Sonderforschungsbereich 902

19F-labeling of the adenine H2-site to study large RNAs by NMR spectroscopy.

Sochor F, Silvers R, Müller D, Richter C, Fürtig B, Schwalbe H. J Biomol NMR. 2015 Dec 24. Abstract Read more …

The three possible 2-(pyrenylethynyl) adenosines: rotameric energy barriers govern the photodynamics of these structural isomers.

Reuss AJ, Grünewald C, Braun M, Engels JW, Wachtveitl J. Chemphyschem. 2015 Dec 4. Abstract Read more …

Date: Tuesday, 10/11/ till Saturday, 11/11/2013.
Location: Forschungskolleg Humanwissenschaften in Bad Homburg.

Progam of the Kick-off Meeting.

The event will start at 11 am on Tuesday, followed by a get-to-gether dinner. On Wednesday, the meeting will be closed around 2:00 pm.

Plant-Specific Features of Ribosome Biogenesis.

Weis BL, Kovacevic J, Missbach S, Schleiff E. Trends Plant Sci. 2015 Nov. Abstract Read more …

Ultrafast Spectroscopy of Hydroxy-Substituted Azobenzenes in Water.

Steinwand S, Halbritter T, Rastädter D, Ortiz-Sánchez JM, Burghardt I, Heckel A, Wachtveitl J. Chemistry. 2015 Oct 26. Abstract Read more …

Dynamic nuclear polarization of nucleic acid with endogenously bound manganese.

Wenk P, Kaushik M, Richter D, Vogel M, Suess B, Corzilius B. J Biomol NMR. 2015 Sept. Abstract Read more …

Dr. Jan Medenbach, University of Regensburg, gives a talk titled “Sex and Drugs and Regulation – Translational Control in Drosophila melanogaster“.

Tuesday, 14/07/15 at 5:15 pm
TUD, Schnittspahnstraße 3, B1|01, room 52

Mechanistic insights into temperature-dependent regulation of the simple cyanobacterial hsp17 RNA thermometer at base-pair resolution.

Wagner D, Rinnenthal J, Narberhaus F, Schwalbe H. Nucleic Acids Res. 2015 Jun 23. Abstract Read more …

Roland Hartmann, Universität Marburg, gives a talk titled “Control of Ebola virus (EBOV) transcription – function of the viral protein VP30“.

Wednesday, 17/06/15 at 5 pm
Campus Riedberg, Biozentrum N100 / 0.15

Christoph Kreutz, Leopold Franzens Universität Innsbruck, gives a talk titled “Advanced stable isotope labeling methods for RNA NMR spectroscopy“.

Wednesday, 10/06/15 at 5 pm
Campus Riedberg, Biozentrum N100 /1.14

Our research is focused on the development of advanced stable isotope labelling protocols for nucleic acids. Using chemo-enzymatic transformations site-specifically ¹³C/¹⁵N/²H- modified building blocks are amenable that can be either used for the solid phase chemical synthesis of RNA (i.e. synthesis of phosphoramidite building blocks) or for the enzymatic production of RNA by in vitro transcription (i.e. synthesis of ribonucleotide triphosphate building blocks). The building blocks currently available in our laboratory will be presented along with selected applications including CPMG relaxation dispersion experiments, ZZ- exchange NMR and paramagnetic relaxation enhancements studies.

References

• Wunderlich C, Santner T, Fauster K, Spitzer R, Tollinger M and Kreutz C* (2012). Synthesis of 6-13C-pyrimidine nucleotides as Spin-Labels for RNA dynamics. J. Am. Chem. Soc. 134:7558-7569.
• Moschen T, Wunderlich C, Spitzer R, Levic J, Micura R, Tollinger M* and Kreutz C* (2014). Ligand-detected Relaxation Dispersion NMR Spectroscopy : Dynamics of preQ1-RNA binding. Angew. Chem. Int. Ed. published online.
• Wunderlich C, Huber RG, Spitzer R, Liedl KR, Kloiber K* and Kreutz C* (2013). Novel paramagnetic relaxation enhancement tag for nucleic acids: A tool to study structure and dynamics of RNA. ACS Chemical Biology 8:2697-2706.

Direct visualization of newly synthesized target proteins in situ.

