Biochemie und Chemie
Refine
Year of publication
Document Type
- Article (1112)
- Doctoral Thesis (728)
- Book (46)
- Preprint (32)
- Contribution to a Periodical (14)
- Conference Proceeding (11)
- Report (11)
- Review (9)
- diplomthesis (3)
- Part of a Book (2)
Has Fulltext
- yes (1974)
Is part of the Bibliography
- no (1974)
Keywords
- crystal structure (37)
- Crystal Structure (25)
- Synthesis (15)
- ESR Spectra (14)
- RNA (14)
- NMR-Spektroskopie (12)
- hydrogen bonding (11)
- IR Spectra (10)
- NMR spectroscopy (10)
- RNS (9)
Institute
- Biochemie und Chemie (1974)
- Medizin (83)
- Exzellenzcluster Makromolekulare Komplexe (68)
- Biowissenschaften (64)
- Präsidium (64)
- Zentrum für Biomolekulare Magnetische Resonanz (BMRZ) (63)
- Pharmazie (52)
- MPI für Biophysik (49)
- Sonderforschungsbereiche / Forschungskollegs (48)
- Georg-Speyer-Haus (22)
In the paper by Bolte [Acta Cryst. (2006), E62, m1609-m1610], the chemical name in the title and the chemical diagram are incorrect. The correct title is {5-[4'-(2,2,5,5-Tetramethyl-3-pyrroline-1-oxyl-3-carbonyloxy)biphenyl-4-ylethynyl]-2,3,7,8,12,13,17,18-octaethylporphyrinato}copper(II) benzene solvate' and the correct diagram is given below.
The isolation of transcribed DNA sequences of P815 cells and the partial characterization with respect to their sequence composition and relative rates of enzymatic DNA methylation are reported in this paper. Transcribed regions were purified by affinity chromatography using immobilized heterogenous nuclear RNA of P815 cells. About 10% of total genome was found in this fraction. Reassociation analyses showed differences in sequence composition of transcribed versus non-transcribed DNA fractions. The relative proportion of inverted repeats was doubled in the transcribed fraction whereas ordinary highly repetitive sequences comprising mainly of satellite DNA were found almost exclusively in the non-transcribed regions of the P815 genome. About 70% of transcribed portions corresponds to unique and intermediary DNA sequences. After labelling of cells with L-[Methyl-3H]methionine and [14C]deoxycytidine relative rates of enzymatic DNA methylation were computed for different kinetic components of transcribed and non- transcribed portions of P815 genome. No difference was found except in inverted repeats. In transcribed DNA the relative rate of enzymatic DNA methylation was only about 40% of that of the non-transcribed ones. We have quantitated this hypomethylation and found that there is, in average, about one 5-methylcytosine residue in 100 nucleotides of transcribed inverted repeats, compared to about 2.5 5-methylcytosines in non-transcribed fractions. In view of these data we propose that the enzymatic methylation of inverted DNA repeats negatively controls the transcriptional process in a given genomic region.
A specific class of DNA sequences, the inverted repetitive sequences, forms a double-stranded structure within a single linear polynucleotide chain in denatured DNA. The reassociation process is unimolecular and occurs very fast. Quantitative analyses have shown that these sequences com-E rise about 4-5% of the nuclear DNA of various mammalian cells (P815 mouse mastocytoma, Hela, L cells, Raji and Chang cells, and human embryonic hepatocytes) and are interspersed within sequences of other degrees of repetitiveness.
After labeling the cells with L-[Metnyl-3H]methionine and [14C]deoxycytidine, relative rates of enzymic DNA methylation were computed on the basis of 3H and 14C radioactivities found in py rimidine residues of the nuclear DNA. The results indicate that DNA of inverted repetitive sequences is methylated to a level about 50% higher than the ordinary repetitive sequences and to about 300% higher than the unique and intermediary sequences.
The biological function of the inverted repeats as well as the role of their enzymic hypermethyl ation is unknown.
