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Plamena Dogandzhiyski

  • PhD student
  • Group of Prof. Michael Goebel
  • Department of Chemical and Pharmaceutical Sciences, Institute of Organic Chemistry and Chemical Biology, Goethe University, Frankfurt
  • Contact email: vasilevaivanova (please add

Background: I graduated Sofia University with a Bachelor’s degree of Chemistry and a Master’s degree of Medical Chemistry. I did my master thesis in the Laboratory of Computational Chemistry and Spectroscopy in Sofia University, the topic of my research was to find a theoretical model to predict the absorption and fluorescence properties of 1,8-naphthalimide hydrazone derivatives for enzyme activity localization.

Training and Technical skills:
- performing footprint analysis and HPLC

Research Projects:The major goal of my PhD work is to find ways for a control of substrate conformations in artificial nucleases in order to obtain site-specific RNA-cleavage. I want to achieve this by rigid spacer units carried from a suitable nucleic acid recognition system. The research project includes the synthesis of modified PNA’s, secondary structure analysis of their complexes with target RNA, and their evaluation as RNA cleavers.
Why this topic is important?
It’s known that the mechanism of typical RNA cleaving enzymes or ribozymes involves a whole set of catalytic strategies, such as general acid / base catalysis and electrophilic phosphate activation. Most RNA cleavers make use of the 2’ hydroxyl group as an intramolecular nucleophile thus leading to fragments with 2’,3’-cyclic phosphates. The same strategies also account for the efficiency of artificial ribonucleases. However, a major advantage of the natural catalysts is their ability to control the conformation of the phosphodiester group to be cleaved. The stereoelectronic requirement of nucleophilic substitution at phosphates is an in-line orientation of nucleophile (2’-OH), phosphorous and leaving group (5’-OH). Restraining the substrate in conformations close to the transition state may result in rate increases of several orders of magnitude.