discussed. It appears that the double cation adduction was due to the electron deficient nature of the derivatives, and formed by taking up two singly charged cations and one electron. Substituents on the anthraquinone ring were found to have a significant effect on the double cation adduction. In contrast, no considerable influence of the acidity of MALDI matrix/solution was observed, even on the double proton adduction. Furthermore, it was demonstrated that double cation adduction might occur in the MALDI gas-phase plume. In addition to the anthraquinones, three more electron deficient compounds of different types, i.e. a perylene bisimide derivative (PB), 3,7-decanoylamino-4,8-dihydrobenzo[1,2-b:4,5-b']dithiophene-4,8-dione (TQ) and 6,6-phenyl C61-butyric acid methyl ester (PCBM), were also analyzed with MALDI TOF MS. The results indicate that the 'abnormal' double cation adduction might be a 'normal' phenomenon in the MALDI TOF MS analysis of many electron deficient compounds.

Directing energy transfer in discrete one-dimensional oligonucleotide-templated assemblies.

Monodisperse DNA-templated one dimensional dye assemblies have been constructed in which the energy transfer can be directed. Fluorescence experiments suggest an optimum transfer efficiency for stacks of 30 bases long.

DNA-templated assembly of dyes and extended π-conjugated systems.

This feature article reports on the use of DNA as a template to assemble dyes and π-conjugated systems with the aim to construct functional multicomponent nanostructures that have a well-defined size, shape and sequence.

ssPNA templated assembly of oligo(p-phenylenevinylene)s.

A single-stranded oligothymine peptide nucleic acid (PNA) was used as a template for the assembly of a chiral oligo(p-phenylenevinylene) diaminotriazine derivative (OPV) in methylcyclohexane (MCH) revealing nanostructures in which the size is controlled by the template.