The sequence complexity of nuclear RNA from mouse liver, mouse spleen and highly malignant P815 mastocytoma was measured by nRNA driven hybridization to unique DNA sequences of P815 cells. The unique DNA sequences represent 63% of the total nuclear DNA of P815 cells and their availibility in hybridization experiments was found to be 76%. Of these sequences 7.8% formed hybrids with nuclear RNA of this cell, about 11.5% with mouse spleen and about 14.5% with mouse liver nuclear RNA. Assuming an asymmetrical transcription, the complexities of these transcripts are 2.8 × 108 nucleotides for mouse P815 mastocytoma, 4.3 × 108 for mouse spleen and about 5.3 × 108 nucleotides for mouse liver.
Cellular specifity of the transcribed information was analyzed in additivity experiments, in which unique DNA sequences, not complementary to the nuclear RNA of one cell were annealed to the nuclear RNAs of the two other tissues/cells. In these experiments most of the nuclear RNA se quences of P815 cells were found to be also present in the nucleus of mouse liver and spleen. Only a small portion of the unique DNA sequences of P815 mastocytoma (about 1.2% corresponding to 4.4 ×107 nucleotides) was found to be complementary only to P815 mastocytoma nuclear RNA.
In den letzten zwei Dekaden wurde die Rolle der RNA in biologischen Prozessen intensiv untersucht. Man erkannte immer deutlicher, dass ihre Funktion über die einfache Vermittlung von Information von der DNA hin zum Protein weit hinausgeht. So spielt sie eine entscheidende Rolle bei der Genexpression und besitzt darüber hinaus auch katalytische Eigenschaften. Die Entdeckung der reversen Transcriptase beim HI-Virus konnte zeigen, dass genetische Informationen nicht nur in Richtung von DNA zu RNA, sondern auch in Entgegengesetzter Richtung übertragen werden kann. Diese Schlüsselrolle in vielen wichtigen biochemischen Prozessen macht die RNA zu einem viel versprechenden Ziel für die Entwicklung neuer Wirkstoffe, um in diese Prozesse eingreifen zu können. RNA bildet eine Vielzahl von stabilen Sekundär- und Tertiärstrukturen aus, die es Proteinen und Antibiotika ermöglicht, sie zu adressieren. Die bis heute wohl mit Ausnahme des Ribosoms und der tRNAs am besten aufgeklärte Struktur einer RNA ist die der HIV TAR-RNA (transaktivierende Region). Ein essentieller Bestandteil für die virale Genexpression ist die so genannte TAR-RNA. Diese befindet sich am 5-Ende aller viraler Transcripte und bildet eine aus 59 Basen bestehende stem-bulge-loop hairpin Struktur. Diese tritt in Wechselwirkung mit dem tat-Protein. Die Grundlage für die Erkennung des hierbei entstehenden Komplexes ist eine Wechselwirkung von tat mit der bulge- und loop-Region von TAR. Durch Interaktion mit der loop- Region kommt es zur Ausbildung eines CyclinT1/tat Komplexes, der im weiteren dafür verantwortlich ist, dass sich die Rate der Transkription um das mehrere hundertfache erhöht. Ziel der vorliegenden Arbeit war es, Liganden zu synthetisieren, die spezifische Bindungen mit der TAR-RNA aus HIV-1 eingehen. Durch eine solche Bindung ist es möglich, den viralen Replikationszyklus zu unterbrechen. Ausgehend von einem relativ rudimentären Design, basierend auf dem Arginin-Fork-Model von Frankel, gelang es, mit Triaminopyrazol und verschiedenen seiner Derivaten dieses Ziel zu erreichen. Nach erfolgreicher Synthese der Zielstrukturen wurden diese in einem FRET-Assay im Hinblick auf ihre Affinität zu der TAR-RNA getestet. 3,4,5-Triaminopyrazol übertraf trotz seiner geringen Größe und Ladung mit einem IC50-Wert von 30 µM die Werte vieler tetrakationischer Tripeptide (FRET). Nach erfolgreicher Bestimmung der TAR-Affinität von Triaminopyrazol wurde seine Wirkung auf HIV-infizierte Hela P4-Zellen untersucht, die ein Tat-TAR-kontrolliertes Reportergen exprimierten. Dabei zeigte Triaminopyrazol eine Inhibierung mit IC50 = 50 µM. Bis zu einer Konzentration von 500 µM traten hierbei keine toxischen Effekte auf. Dies legt die Vermutung nahe, dass es sich bei Triaminopyrazol tatsächlich um einen tat- Antagonisten handelt. Ebenso konnte gezeigt werden, dass die Wirkung von Triaminopyrazol nicht die eines Entryinhibitors ist, sondern dass die Verbindung in der Lage ist, die Zellmembran zu durchdringen.
