Integrated Calendar

Our laboratory is applying an interdisciplinary and multi scalar approach to characterise the molecular mechanisms of transcription and in particular of multisubunit RNA polymerases (RNAPs). We explore model systems from the third domain of life, the Archaea, not only because they are fascinating organisms in their own right but because their transcription apparatus is a model system for – and more biochemically tractable than - eukaryotic RNAPII. Today I will present progress in our understanding of (i) the architecture of transcription initiation complexes, (ii) conformational dynamics of RNAP during the transcription cycle, and (iii) the whole genome-distribution of the basal transcription apparatus and transcription start site mapping. This analysis reveals the underlying molecular nature of the spontaneous DNA melting in archaea, which requires ATP hydrolysis in the RNAPII system. Our data furthermore show that the dynamic recruitment and release of basal factors that guide RNAP through the transcription cycle is modulated by the coupling of transcription and translation, of RNAPs and ribosomes.

The study of molecular collisions with the highest possible detail has been an important research theme in physical chemistry for decades. Over the last years we have developed methods to get improved control over molecules in a molecular beam [1]. With the Stark decelerator, a part of a molecular beam can be selected to produce bunches of molecules with a computer-controlled velocity and with longitudinal temperatures as low as a few mK. The molecular packets that emerge from the decelerator have small spatial and angular spreads, and have almost perfect quantum state purity. These tamed molecular beams allow for crossed beam scattering experiments with unprecedented levels of precision and sensitivity [2,3].

I will discuss our most recent results on the combination of Stark deceleration and velocity map imaging. The narrow velocity spread of Stark-decelerated beams results in scattering images with an unprecedented sharpness and angular resolution. This has facilitated the observation of diffraction oscillations in the state-to-state differential cross sections for collisions of NO with rare gas atoms [4]. Observed features in the diffraction pattern result from subtle quantum interference effects, and appear extremely sensitive to the potential energy surfaces governing the scattering process [5].

[1] S.Y.T. van de Meerakker, H.L. Bethlem, G. Meijer, Nature Physics 4, 595 (2008).
[2] J.J. Gilijamse, S. Hoekstra, S.Y.T. van de Meerakker, G.C. Groenenboom, G. Meijer,
Science 313, 1617 (2006).
[3] M. Kirste, X. Wang, H.C. Schewe, G. Meijer, K. Liu, A. van der Avoird, L.M.C.
Janssen, K.B. Gubbels, G.C. Groenenboom, S.Y.T. van de Meerakker,
Science 338, 1060 (2012).
[4] A. von Zastrow, J. Onvlee, S.N. Vogels, G.C. Groenenboom, A. van der Avoird,
S.Y.T. van de Meerakker, Nature Chemistry 6, 216 (2014).
[5] S.N. Vogels, J. Onvlee, A. von Zastrow, G.C. Groenenboom, A. van der Avoird,
S.Y.T. van de Meerakker, Phys. Rev. Lett. 113, 263202 (2014).

In the last decade advances in Next Generation Sequencing and bioinformatics enabled the unraveling of global RNA modifications and editing. The evolving field of epitranscriptomics proved to be important in cell fate decisions, normal development and disease.
The lecture will deal with A to I editing-based mechanisms relevant to cancer and with the emerging role
of m6A methylation in the precise regulation of early embryonic development.

Several ways to search for time-reversal-violation in beta decay of trapped nuclei will be reviewed. The newly upgraded TRINAT trap system will be described showing the high sensitivity required for such a search. The experimental plans for such experiments will be described.