Synthesis of 'head-to-tail' cyclized peptides on solid support using a chelating amide as new orthogonal protecting group.

The synthesis of 'head-to-tail' cyclized peptides requires orthogonal protecting groups. Herein, we report on the introduction of bis(2-pyridylmethyl)amine (Bpa) as a new protecting group for carboxylic functions in SPPS. The synthesis of the Bpa-protected aspartic acid was straightforward, and its utility was investigated under standard peptide synthesis conditions. The new protecting group was cleaved in a very mild way using Cu(OAc)2 and 2-(trimethylsilyl)ethanol as nucleophile in a microwave oven without affecting other groups. Hence, the new group is ideally suited for the synthesis of 'head-to-tail' cyclic peptides, as demonstrated for a cyclic pentapeptide and cyclic hexapeptides.

Unusual orthogonality in the cleavage process of closely related chelating protecting groups for carboxylic acids by using different metal ions.

Three structurally related relay protecting groups for carboxylic acids that are based on chelating amines have been developed. These protecting groups can easily be introduced by coupling the carboxylic acid and the corresponding amine in the presence of 2-(1H-benzotriazole-1-yl)-1,1,3,3-tetramethyluronium tetrafluoroborate (TBTU). In addition to being stable to a whole array of reaction conditions, these protecting groups are also stable under acidic and basic conditions, allowing them to be used in combination with the ester protection of carboxylic acids. The cleavage of these protecting groups is activated by the chelation of metal ions, involving an unusual coordination of the amide nitrogen. Despite their similarity, cleavage of these protecting groups is possible in both a stepwise and an orthogonal fashion by applying different metal salts.

A novel method for the labelling of peptides and proteins through a bioorthogonal Staudinger reaction by using 2-cyanoethyl phosphoramidites.

Chemoselective modification of biomolecules: The reaction between 2-cyanoethyl phosphoramidites and azides is economical and can be performed in different solvents, including aqueous buffers. The course of the reaction with azido-modified amino acids, peptides or proteins and different label molecules was followed by (31)P NMR spectroscopy.

Modification and optimization of the bis-picolylamide-based relay protection for carboxylic acids to be cleaved by unusual complexation with Cu2+ salts.

A simple modification of our recently published protection scheme for carboxylic acids as amides resulted in a new protecting group with significantly improved properties. It requires shorter reaction times for deprotection and allows us to replace Cu(OTf)(2) by CuCl(2), indicating at the same time the importance of the nature of the anion of the Cu(2+) source. Since the new scheme fulfills all criteria required for an ideal protection group it should find widespread application in synthetic organic chemistry.

Site specific chemoselective labelling of proteins with robust and highly sensitive Ru(II) bathophenanthroline complexes.

The bioorthogonal and chemoselective fluorescence labelling of several cell-free synthesized proteins containing a site-specifically incorporated azido amino acid was possible using different alkyne-functionalized Ru(II) bathophenanthroline complexes. We were able to achieve a selective labelling even in complex mixtures of proteins despite the fact that ruthenium dyes normally show a high tendency for unspecific interactions with proteins and are commonly used for total staining of proteins. Since the employed Ru complexes are extremely robust, photo-stable and highly sensitive, the approach should be applicable to the production of labelled proteins for single molecule spectroscopy and fluorescence-based interaction studies.

Accurate distance determination of nucleic acids via Förster resonance energy transfer: implications of dye linker length and rigidity.

