The layer-by-layer growth of a surface-attached metal-organic framework (SURMOF), [Cu2(F4bdc)2(dabco)] (F4bdc = tetrafluorobenzene-1,4-dicarboxylate and dabco = 1,4-diazabicyclo-[2.2.2]octane), on carboxylate- and pyridine-terminated surfaces has been investigated by various surface characterization techniques. Particular attention was paid to the dependency of the crystal orientation and morphology on surface functionality, deposition temperature, and first layer order. For the fully oriented deposition of SURMOFs, not only a suitable surface chemistry but also the appropriate temperature has to be chosen. In the case of carboxylate-terminated surfaces, the expected [100] oriented [Cu2(F4bdc)2(dabco)] SURMOF can be achieved at low temperatures (5 °C). In contrast, the predicted [001] oriented SURMOF on pyridine-terminated surface was obtained only at high deposition temperatures (60 °C). Interestingly, we found that rearrangement processes in the very first layer determine the final orientation (distribution) of the growing crystals. These effects could be explained by a surprisingly hampered substitution at the apical position of the Cu2-paddle wheel units, which requires significant thermal activation, as supported by quantum-chemical calculations.

The cocaine aptamer is a DNA three-way junction that binds cocaine at its helical junction. We studied the global conformation and overall flexibility of the aptamer in the absence and presence of cocaine by pulsed electron-electron double resonance (PELDOR) spectroscopy, also called double electron-electron resonance (DEER). The rigid nitroxide spin label Ç was incorporated pairwise into two helices of the aptamer. Multi-frequency 2D PELDOR experiments allow the determination of the mutual orientation and the distances between two Çs. Since Ç is rigidly attached to double-stranded DNA, it directly reports on the aptamer dynamics. The cocaine-bound and the non-bound states could be differentiated by their conformational flexibility, which decreases upon binding to cocaine. We observed a small change in the width and mean value of the distance distribution between the two spin labels upon cocaine binding. Further structural insights were obtained by investigating the relative orientation between the two spin-labeled stems of the aptamer. We determined the bend angle between this two stems. By combining the orientation information with a priori knowledge about the secondary structure of the aptamer, we obtained a molecular model describing the global folding and flexibility of the cocaine aptamer.

Distance measurements are performed between a pair of spin labels attached to nucleic acids using Pulsed Electron-Electron Double Resonance (PELDOR, also called DEER) spectroscopy which is a complementary tool to other structure determination methods in structural biology. The rigid spin label Ç, when incorporated pairwise into two helical parts of a nucleic acid molecule, allows the determination of both the mutual orientation and the distance between those labels, since Ç moves rigidly with the helix to which it is attached. We have developed a two-step protocol to investigate the conformational flexibility of flexible nucleic acid molecules by multi-frequency PELDOR. In the first step, a library with a broad collection of conformers, which are in agreement with topological constraints, NMR restraints and distances derived from PELDOR, was created. In the second step, a weighted structural ensemble of these conformers was chosen, such that it fits the multi-frequency PELDOR time traces of all doubly Ç-labelled samples simultaneously. This ensemble reflects the global structure and the conformational flexibility of the two-way DNA junction. We demonstrate this approach on a flexible bent DNA molecule, consisting of two short helical parts with a five adenine bulge at the center. The kink and twist motions between both helical parts were quantitatively determined and showed high flexibility, in agreement with a Förster Resonance Energy Transfer (FRET) study on a similar bent DNA motif. The approach presented here should be useful to describe the relative orientation of helical motifs and the conformational flexibility of nucleic acid structures, both alone and in complexes with proteins and other molecules.

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