Pulsed electron-electron double resonance (PELDOR) is a well established method concerning nanometer distance measurements involving two nitroxide spin-labels. In this thesis the applicability of this method to count the number of spins is tested. Furthermore, this work explored the limits, up to which PELDOR data obtained on copper(II)-nitroxide complexes can be quantitatively interpreted. Spin counting provides access to oligomerization studies – monitoring the assembly of homo- or hetero-oligomers from singly labeled compounds. The experimental calibration was performed using model systems, which contain one to four nitroxide radicals. The results show that monomers, dimers, trimers, and tetramers can be distinguished within an error of 5% in the number of spins. Moreover, a detailed analysis of the distance distributions in model complexes revealed that more than one distance can be extracted from complexes bearing several spins, as for example three different distances were resolved in a model tetramer – the other three possible distances being symmetry related. Furthermore, systems exhibiting mixtures of oligomeric states complicate the analysis of the data, because the average number of spin centers contributes nonlinearly to the signal and different relaxation behavior of the oligomers has to be treated explicitly. Experiments solving these problems are proposed in the thesis. Thus, for the first time spin counting has been experimentally calibrated using fully characterized test systems bearing up to four spins. Moreover, the behavior of mixtures was quantitatively interpreted. In addition, it has been shown that several spin-spin distances within a molecule can be extracted from a single dataset. In the second part of the thesis PELDOR experiments on a spin-labeled copper(II)-porphyrin have been quantitatively analyzed. Metal-nitroxide distance measurements are a valuable tool for the triangulation of paramagnetic metal ions. Therefore, X-band PELDOR experiments at different frequencies have been performed. The data exhibits only weak orientation selection, but a fast damping of the oscillation. The experimental data has been interpreted based upon quantitative simulations. The influence of orientation selection, conformational flexibility, spin-density distribution, exchange interaction J, as well as anisotropy and strains of the g-tensor has been examined. An estimate of the spin-density delocalization has been obtained by density functional theory calculations. The dipolar interaction tensor was calculated from the point-charge model, the extension of the point-dipole approximation to several spin bearing centers. Even assuming asymmetric spin distributions induced by an ensemble of asymmetrically distorted porphyrins the effect of delocalization on the PELDOR time trace is weak. The observed damping of dipolar oscillations has been only reproduced by simulations, if a small distribution in J was assumed. It has been shown that the experimental damping of dipolar modulations is not solely due to conformational heterogeneity. In conclusion the quantitative interpretation of PELDOR data is extended to copper-nitroxide- and multi-spin-systems. The influence of the mean distance, of the number of coupled spins, of the conformational flexibility, of spin-density distribution and of the electronic structure of the spin centers has been analyzed using model systems. The insights on model compounds mimicking spin-labeled biomacromolecules – in oligomeric or metal bound states – calibrate the method with respect to the information that can be deduced from the experimental data. The resulting in-depth understanding allows correlating experimental results (from for example biological systems) with models of structure and dynamics. It also opens new fields for PELDOR as for example triangulation of metal centers and oligomerization studies. In general, this thesis has demonstrated that modern pulsed electron paramagnetic resonance techniques in combination with quantitative data analysis can contribute to a detailed insight into molecular structure and dynamics.