In Förster resonance energy transfer (FRET) experiments, the donor (D) and acceptor (A) fluorophores are usually attached to the macromolecule of interest via long flexible linkers of up to 15 Å in length. This causes significant uncertainties in quantitative distance measurements and prevents experiments with short distances between the attachment points of the dyes due to possible dye-dye interactions. We present two approaches to overcome the above problems as demonstrated by FRET measurements for a series of dsDNA and dsRNA internally labeled with Alexa488 and Cy5 as D and A dye, respectively. First, we characterize the influence of linker length and flexibility on FRET for different dye linker types (long, intermediate, short) by analyzing fluorescence lifetime and anisotropy decays. For long linkers, we describe a straightforward procedure that allows for very high accuracy of FRET-based structure determination through proper consideration of the position distribution of the dye and of linker dynamics. The position distribution can be quickly calculated with geometric accessible volume (AV) simulations, provided that the local structure of RNA or DNA in the proximity of the dye is known and that the dye diffuses freely in the sterically allowed space. The AV approach provides results similar to molecular dynamics simulations (MD) and is fully consistent with experimental FRET data. In a benchmark study for ds A-RNA, an rmsd value of 1.3 Å is achieved. Considering the case of undefined dye environments or very short DA distances, we introduce short linkers with a propargyl or alkenyl unit for internal labeling of nucleic acids to minimize position uncertainties. Studies by ensemble time correlated single photon counting and single-molecule detection show that the nature of the linker strongly affects the radius of the dye's accessible volume (6-16 Å). For short propargyl linkers, heterogeneous dye environments are observed on the millisecond time scale. A detailed analysis of possible orientation effects (κ(2) problem) indicates that, for short linkers and unknown local environments, additional κ(2)-related uncertainties are clearly outweighed by better defined dye positions.

Novel three-color FRET tool box for advanced protein and DNA analysis.

We report on a new three-color FRET system which we were able to verify in peptides as well as in synthetic DNA. All three chromophores could be introduced by a building block approach avoiding postsynthetic labeling. Additional features are robustness, matching spectroscopic properties, high-energy transfer, and sensitivity. The system was investigated in detail on a set of peptides as well as an array of tailored oligonucleotides. The detailed analysis of the experimental data and comparison with theoretical considerations were in excellent agreement. It is shown that in the case of polypeptides specific interaction with the fluorescence probes has to be considered. In contrast with DNA, the fluorescence probes did not show any indications of such interactions. The novel three-color FRET toolbox revealed the potential for applications studying fundamental processes of three interacting molecules in life science applications.

Photophysical characterization of a FRET system using tailor-made DNA oligonucleotide sequences.

We have carried out a detailed photophysical study of the FRET D/A pair consisting of a carbostyril donor and a Ru(II)bathophenanthroline complex acceptor in double-stranded synthetic DNA. Altogether 13 different double-stranded 30 base pair DNAs showing small incremental differences in the distances between donor and acceptor were synthesized. Using the fluorescence of the donor as well as of the acceptor, D/A separations were determined and compared to those derived from a well-established model for DNA distance calculations. The model calculations and anisotropy studies revealed that the donor can nearly be seen as a free rotator allowing the application of the established FRET data evaluation.

Size-tunable micron-bubbles based on fluorous-fluorous interactions of perfluorinated dendritic polyglycerols.

This paper describes the behavior of various generations of polyglycerol dendrimers that contain a perfluorinated shell. The aggregation in organic solvents is based on supramolecular fluorous-fluorous interactions, which can be described by means of (19)F NMR spectroscopy. In order to study the interaction and aggregation phenomena of dendrimers with perfluorinated shell and perfluoro-tagged guest molecules we investigated [G3.5]-dendrimer with a perfluorinated shell in the presence of perfluoro-tagged disperse red. Noteworthy, the interaction intensities varied in an unexpected manner depending on the equivalents of perfluoro-tagged guest molecules added to the dendrimers in solution which then formed supramolecular complexes based on fluorous-fluorous interactions. We found that these complexes aggregated around residual air in the solvent to form stable micron-sized bubbles. Their sizes correlated with the interaction intensities measured for certain dendrimer-guest molecule ratios. Degassing of the solutions led to a quasi phase separation between organic and fluorous phase, whereby the dendrimers formed the fluorous phases. Regassing the sample with air afforded bubbles of the initial size again.

