Two-dimensional supramolecular polymers

One of the biggest issues of modern materials science is developing of strategies to create large and ordered assemblies in the form of discrete nanoscale objects. Oligopyrenotides (OPs) represent novel class of amphiphilic molecules which tend to self-assemble forming highly ordered structures. As has been already shown OPs are able to form 1D («rod-like») supramolecular polymer [1]. Since programmed arraying of polyaromatic hydrocarbons in structurally defined objects could offer enhanced performance over the individual components, prediction and controlling of their spatial arrangement remains challenging. Herein we demonstrate that certain changes to design of pyrene’s molecular core allow Py3 form 2D supramolecular assemblies («nanosheets») instead of 1D. Two dimensional supramolecular polymers are attractive objects due to their exceptional properties which originate from in-plan alignment of molecular units in the sheets with constant thickness ~ 2 nm [2]. These assemblies have high degree of internal order: the interior consists of hydrophobic pyrenes and alkyl chains, whereas the exterior exists as a net of hydrophilic, negatively charged phosphates. The Py3 units are hold up by non-covalent interactions what makes these assemblies totally reversible. Moreover the polymerization occurs via nucleation-elongation mechanism. To study Py3 self-assembly, we carried out whole set of spectroscopic (UV/vis, fluorescence, DLS) and microscopic experiments (AFM)

Two-dimensional supramolecular polymers

One of the biggest issues of modern materials science is developing of strategies to create large and ordered assemblies in the form of discrete nanoscale objects. Oligopyrenotides (OPs) represent novel class of amphiphilic molecules which tend to self-assemble forming highly ordered structures. As has been already shown OPs are able to form 1D («rod-like») supramolecular polymer [1]. Since programmed arraying of polyaromatic hydrocarbons in structurally defined objects could offer enhanced performance over the individual components, prediction and controlling of their spatial arrangement remains challenging. Herein we demonstrate that certain changes to design of pyrene’s molecular core allow Py3 form 2D supramolecular assemblies («nanosheets») instead of 1D. Two dimensional supramolecular polymers are attractive objects due to their exceptional properties which originate from in-plan alignment of molecular units in the sheets with constant thickness ~ 2 nm [2]. These assemblies have high degree of internal order: the interior consists of hydrophobic pyrenes and alkyl chains, whereas the exterior exists as a net of hydrophilic, negatively charged phosphates. The Py3 units are hold up by non-covalent interactions what makes these assemblies totally reversible. Moreover the polymerization occurs via nucleation-elongation mechanism. To study Py3 self-assembly, we carried out whole set of spectroscopic (UV/vis, fluorescence, DLS) and microscopic experiments (AFM)

DNA-multiporhyrinic systems: promising objects for materials science

Porphyrin-containing materials are attractive objects for advanced light-harvesting systems [1]. Despite existence of numerous approaches to arrange porphyrines in a controlled and programmed way and therefore mimic natural photosynthetic systems, the problem of porphyrin`s arraying remains challenging [2]. Herein, we present an approach based on using DNA as a scaffold to hold porphyrines together. The whole spectroscopic investigation of the compounds containing several porphyrines and a possibility of their usage as molecular blocks for functional supramolecular architectures is discussed [3].

2D supramolecular polymers: nanosized, water-soluble "sheets"

Self – assembly is a powerful tool for the construction of highly organized nanostructures [1]. Therefore, the possibility to control and predict pathways of molecular ordering on the nanoscale level is a critical issue for the production of materials with tunable and adaptive macroscopic properties. Herein, we demonstrate that designed molecule Py3 forms dimensionally - defined supramolecular assemblies under thermodynamic conditions in water [2]. To study Py3 self-assembly, we carried out whole set of spectroscopic and microscopic experiments. The factors influencing stability, morphology and behavior of «nanosheets» in multicomponent systems are discussed

Synthetic versus natural curcumin: bioequivalence in an in vitro oral mucositis model

BACKGROUND Curcumin (CUR) is a dietary spice and food colorant (E100). Its potent anti-inflammatory activity by inhibiting the activation of Nuclear Factor-kappaB is well established. METHODS The aim of this study was to compare natural purified CUR (nCUR) with synthetically manufactured CUR (sCUR) with respect to their capacity to inhibit detrimental effects in an in vitro model of oral mucositis. The hypothesis was to demonstrate bioequivalence of nCUR and sCUR. RESULTS The purity of sCUR was HPLC-confirmed. Adherence and invasion assays for bacteria to human pharyngeal epithelial cells demonstrated equivalence of nCUR and sCUR. Standard assays also demonstrated an identical inhibitory effect on pro-inflammatory cytokine/chemokine secretion (e.g., interleukin-8, interleukin-6) by Detroit pharyngeal cells exposed to bacterial stimuli. There was bioequivalence of sCUR and nCUR with respect to their antibacterial effects against various pharyngeal species. CONCLUSION nCUR and sCUR are equipotent in in vitro assays mimicking aspects of oral mucositis. The advantages of sCUR include that it is odorless and tasteless, more easily soluble in DMSO, and that it is a single, highly purified molecule, lacking the batch-to-batch variation of CUR content in nCUR. sCUR is a promising agent for the development of an oral anti-mucositis agent.

OMA and OPA—Software-Supported Mass Spectra Analysis of Native and Modified Nucleic Acids

The platform-independent software package consisting of the oligonucleotide mass assembler (OMA) and the oligonucleotide peak analyzer (OPA) was created to support the analysis of oligonucleotide mass spectra. It calculates all theoretically possible fragments of a given input sequence and annotates it to an experimental spectrum, thus, saving a large amount of manual processing time. The software performs analysis of precursor and product ion spectra of oligonucleotides and their analogues comprising user-defined modifications of the backbone, the nucleobases, or the sugar moiety, as well as adducts with metal ions or drugs. The ability to expand the library of building blocks and to implement individual structural variations makes it extremely useful for supporting the analysis of therapeutically active compounds. The functionality of the software tool is demonstrated on the examples of a platinated doublestranded oligonucleotide and a modified RNA sequence. Experiments also reveal the unique dissociation behavior of platinated higher-order DNA structures.

MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13

The MQN-mapplet is a Java application giving access to the structure of small molecules in large databases via color-coded maps of their chemical space. These maps are projections from a 42-dimensional property space defined by 42 integer value descriptors called molecular quantum numbers (MQN), which count different categories of atoms, bonds, polar groups, and topological features and categorize molecules by size, rigidity, and polarity. Despite its simplicity, MQN-space is relevant to biological activities. The MQN-mapplet allows localization of any molecule on the color-coded images, visualization of the molecules, and identification of analogs as neighbors on the MQN-map or in the original 42-dimensional MQN-space. No query molecule is necessary to start the exploration, which may be particularly attractive for nonchemists. To our knowledge, this type of interactive exploration tool is unprecedented for very large databases such as PubChem and GDB-13 (almost one billion molecules). The application is freely available for download at www.gdb.unibe.ch.

Observation of the rare chrysene excimer

Formation of the so far elusive chrysene excimer in solution is achieved by using DNA as a supramolecular scaffold. Oligonucleotides possessing one or two chrysene building blocks have been synthesized. Chrysene excimer fluorescence has been unambiguously observed in DNA double strands, as well as in single strands containing two neighbouring chrysenes.