Erfolgreich wurde die biochemische Synthese eines Kernbereiches der spleißosomalen U4/U6-RNA etabliert und die Sekundärstruktur mittels NMR-spektroskopischer Methoden charakterisiert. Die Konformationen von zwei molekularen Regeleinheiten, des auf Gramicidin A basierenden Ionenkanals Minigramicidin sowie einem aus zwei cis-Dekalinen aufgebautenmolekularen Schalters konnten in unterschiedlichen Umgebungen mit Hilfe der NMR-Spektroskopie erfolgreich bestimmt werden. Die Synthese des RNA-Konstruktes u4u6a46phh2 erfolgte durch Transkription von plasmidischer Templat-DNA mit T7-Polymerase und anschließender Aufreinigung mittels Gelelektrophorese und Homogenisierung am 3’-Ende mit Hilfe eines passenden Hammerhead-Ribozyms. u4u6a46phh2-RNA kann als Konstrukt für die Synthese von 13C/15N-gelabelter RNA dienen, da die Schneidreaktion und die daraus resultierende RNA definiert ist und die Integrale der Iminoprotonen für eine einzige Konformation der RNA sprechen. Das von Dr. Hans-Dieter Arndt in der Arbeitsgruppe von Prof. Dr. Koert an der Humboldt-Universität zu Berlin hergestellte Minigramicidin ist aus zwei verkürzten Gramicidin A-Einheiten aufgebaut, die in einer Kopf-an-Kopf Anordnung durch einen Bernsteinsäure-Linker kovalent verknüpft sind. In dieser Arbeit wurden die Strukturen von Minigramicidin in zwei unterschiedlichen Umgebungen aufgeklärt: in Benzol/Aceton (10:1, v/v) ohne Zusatz von Kationen und in gesättigter Cäsiumchlorid-Chloroform/Methanol (3:1, v/v)-Lösung. Im ersten Fall findet man ein doppelt helikales linksgängiges Dimer von Minigramicidin mit ca. 5.7 Resten pro Windung. Diese Struktur hat eine Länge von ca. 38 Å und einen Durchmesser von ca. 1.2 Å. Mit Cäsium-Kationen liegt die Verbindung als Monomer vor. Sie bildet eine rechtsgängige pi-Helix mit ca. 6.3 Resten pro Windung. Die Struktur hat eine Länge von 17 Å und einen Durchmesser von ca. 4.5 Å. Es konnte erstmals eine zur ionenkanalaktiven Form des gA ähnliche Konformation eines auf gA basierenden künstlichen Ionenkanals in organischen Lösemitteln nachgewiesen werden. Der von Dr. Michael Karle aus der Arbeitsgruppe von Prof. Koert an der Philipps-Universität Marburg synthetisierte molekulare Schalter besteht aus zwei cis-Dekalineinheiten, die durch einen 14-gliedrigen Bislactam-Ring miteinander gekoppelt sind. Der Schaltprozeß wurde dabei durch die saure Spaltung des Ley-Acetals in 13 ausgelöst. Es wurde für die Verbindung 13 eine all-axial Stellung für den Makrozyklus gefunden. Diese Struktur wird auch durch die gefundenen Kopplungskonstanten gestützt. Nach dem Schaltprozeß wurde die Struktur von 16 ermittelt. Wie erwartet, wurde durch das Lösen der konformativen Klammer ein Doppelringflip im linken Dekalingerüst ausgelöst und durch den Makrozyklus auf das rechte Dekalingerüst übertragen. Die gefundenen ROE-Abstände und Kopplungskonstanten für bestimmte Dekalinprotonen bestätigen die umgeschaltete Struktur.
The following mixed-stack donor/acceptor complexes {D···A}∞ have been crystallized and their structures determined: {hexamethylbenzene···3,5-dicyano-1-nitrobenzene hexamethylbenzene···3,5-dinitro-1-cyanobenzene}∞, {pyrene···3,5-dinitro-1-cyanobenzene}∞, {anthracene···(3,5-dinitro-1-cyanobenzene)2}∞, {N,N-dimethylanilin···3,5-dinitro- 1-cyanobenzene}∞ and { 1-3-phenylenediamine···3,5-dinitro-1-cyanobenzene}∞. Their lattice packing consists of parallel layers, which contain either donors and acceptors as for hexamethylbenzene and pyrene or composite ones as in the 1:2 complex of anthracene with each one of the acceptors above and below its peripheral rings. The isostructural hexamethylbenzene complexes exhibit almost identical packing coefficients as well as a hexagonal coplanar arrangement of the C6(CH3)6 donors. Weak intermolecular van der Waals interactions are also observed between antiparallel cyano substituents. The interplanar n distances range between 334 and 353 pm, i. e. around 340 pm of two van der Waals n radii. In none of the complexes, however, significant structural changes in either the donor or the acceptor components due to the complex formation are observed. In both the crystals as well as in solution, the donor/acceptor complexes exhibit colours between yellow and red; their long-wavelength charge transfer absorption maxima, therefore, correspond to a lowering in excitation energy of only up to 1 eV relative to that of the components. The different charge transfer in the ground and the CT excited states is also discussed referring to other data such as vertical first ionization energies or interplanar distances {D···A}, as well as to results from semiempirical calculations based on the crystal structure data determined and including approximate configuration interaction.
