Prof. Dr. Karim Fahmy
Head Biophysics
Phone: +49 351 260 - 2952, 3601
Fax: 12952, 3553

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Paramagnetic DNA Nanostructures

DNA origami triangles magnetic circular dichroism (MCD) of DNA origami

DNA-origami are nanostructures that are formed by the rational design of DNA scaffold and staple strands, using base complementarity to fold the scaffold into a predicted arbitrary shape. We have studied the potential of paramagnetic decoration to confer magnetic properties to such nanostructures. We show that Eu3+, a paramagnetic lanthanide, is strongly coordinated by two differently shaped DNA nanostructures. Whereas natural DNA double strands would change their geometry and aggregate upon neutralization of heir surface charge by Eu3+, the DNA-origami exhibit sufficient rigidity to preserve their structure even when their molecular surfaces are are close to saturated with the trivalent lanthanide. This allows producing DNA-based structures with magnetic properties based on the paramagnetism of a trivalent lanthanide. Lars Opherden et al., Langmuir, 2014, 30: pp 8152–8159 (2015).

Figure 1 (left): DNA origami triangles(left AFM image) preserve their shape when they bind large amounts of Eu3+ (about 2000 per DNA origami) before they aggregate (obvious from the sudden decrease of their UV-vis absorption, red curve). The shape of the DNA-origami is preserved even under conditions of excess Eu3+ (right AFM image). (One arm of the triangle is ~130 nm long). (Move mouse over image to enlarge.)

Figure 2 (right): Eu3+ affects the magnetic circular dichroism (MCD) of DNA origami in a superstructure-dependent manner. The replacement of the natural Mg2+ counterion to the DNA phosphate backbone by Eu3+ strongly affects the MCD of DNA origami triangles below 225 nm, whereas in six-helical bundles, only the weak change between 280 and 300 nm is observed. The Eu3+ effect on the MCD of of both superstructures differs from that of on genomic DNA, evidencing a superstructure-dependent interaction of the lanthanide with the DNA structures. In addition, time-resolved luminescence of Eu3+ bound to the DNA origami supports the conclusion that the coordination geometry of Eu3+ is different in the two superstructures and exhibits an asymmetric coordination environment. Such binding site asymmetries form the basis for exploiting the paramagnetism of the lanthanide to orient DNA-based nanostructures in external magnetic fields. (Move mouse over image to enlarge.)

Calorimetric monitoring of metal toxicity in organisms

The toxicity of heavy metals and radionuclides cannot be assessed from environmental concentrations of the respective elements alone because many factors affect their bioavailability. The relevant parameters are largely unknown in the environment and molecular mechanisms of metal uptake not generally elucidated. We have initiated experiments that use the organism itself to determine the concentration threshold above which a metabolic response to the metal can be detected. This response can be accurately determined by microcalorimetry in complex synthetic and natural growth media. In addition to uranium, we are currently studying the chemitoxic effect of europium as a model for trivalent actinides using a variety of bacteria including isolates from nuclear waste piles.

Structure and Energetics of Europium Polycarboxylate Complexes

The mobility of actinides and other metal ions in the environment is largely influenced by their interaction with humic acids. The latter bind multivalent cations at their multiple carboxylic functions. We have studied the binding of the lanthanide Eu3+, a non-radioactive model for the physico-chemical behaviour of trivalent actinides, to benzenetetracarboxylic acid (BTC), a polycarboxylate model for humic acids. The figure shows the heat uptake during Eu BTC complex formation measured by isothermal titration calorimetry upon injection of BTC into a 1 mM Eu3+ solution. The integrated heats (lower panel) of the fast (red) and slow (blue) calorimetric response were evaluated separately and assigned to a 1:1 complex formation and an ensuing metal-mediated polymerization, respectively. Both processes are entropy-driven with ΔH of 14-17 kJ mol-1 and ΔS of 130-160 J mol-1 K-1. In combination with infrared, fluorescence spectroscopy and DFT calculations an energetically and structurally consistent model of the lanthanide-BTC interaction and polymerization (reaction scheme) has been derived (Barkleit et al. 2011).

Infrared spectroscopy reveals the physical basis of desiccation tolerance in an anhydrobiotic organism.

We have used FTIR-difference spectroscopy to study the effect of desiccation stress on the physical state of C.elegans larvae that are either competent or defficient of trehalose synthesis. The spectra indicate a critical role of trehalose on the reversibility of dessication-induced packing changes in lipidic components of the organism. The vibrational frequency of the CH2 stretching modes (dominated by lipidic acyl chains) change during desiccation of the live organism. Only in the presence of trehalose, these changes are reversed by subsequent rehydration. The physiological, morphological and spectroscopic traits of different C.elegans strains are well correlated (Erkut et al. CurrBiol 2011; Erkut et al. Worm 2012).

Picture (right): Infrared absorption spectra in the range of CH2 stretching modes of live C.elegans Dauer larvae. Top to bottom: initial IR absorption spectrum; absorption changes upon rehydration of dessicated larvae; absorption changes during dessication of larvae; absorption changes during dessication of extracted C.elegans lipids. Irreversible changes in hdyration / dehydration spectra of this trehalose defficient strain can be seen at 2858 and 2916 cm-1. (Move mouse over image to enlarge.)

Aqueous coordination chemistry and photochemistry of uranyl(VI) oxalate.

uranyl(VI) oxalate

The bioavailability of uranyl in contaminated soils and waters depends on its solubility. The latter is strongly affacted by the uranyl redox state as U(VI) complexes exhibit high solubility as compared to the essentially unsoluble reduced U(IV) state. Light can additionally affect the redox state through photochemical reactions in uranyl complexes with organic ligands as in light exposed soils or plant tissues of contaminated areas. Using density functional theory (DFT) calculations, we revisited a classical problem of uranyl(VI) oxalate photochemical decomposition. Photoreactivities of uranyl(VI) oxalate complexes are found to correlate largely with ligand-structural arrangements. Importantly, the intramolecular photochemical reaction is inhibited when oxalate is bound to uranium exclusively in chelate binding mode. Previously proposed mechanisms involving a UO2(C2O4)22− (1:2) complex as the main photoreactive species are thus unlikely to apply, because the two oxalic acids are bound to uranium in a chelating binding mode. Our DFT results suggest that the relevant photoreactive species are UO2(C2O4)34− (1:3) and (UO2)2(C2O4)56− (2:5) complexes binding uranium in an unidentate fashion. These species go through decarboxylation upon excitation to the triplet state, which ensues the release of CO2 and reduction of U(VI) to the U(V) state (Tsushima et al., 2010).

Picture (right): DFT-result for the ground state geometry (bond lengths in Angstrom) of a uranyl:oxalate 2:5 complex. The oxalates in unidentate coordination (lower left and upper right) undergo decarboxylation upon photon-induced electron transfer and U(V) formation in the excited state of the actinide. (Move mouse over image to enlarge.)

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