Palladium nanoparticles on graphite oxide and its functionalized graphene derivatives as highly active catalysts for the Suzuki-Miyaura coupling reaction.

Pd(2+)-exchanged graphite oxide and chemically derived graphenes therefrom were employed as supports for Pd nanoparticles. The influence of catalyst preparation, carbon functionalization, and catalyst morphology on the catalytic activity in the Suzuki-Miyaura coupling reactions was investigated. The catalysts were characterized by means of spectroscopy (FT-IR, solid-state (13)C NMR, AAS, XPS), X-ray scattering (WAXS), surface area analysis (BET, methylene blue adsorption), and electron microscopy (TEM, ESEM). In contrast to the conventional Pd/C catalyst, graphite oxide and graphene-based catalysts gave much higher activities with turnover frequencies exceeding 39,000 h(-1), accompanied by very low palladium leaching (<1 ppm).

A new assay format for NF-kappaB based on a DNA triple helix and a fluorescence resonance energy transfer.

Herein we report a feasibility study for a new concept to detect DNA binding protein NF-kappaB based on a DNA triple helix formation in combination with a fluorescence resonance energy transfer (FRET). The new principle avoids expensive antibodies and radioactivity and might have implications for assays of other DNA binding proteins.

Amphiphilic conetworks as activating carriers for the enhancement of enzymatic activity in supercritical CO2.

Enzymatic reactions in supercritical carbon dioxide (scCO2) represent a way of combining the advantages of biocatalysis with the environmental benign nature of scCO2 as a solvent. Here we demonstrate that activities of enzymes in scCO2 can be greatly enhanced by incorporating them into amphiphilic conetworks (APCNs), a novel type of enzyme support. Two sets of hydrophilic/scCO2-philic APCNs, poly(2-hydroxyethyl acrylate)-linked by-poly(dimethylsiloxane) (PHEA-l-PDMS) and poly(2-hydroxyethyl acrylate)-linked by-perfluoropolyether (PHEA-l-PFPE), were prepared and loaded with the synthetically relevant lipase from Rhizomucor miehei. The effect of the APCNs' composition on the amount of the absorbed lipase was studied. It is observed that both sets of lipase-loaded APCNs enhance the catalytic activity of the enzyme in scCO2. The chemical nature of the scCO2-philic phase as well as the conetworkscomposition greatly influences the activity of the lipase in the conetworks. Activities obtained with PFPE-basedAPCNS were up to 10-fold higher than those obtained with PDMS-based conetworks. The highest specific activity measured corresponds to a 2,000-fold activation compared to the lyophilized enzyme powder. This activity is 10 times higher than the specific activity of the lipase immobilized on an optimized commercial carrier.

Synthesis of a new pair of fluorescence resonance energy transfer donor and acceptor dyes and its use in a protease assay.

A new, efficient and very robust fluorescence resonance energy transfer (FRET) system, which can be measured in a normal as well as in a time-resolved mode, was developed and its feasibility demonstrated in a protease assay format.

Modern separation techniques for the efficient workup in organic synthesis.