Tom Dieck S, Kochen L, Hanus C, Heumüller M, Bartnik I, Nassim-Assir B, Merk K, Mosler T, Garg S, Bunse S, Tirrell DA, Schuman EM. Nat Methods. 2015 May. Abstract Read more …

Thomas Schubert, 2bind GmbH, Regensburg, gives a talk titled “Fast and quantitative analysis of aptamer-target interactions using MicroScale Thermoporesis (MST)“.

Thursday, 28/05/15 at 4:15 pm
Campus Riedberg, Biozentrum N100 / B2

Ciara O‘Sullivan, Universitat Rovira i Virgili, Tarragona, gives a talk titled “High affinity beta-conglutin binding aptamers“.

Thursday, 28/05/15 at 4:15 pm
Campus Riedberg, Biozentrum N100 / B2

Differential scanning fluorimetry for monitoring RNA stability.

Silvers R, Keller H, Schwalbe H, Hengesbach M. Chembiochem 2015 May.
Full publication here. Read more …

Prof. Rolf Backofen, Albert-Ludwigs-Universität Freiburg, gives a talk titled “How to make sense out of CLIP-seq data“.

Wednesday, 15/04/15 at 5:15 pm

Campus Riedberg, Biozentrum N260/3.13

Abstract:

It is becoming increasingly clear that a RNA-binding proteins are key elements in regulating the cell’s transcriptome. Thus, unraveling the interaction network of the RNA-binding proteins by determining their binding sites is becoming an increasingly important topic. There are several high-throughput methods available to detect binding sites such as CLIP-seq. Since not all possible binding sites are covered due to differential expression in tissues and developmental states, the main problem is to come up with good motif descriptions to find missing binding sites and to evaluate the binding strength. Our new approach GraphProt uses an advanced machine learning approach based on our graph-kernel, and is able to use both structural profiles as well as detailed 2D-structures, and predicts missing binding sites with an high accuracy./blockquote>

atBRX1-1 and atBRX1-2 are involved in an alternative rRNA processing pathway in Arabidopsis thaliana.

Weis BL, Palm D, Missbach S, Bohnsack MT, Schleiff E. RNA. 2015 Mar. Abstract Read more …

Multiple conformational states of riboswitches fine-tune gene regulation.

Fürtig B, Nozinovic S, Reining A, Schwalbe H. Curr Opin Struct Biol. 2015 Feb. Abstract Read more …

Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity.

You X, Vlatkovic I, Babic A, Will T, Epstein I, Tushev G, Akbalik G, Wang M, Glock C, Quedenau C, Wang X, Hou J, Liu H, Sun W, Sambandan S, Chen T, Schuman EM, Chen W. Nat Neurosci. 2015 Feb 25. Press release Read more …

Reversible photoswitching of RNA hybridization at room temperature with an azobenzene C-nucleoside.

Goldau T, Murayama K, Brieke C, Steinwand S, Mondal P, Biswas M, Burghardt I, Wachtveitl J, Asanuma H, Heckel A. Chemistry. 2015 Feb 9. Abstract Read more …

Prof. Vikram Panse, ETH Zürich, gives a talk titled “Exploring the interface between ribosome assembly and nucleocytoplasmic transport“.

Wednesday, 04/02/15 at 5 pm

Campus Riedberg, Biozentrum N100/0.15

Abstract: Eukaryotic ribosome assembly is a spectacular example of a highly dynamic and regulated process that spans different cellular territories: the nucleus, nucleoplasm and the cytoplasm. This poorly understood process, which begins in the nucleolus, requires >350 conserved transiently associating assembly factors, whose site(s) of action and precise function(s) on pre-ribosomal particles are beginning to be elucidated.

Further, production of ribosomes relies on an active functional nucleocytoplasmic transport machinery: the nuclear import machinery ensures delivery of newly synthesized ribosomal proteins to assembling pre-ribosomal particles in the nucleolus, the site of biogenesis, and the nuclear export machinery catalyses the transport of correctly assembled pre-ribosomal particles through nuclear pore complexes into the cytoplasm, the site of function. I will elaborate on two recent works from my laboratory that are beginning to illuminate the unchartered interface between the nucleocytoplasmic transport machinery and the ribosome assembly pathway.

Dr. Juliane Soukup, University of Nebraska, gives a talk titled “Phosphatase-Inert Glucosamine 6‑Phosphate Mimics serve as Actuators of the glmS Riboswitch“.

Wednesday, 21/01/15 at 5 pm

Campus Riedberg, Biozentrum N100/0.15