Hannover 2013 – scientific programme

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MO: Fachverband Molekülphysik

MO 22: Biomolecules

MO 22.1: Talk

Thursday, March 21, 2013, 11:00–11:15, F 107

Influence of bulged nucleotides on the overall structure of RNA junctions - Precise structural modeling via single molecule FRET — •Sascha Fröbel, Hayk Vardanyan, Simon Sindbert, Stanislav Kalinin, Christian Hanke, Holger Gohlke, and Claus A. M. Seidel — Heinrich-Heine-Universität Düsseldorf, Germany

Recently, our group presented a powerful method for the determination of biomolecular structures via Förster resonance energy transfer (FRET) called FRET-restrained high-precision structural modeling [1]. The technique is based on single molecule FRET measurements of dye labeled biomolecules freely diffusing in solution. By explicitly considering dye position distributions the accuracy of the extracted distance information and of the final structural models is increased significantly.

Here, FRET-restrained high-precision structural modeling is applied to three structurally related RNA three-way junctions. The molecules differ by the number of unpaired nucleotides at the junction region, referred to as bulges. Starting with a fully Watson-Crick paired molecule, the influence of a two- and a five-nucleotide bulge on the overall structure is investigated. Changing the bulge size leads to clearly distinct structures, which reveals the strong influence of this structural element on helix orientations. Apparently, this influence is stronger than that of the secondary structure next to the junction region.

[1] S. Kalinin, T. Peulen, S. Sindbert, P.J. Rothwell, S. Berger, T. Restle, R.S. Goody, H. Gohlke and C.A.M. Seidel, Nature Methods 9, 1218-1225 (2012).