Berlin 2015 – scientific programme

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BP: Fachverband Biologische Physik

BP 44: DNA/RNA and related enzymes

BP 44.4: Talk

Thursday, March 19, 2015, 16:00–16:15, H 1058

Gene regulation on the RNA level. The B12 dependent btuB riboswitch studied with single molecule FRET. — •Richard Börner, Michelle Schaffer, Sofia Gallo, and Roland K.O. Sigel — Department of Chemistry, University Zurich, Switzerland

The btuB riboswitch is one of the promising candidates for understanding the gene regulation at the RNA level (1). This B12 specific RNA is encoded in the 5’-untranslated region (UTR) of the btuB gene encoding a coenzyme B12 (AdoCbl) transporter found among other bacteria, especially in E. coli. Upon the binding of B12, a conformational switch of the btuB aptamer occurs, thus inhibiting the expression of the cellular B12 transporter. Although studied intensively on a bulk level (2), the kinetics and in particular the exact structural information of this riboswitch is still missing, as neither a crystal nor a NMR structure exists.

Herein, we use Förster resonance energy transfer on a single molecule level (smFRET) as a versatile tool to characterize the conformational states and the folding kinetics of the aptamer region of the btuB riboswitch. Thereby, we will especially focus on the influence of AdoCbl and the function of Mg2+ for folding and switching. As FRET is known to be used as molecular ruler, we are aiming at absolute rather than apparent distance measurements (3). Thus, a study of the global structure of the btuB riboswitch will complement our experiments.

1. Perdrizet, G. A., et al. 2012. Proc. Natl. Acad. Sci. U. S. A. 109:3323-3328. 2. Choudhary, P. K. and R. K. Sigel. 2014. RNA 20:36-45. 3. Sindbert, S., et al. 2011. J. Am. Chem. Soc. 133:2463-2480.