Nonenzymatic synthesis of anomerically pure, mannosyl-based molecular probes for scramblase identification studies.

The chemical synthesis of molecular probes to identify and study membrane proteins involved in the biological pathway of protein glycosylation is described. Two short-chain glycolipid analogs that mimic the naturally occurring substrate mannosyl phosphoryl dolichol exhibit either photoreactive and clickable properties or allow the use of a fluorescence readout. Both probes consist of a hydrophilic mannose headgroup that is linked to a citronellol derivative via a phosphodiester bridge. Moreover, a novel phosphoramidite chemistry-based method offers a straightforward approach for the non-enzymatic incorporation of the saccharide moiety in an anomerically pure form.

Assembly and functionalization of supramolecular polymers from DNA-conjugated squaraine oligomers.

DNA conjugated oligomers of organic molecules are candidates for applications in the materials and medical sciences, in diagnostics, in optical devices, for delivery or for the design of complex molecular architectures. Herein, we describe the synthesis and properties of DNA-conjugated squaraine (Sq) oligomers. The oligomers self-assemble into supramolecular polymers that are amenable to further functionalization via DNA hybridization, as shown by the attachment of gold nanoparticles (AuNPs).

Supramolecular Assembly of DNA-Phenanthrene Conjugates into Vesicles with Light-Harvesting Properties.

Vesicle-shaped supramolecular polymers are formed by self-assembly of a DNA duplex containing phenanthrene overhangs at both ends. In the presence of spermine, the phenanthrene overhangs act as sticky ends linking the DNA duplexes together. In aqueous solution, the assembly leads to vesicles with a diameter in the range of 50-200 nm. Fluorescence measurements show that the assembled phenanthrene units act as light-harvesting complexes and transfer absorbed energy to an acceptor, such as pyrene or Cy3, which can either be directly added to the polymer or attached via a complementary DNA strand. The presence of DNA in the nanostructures allows the construction of light-harvesting vesicles that are amenable to derivatization with different functional groups.

Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease.

The use of the DNA duplex as a supramolecular scaffold is an established approach for the assembly of chromophore aggregates. In the absence of detailed structural insight, the characterization of thus assembled oligochromophores is, today, largely based on solution-phase spectroscopy. Here, we describe the crystal structures of three DNA-organized chromophore aggregates. DNA hybrids containing non-nucleosidic pyrene and phenanthrene building blocks were co-crystallized with the recently described binding domain of the restriction enzyme BpuJI. Crystal structures of these complexes were determined at 2.7, 1.9 and 1.6 Å resolutions. The structures reveal aromatic stacking interactions between pyrene and/or phenanthrene units within the framework of the B-DNA duplex. In hybrids containing a single modification in each DNA strand near the end of the duplex, the two polyaromatic hydrocarbons are engaged in a face-to-face stacking orientation. Due to crystal packing and steric effects, the terminal GC base pair is disrupted in all three crystal structures, which results in a non-perfect stacking arrangement of the aromatic chromophores in two of the structures. In a hybrid containing a total of three pyrenes, crystal lattice induced end-to-end stacking of individual DNA duplexes leads to the formation of an extended aromatic π-stack containing four co-axially arranged pyrenes. The aromatic planes of the stacked pyrenes are oriented in a parallel way. The study demonstrates the value of co-crystallization of chemically modified DNA with the recombinant binding domain of the restriction enzyme BpuJI for obtaining detailed structural insight into DNA-assembled oligochromophores.

A modular LHC built on the DNA three-way junction.

A light-harvesting complex composed of a π-stacked multichromophoric array in a DNA three-way junction is described. The modular design allows for a ready exchange of non-covalently attached energy acceptors.

The DNA three-way junction as a mould for tripartite chromophore assembly.

The DNA three-way junction serves as a scaffold for the molecular organization of non-nucleosidic alkynylpyrene and perylenediimide chromophores located at the branch point of the structure. Depending on the composition of the tripartite assembly, the constructs possess distinct spectroscopic properties, ranging from monomer or excimer fluorescence to completely quenched tripartite aggregates.

Interactive blood damage analysis for ventricular assist devices.

Ventricular Assist Devices (VADs) support the heart in its vital task of maintaining circulation in the human body when the heart alone is not able to maintain a sufficient flow rate due to illness or degenerative diseases. However, the engineering of these devices is a highly demanding task. Advanced modeling methods and computer simulations allow the investigation of the fluid flow inside such a device and in particular of potential blood damage. In this paper we present a set of visualization methods which have been designed to specifically support the analysis of a tensor-based blood damage prediction model. This model is based on the tracing of particles through the VAD, for each of which the cumulative blood damage can be computed. The model's tensor output approximates a single blood cell's deformation in the flow field. The tensor and derived scalar data are subsequently visualized using techniques based on icons, particle visualization, and function plotting. All these techniques are accessible through a Virtual Reality-based user interface, which features not only stereoscopic rendering but also natural interaction with the complex three-dimensional data. To illustrate the effectiveness of these visualization methods, we present the results of an analysis session that was performed by domain experts for a specific data set for the MicroMed DeBakey VAD.

Recruitment of the NCoA/SRC-1/p160 family of transcriptional coactivators by the aryl hydrocarbon receptor/aryl hydrocarbon receptor nuclear translocator complex.

The aryl hydrocarbon receptor complex heterodimeric transcription factor, comprising the basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain aryl hydrocarbon receptor (AHR) and aryl hydrocarbon receptor nuclear translocator (ARNT) proteins, mediates the toxic effects of TCDD (2,3,7,8 tetrachlorodibenzo-p-dioxin). The molecular events underlying TCDD-inducible gene activation, beyond the activation of the AHRC, are poorly understood. The SRC-1/NCoA-1, NCoA-2/GRIP-1/TIF-2, and p/CIP/AIB/ACTR proteins have been shown to act as mediators of transcriptional activation. In this report, we demonstrate that SRC-1, NCoA-2, and p/CIP are capable of independently enhancing TCDD-dependent induction of a luciferase reporter gene by the AHR/ARNT dimer. Furthermore, injection of anti-SRC-1 or anti-p/CIP immunoglobulin G into mammalian cells abolishes the transcriptional activity of a TCDD-dependent reporter gene. We demonstrate by coimmunoprecipitation and by a reporter gene assay that SRC-1 and NCoA-2 but not p/CIP are capable of interacting with ARNT in vivo after transient transfection into mammalian cells, while AHR is capable of interacting with all three coactivators. We confirm the interactions of ARNT and AHR with SRC-1 with immunocytochemical techniques. Furthermore, SRC-1, NCoA-2, and p/CIP all associate with the CYP1A1 enhancer region in a TCDD-dependent fashion, as demonstrated by chromatin immunoprecipitation assays. We demonstrate by yeast two-hybrid, glutathione S-transferase pulldown, and mammalian reporter gene assays that ARNT requires its helix 2 domain but not its transactivation domain to interact with SRC-1. This indicates a novel mechanism of action for SRC-1. SRC-1 does not require its bHLH-PAS domain to interact with ARNT or AHR, but utilizes distinct domains proximal to its p300/CBP interaction domain. Taken together, these data support a role for the SRC family of transcriptional coactivators in TCDD-dependent gene regulation.