Raney nickel, a highly reactive and air-sensitive solid, if prepared and investigated under oxygen-free conditions, exhibits interesting catalytic properties. Using photoelectron spectroscopy for real-time gas analysis in a flow reactor, the following results are obtained with alkyl and acylhalides: Dehydrohalogenation temperatures are lowered relative to thermal HHal elimination up to 350 K. Monochloro and bromo propanes and butenes yield propene and butadiene, respectively. 1,1-Dichloro ethane or 1,1-dibromo propane only split off one HHal and form chloroethene or 1-bromopropene-2. HCl elimination from 2-methyl propionic acid chloride, expectedly, produces dimethyl ketene. Most interesting, however, is the ring opening of monobromo cyclobutane to 1-bromo-butene-3, observed already at room temperature, which strongly suggests the intermediate formation of a chemisorbed surface carbene at Raney nickel. The formation of hexadiene-1,5 as a by-product in the HCl elimination of 1-chloropropane, i. e. a surface carbene dimer, indicates their presence also in other dehydrohalogenations heterogeneously catalyzed by Raney nickel.
Raney nickel, a highly reactive and air-sensitive solid, if prepared and investigated under oxygen-free conditions, exhibits interesting catalytic properties. Using photoelectron spectroscopy for real-time gas analysis in a flow reactor, the following results are obtained with alkyl and acylhalides: Dehydrohalogenation temperatures are lowered relative to thermal HHal elimination up to 350 K. Monochloro and bromo propanes and butenes yield propene and butadiene, respectively. 1,1-Dichloro ethane or 1,1-dibromo propane only split off one HHal and form chloroethene or l-brom opropene-2. HCl elim ination from 2-methyl propionic acid chloride, expectedly, produces dimethyl ketene. Most interesting, how ever, is the ring opening of monobromo cyclobutane to 1-brom o-butene-3, observed already at room temperature, which strongly suggests the intermediate formation of a chem isorbed surface carbene at Raney nickel. The formation of hexadiene-1,5 as a by-product in the HCl elim ination of 1-chloropropane, i.e. a surface carbene dimer, indicates their presence also in other dehydrohalogenations heterogeneously catalyzed by Raney nickel.
The following mixed-stack donor/acceptor complexes {D · · · A }∞ have been crystallized and their structures determined: { 1 ,2,4,5-tetramethylbenzene · · · tetrabromo-p -benzoquinone}∞ , {hexamethylbenzene · · · tetrabromo-p-benzoquinone}∞ , { ( 1 ,2 ,4,5-tetramethyl-benzene)2 · · · tetrachloro -p -benzoquinone}∞ , {pyrene · · · tetrafluoro-p-benzoquinone}∞ , {pyrene · · · tetrabromo-p-benzoquinone}∞ and {perylene · · · tetrabromo-p-benzoquinone}∞ . They exhibit an interesting lattice packing, especially the 2:1 tripeldecker sandwich of tetrachloro-p-benzoquinone, which crystallizes in a herringbone pattern. Their interplanar distances are around 340 pm, i. e. two van der Waals π radii. None of them , however, exhibits in neither the donor nor the acceptor components significant structural changes due to complex formation. Their colours range from orange-red to black in the crystal and to green in H2CCl2 solution. Their long-wavelengths charge transfer absorption maxim a correspond to a lowering in excitation energy of up to 2 eV relative to that of the components. The different charge transfer in the ground and excited states of the donor/acceptor complexes investigated is further discussed referring to data such as cyclovoltammetric reduction potentials as w ell as to results from semiempirical calculations based on the crystal structure data determined and including configuration interaction.