Mr. Simon Sindbert

Photo of Simon  Sindbert

Dr. Simon Sindbert

hat die Gruppe im Oktober 2013 verlassen /
left the group: October 2013

Building: 26.32.
Floor/Room: 02.36
Phone +49 211 81-11469
Fax +49 211 81-12803

Mini Academic CV

University degrees:

First degree or intermediate examination:

  • Vordiplom(Physics), 2004, Ruprecht-Karls University, Heidelberg, Germany

Second degree and/or intermediate examination:

  • Diplom(Physics), 2008, Ruprecht-Karls University, Heidelberg, Germany

Further degrees and/or interemediate examinations:

  • M.Sc.(Medical Physics), 2008, Ruprecht-Karls University, Heidelberg, Germany

Attended conferences:

  • conference poster "Interferometric resolution and efficiency enhancement for scanning fluorescence microscopes" authors: Simon Sindbert, Kai Wicker, Rainer Heintzmann, 2008, Micro Science, London, UK

Prices/Scholarships:

  • Scholarship "Landesstiftung Baden-Württemberg"

BioStruct PhD project

Analysis of the three-dimensional architecture and dynamics of helical structures in biomolecules using single molecule fluorescence spectroscopy with multiparameter fluorescence detection
Many biomolecules, e.g. DNA, RNA or membrane proteins, have helical structure elements and it is often difficult to analyze their structural dynamics with techniques such as NMR or X-ray crystallography. Fluorescence spectroscopy of single molecules using Multiparameter Fluorescence Detection (MFD) was chosen to analyze molecules for following reasons:

  • As single molecules are measured, subpopulations are made visible and, therefore, one has direct access to molecular dynamics and mechanisms.
  • The technique allows for direct measurements of distances between two positions in a molecule via Fluorescence Resonance Energy Transfer (FRET).
  • Only small amounts of sample are needed. Typically, concentrations in the fM-range.
  • The technique has a high sensitivity and specificity.
  • Also, compared to e.g. X-ray and NMR, it is inexpensive.

The obtained data is compared and complemented with data from e.g. X-ray crystallography, NMR, bioinformatics and computer simulations and, finally, a unified structural model of the molecule is established. As a first model system for analysis non-coding RNA was chosen because:

  • There is very little known about RNA/Protein interactions.
  • One has the possibility of a controlled buildup of the single RNA stemloops and can, thus, analyze the regulation of the RNA’s self-expression.
  • They are simple to synthesize and, therefore, easily accessible.

Transmembrane helices of membrane proteins, e.g. ABC-transporters, would also be suitable for examination with this technique. They are difficult to produce in high concentrations and are hard to crystallize, which makes them hard to analyze with NMR and X-ray crystallography, respectively.

Supervisors

Topic Supervisor:

undefinedProf. Dr. Claus Seidel, Institute for physical chemistry, Seidel Group

Complementary Supervisor:

undefinedProf. Dr. D. Willbold, Institute for physical biology, Willbold Group

Complementary Supervisor:

PD Dr. Bernd König, Institute for physical biology

Responsible for the content: E-MailBioStruct Office