The shift of paradigm in combinatorial chemistry, from large compound libraries (of mixtures) on a small scale towards defined compound libraries where each compound is prepared in an individual well, has stimulated the search for alternative separation approaches. The key to a rapid and efficient synthesis is not only the parallel arrangement of reactions, but simple work-up procedures so as to circumvent time-consuming and laborious purification steps. During the initial development stages of combinatorial synthesis it was believed that rational synthesis of individual compounds could only be achieved by solid-phase strategies. However, there are a number of problems in solid-phase chemistry: most notably there is the need for a suitable linker unit, the limitation of the reaction conditions to certain solvents and reagents, and the heterogeneous reaction conditions. Further disadvantages are: the moderate loading capacities of the polymeric support and the limited stability of the solid support. In the last few years several new separation techniques have been developed. Depending on the chemical problem or the class of compounds to be prepared, one can choose from a whole array of different approaches. Most of these modern separation approaches rely on solution-phase chemistry, even though some of them use solid-phase resins as tools (for example, as scavengers). Several of these separation techniques are based on liquid-liquid phase separation, including ionic liquids, fluorous phases, and supercritical solvents. Besides being benign with respect to their environmental aspects, they also show a number of advantages with respect to the work-up procedures of organic reactions as well as simplicity in the isolation of products. Another set of separation strategies involves polymeric supports (for example, as scavengers or for cyclative cleavage), either as solid phases or as soluble polymeric supports. In contrast to solid-phase resins, soluble polymeric supports allow reactions to be performed under homogeneous conditions, which can be an important factor in catalysis. At the same time, a whole set of techniques has been developed for the separation of these soluble polymeric supports from small target molecules. Finally, miscellaneous separation techniques, such as phase-switchable tags for precipitation by chemical modification or magnetic beads, can accelerate the separation of compounds in a parallel format.

Reactions in unusual media.

This review provides an introduction to three of the most well-developed solvent replacement strategies currently under investigation for synthetic chemistry: Ionic liquids, fluorous phase techniques, and supercritical carbon dioxide. They are all fascinating reaction media, and have considerable potential for use in pharmaceutical synthesis. However, this has to be balanced with problems and limitations of the new methods. This review aims to provide an overall account of recent advances in the use of unusual media for synthetic chemistry, with an emphasis on highlighting potential benefits, but also limitations, of each of the methods described.

Combinatorial Solid-Phase Synthesis of Structurally Complex Thiazolylhydantoines.

A nine-step (!) solid-phase synthesis and subsequent cleavage with cyclization from the polymeric support were the keys to preparing high-quality molecular libraries of thiazolylhydantoines 1 from modified amino acid building blocks. Each step in the synthesis is different. Because the final cyclization cleaves only molecules that have been successfully constructed, the products obtained are pure. R1 , R2 =alkyl; R3 =aryl, arylO; R4 =allyl.

Dye dynamics in three-color FRET samples.

Time-resolved emission data (fluorescence decay and fluorescence depolarization) of two three-color Förster resonance energy transfer (tc-FRET) systems consisting of a carbostyril donor (D), a ruthenium complex (Ru) as relay dye, and a Cy5 derivative (Cy) or, optionally, an anthraquinone quencher (Q) were carefully analyzed using advanced distribution analysis models. Thereby, it is possible to get information on the flexibility and mobility of the chromophores which are bound to double stranded (ds) DNA. Especially the distance distribution based on the analysis of the fluorescence depolarization is an attractive approach to complement data of fluorescence decay time analysis. The distance distributions extracted from the experimental data were in excellent agreement with those determined from accessible volume (AV) simulations. Moreover, the study showed that for tc-FRET systems the combination of dyes emitting on different time scales (e.g., nanoseconds vs microseconds) is highly beneficial in the distribution analysis of time-resolved luminescence data in cases where macromolecules such as DNA are involved. Here, the short lifetimes can yield information on the rotation of the dye molecule itself and the long lifetime can give insight in the overall dynamics of the macromolecule.

Quenching of the long-lived Ru(II)bathophenanthroline luminescence for the detection of supramolecular interactions.

A feasibility study based on tailor-made peptide sequences for a new robust luminescence probe-system using the long-lived luminescence of a Ru(II)-bathophenanthroline complex in combination with an efficient anthraquinone-type quencher is presented. Due do their high chemical stability, both dyes can be introduced during solid-phase peptide synthesis avoiding post-synthetic labelling. Photophysical measurements revealed an intense quenching of the luminescence of the Ru-complex (65-68%) which was also confirmed by calculations resulting from decay time measurements. The long-lived luminescence allows for a time-gated detection scheme, which can reduce any luminescence contribution from matrix components.