Christoph Erben

Rapid Chiral Assembly of Rigid DNA Building Blocks for Molecular Nanofabrication

Practical components for three-dimensional molecular nanofabrication must be simple to produce, stereopure, rigid, and adaptable. We report a family of DNA tetrahedra, less than 10 nanometers on a side, that can self-assemble in seconds with near-quantitative yield of one diastereomer. They can be connected by programmable DNA linkers. Their triangulated architecture confers structural stability; by compressing a DNA tetrahedron with an atomic force microscope, we have measured the axial compressibility of DNA and observed the buckling of the double helix under high loads.

Reconfigurable, braced, three- dimensional DNA nanostructures

DNA nanotechnology makes use of the exquisite self-recognition of DNA in order to build on a molecular scale. Although static structures may find applications in structural biology and computer science, many applications in nanomedicine and nanorobotics require the additional capacity for controlled three-dimensional movement. DNA architectures can span three dimensions and DNA devices are capable of movement, but active control of well-defined three-dimensional structures has not been achieved. We demonstrate the operation of reconfigurable DNA tetrahedra whose shapes change precisely and reversibly in response to specific molecular signals. Shape changes are confirmed by gel electrophoresis and by bulk and single-molecule Förster resonance energy transfer measurements. DNA tetrahedra are natural building blocks for three-dimensional construction; they may be synthesized rapidly with high yield of a single stereoisomer, and their triangulated architecture conveys structural stability. The introduction of shape-changing structural modules opens new avenues for the manipulation of matter on the nanometre scale.

DNA cage delivery to mammalian cells.

DNA cages are nanometer-scale polyhedral structures formed by self-assembly from synthetic DNA oligonucleotides. Potential applications include in vivo imaging and the targeted delivery of macromolecules into living cells. We report an investigation of the ability of a model cage, a DNA tetrahedron, to enter live cultured mammalian cells. Cultured human embryonic kidney cells were treated with a range of fluorescently labeled DNA tetrahedra and subsequently examined using confocal microscopy and flow cytometry. Substantial uptake of tetrahedra into cells was observed both when the cells were treated with tetrahedra alone and when the cells were treated with a mixture of tetrahedra and a transfection reagent. Analysis of the subcellular localization of transfected tetrahedra using confocal microscopy and organelle staining indicates that the cages are located in the cytoplasm. FRET experiments indicate that the DNA cages remain substantially intact within the cells for at least 48 h after transfection. This is a first step toward the use of engineered DNA nanostructures to deliver and control the activity of cargoes within cells.

High-Resolution Structural Analysis of a DNA Nanostructure by cryoEM

Many DNA nanostructures have been produced and a wide range of potential applications have been proposed. However, confirmation of accurate 3D construction is particularly challenging. Here, we demonstrate that cryoEM may be exploited to obtain structural information at sufficient resolution to visualize the DNA helix and reveal the absolute stereochemistry of a 7 nm self-assembled DNA tetrahedron. Structural analysis at such high resolution by cryoEM image analysis is unprecedented for any biological molecule of this size.

A Facile Method for Reversibly Linking a Recombinant Protein to DNA

A simple modification allows DNA to be linked to recombinant proteins. DNA functionalized with three nitrilotriacetic acid groups forms coordination complexes with nickel ions and the His6‐tag of the recombinant protein (here, GFP). This noncovalent linkage is reversible, site‐specific and has a high (nanomolar) affinity.

Non‐covalent Single Transcription Factor Encapsulation Inside a DNA Cage

An elegant approach to the control of gene expression is to reversibly encapsulate the TFs in a drug-delivery cage. Within the cage, the TF cannot bind cellular DNA and is inactive; the cage can then be opened using external triggers, releasing and thus activating the TF. Molecular cages designed for encapsulation vary in size and fabrication method: fullerenes (approximately 1 nm) can encapsulate single atoms; [3] hollow metal nanoparticles [4] (approximately 100 nm) for proteins; and liposomes (100–800 nm) for drugs [5] or fluorescent molecules. [6] TF encapsulation by supramolecular nanoparticles (approximately 50 nm) for intracellular delivery has recently been reported. [7] Herein, we report a novel cage for a TF constructed using DNA. A DNA cage offers many advantages: for example, cages of dimensions similar to protein targets can be designed rationally to self-assemble in a single, rapid, and facile step. Examples of such DNA nanostructures range from polyhedra, [8] to much larger structures based on DNA origami. [9]

ISOPORPHYCENE : THE FOURTH CONSTITUTIONAL ISOMER OF PORPHYRIN WITH AN N4 CORE : OCCURRENCE OF E/Z ISOMERISM

Liberation of the ligand from the nickel complex 1 obtained by template synthesis yielded isoporphycene (as the octaethyl derivative 2), the first constitutional isomer of porphyrin with an N(4) core for which E/Z isomerism is involved: Compound 2 is present as the E isomer, which is in rapid, presumably acid-catalyzed equilibrium with a small amount (2 %) of the Z isomer. The remaining unknown constitutional isomers of porphyrin are considerably higher in energy than the already rather labile isoporphycene, so that the latter should mark the border of existence for this type of structural variant of porphyrin.

Manganese(III) and manganese(IV) corroles: synthesis, spectroscopic, electrochemical and X-ray structural characterization

The synthesis, spectroscopic characterization and electrochemistry of four Mn(III) and Mn(IV) octaethylcorroles are reported and the potentials of the Mn(III)/Mn(IV) and Mn(IV)/Mn(III) processes examined as a function of the axial ligand. The investigated compounds are represented as (OEC)Mn, (OEC)MnCl, (OEC)Mn(py) and (OEC)Mn(C6H5) where OEC is the trianion of octaethylcorrole. The first one-electron oxidation of (OEC)MnIII and (OEC)MnIII(py) in PhCN or pyridine containing 0.1 M TBAP leads to the facile formation of a Mn(IV) species while the first one-electron reduction of (OEC)MnIVCl and (OEC)MnIV(C6H5) in the same two solvents leads to the Mn(III) corrole. All other redox reactions occur at the corrole macrocycle to give π-cation radicals or π-anion radicals and there is no evidence for electrogeneration of a compound with a Mn(II) oxidation state as is the case for manganese(III) porphyrins which are all easily reduced to the Mn(II) state in nonaqueous media. The products of each Mn(III)/Mn(IV) redox reaction were characterized by UV-visible and/or ESR spectroscopy and the structures of (OEC)MnCl, (OEC)Mn(py) and (OEC)Mn(C6H5) were determined by single-crystal X-ray diffraction.

Isoporphycen, das vierte Porphyrin‐Konstitutionsisomer mit N4‐Kern – Auftreten von E/Z‐Isomerie

FreisetzungdesLiganden aus dem durch Templatsynthese gewonnenen Nickelkomplex 1 lieferte Isoporphycen (als Octaethylderivat 2), das erste Porphyrin-Konstitutionsisomer mit einem N4-Kern, bei dem E/Z-Isomerie ins Spiel kommt: 2 liegt als E-Isomer vor, das mit einer gerade noch nachweisbaren Menge (2 %) an Z-Isomer in sehr raschem, vermutlich saurekatalysiertem Gleichgewicht steht. Die verbleibenden unbekannten Porphyrin-Konstitutionsisomere sind noch erheblich energiereicher als das bereits labile Isoporphycen, so das mit diesem die Grenze der Existenzfahigkeit von Porphyrin-Strukturvarianten dieses Typs erreicht sein durfte.