DNA based ligands for use in asymmetric catalysis and development of metallo-(deoxy)ribozymes [Elektronische Ressource] / vorgelegt von Mihaela Caprioara

Mihaela Caprioara

Sujets

• Biologie

Informations

• Publié par: ruprecht-karls-universitat_heidelberg
• Publié le: 01 janvier 2007
• Nombre de lectures: 21
• Langue: English
• Poids de l'ouvrage: 5 Mo

Extrait

Inaugural-Dissertation


zur Erlangung der Doktorwürde
der
Naturwissenschaftlich-Mathematischen Gesamtfakultät
der
Ruprecht-Karls Universität
Heidelberg



vorgelegt von

M. Sc. - Dipl. Chem. Mihaela Caprioara
aus Piatra Neamt/Rumänien




Tag der mündlichen Prüfung: 26.11.2007








DNA-Based Ligands for Use in Asymmetric Catalysis and
Development of Metallo-(deoxy)Ribozymes




















Gutachter: Prof. Dr. Andres Jäschke
Prof. Dr. Nils Metzler-Nolte

Acknowledgments

I thank all my friends and colleagues from the University of Heidelberg and from other
research groups who contributed to the work described in this thesis.
I express my sincere gratitude to my supervisor, Prof. Andres Jäschke, for giving me the
opportunity to work in a very stimulating research group, on a highly interesting project,
as well as for his continuous support, encouragement, and confidence at all stages of my
work. Thank you for all suggestions that helped me to improve the quality of this thesis.
I would like to thank Prof. Nils Metzler-Nolte who agreed to review and co-examine
this thesis.
I want to acknowledge Dr. Roberto Fiammengo and express my recognition for his
guidance, expertise, determination, and understanding, which considerably added to my
experience throughout all these years. He provided me with direction, stimulated me in
being critical with my results, and had always prompt answers to my questions. I
appreciate his work and patience to read the preliminary versions of my writings,
including this thesis, and the assistance he provided through the most difficult
correction steps.
I would like to acknowledge Prof. Nils Metzler-Nolte and Dr. Srecko Kirin who kindly
provided the N,N-bis(2-picolyl)amine derivative, as well as Prof. Lutz Gade for
generously providing the PYRPHOS ligand. I also thank Prof. Roland Krämer and Dr.
Andriy Mokhir for helpful discussion and technical support in performing the MALDI
TOF measurements. I am grateful to Dr. Marianne Engeser, University of Bonn, for our
fruitful collaboration, for recording the electrospray mass spectra of the Rh(I)-
PYRPHOS complex and the DNA-PYRPHOS conjugate, as well as for her help with
the interpretation of the data.
I thank Dr. Mark Helm, Pierre Fournier, Stephanie Pfander and Anna Wiesmayr for
generously offering to proof-read sections of my thesis. I appreciate their support, their
rigorous and constructive corrections. I am grateful to Stephanie Pfander and Alexander
Nierth for the linguistic improvements of the “Zusammenfassung” of my thesis.
I want to acknowledge Pierre Fournier with whom I shared the work in the lab, for the
many helpful discussions about catalysis and for his enthusiasm in the times when
difficult tasks came up.
Special thanks go to Dr. Richard Wombacher, Columbia University, for his continuous
interest in my project and for our scientific debates, knowledge exchange, and venting
of frustration during our breaks. I also thank Dr. Barbara-Sylvia Weigand, Stephanie
Pfander, Markus Petermeier for being supportive and understanding, for their friendship
and encouragement over the last four years. I am grateful to all former and current
colleagues for the stimulating working environment and for their contributions to the
lab research standards.
This work would have been incomplete without the help of Sandra Suhm, Heiko Rudy,
Tobias Timmerman, Besarta Nezaj, Marina Silbereis. I want to thank them for the great
technical assistance in synthesis, mass spectrometry and NMR measurements, as well as
for their excellent job to fulfil the needs of the lab.
My special thanks go to the office staff, in particular to Mrs. Viola Funk and Mrs. Karin
Weiß, for all the instances in which their assistance helped me along the way and for all
their support and advices at times of critical need.
Thanks to my family for their sincere encouragement and support they provided me
through my entire life. In particular, I would like to thank my fiancé and my best friend,
Razvan, for his patient support, encouragement, and for helping me finish this thesis.
This work was financially supported by Deutsche Forschungsgemeinschaft (SFB 623).



























To my family
Summary Caprioara, Mihaela; M. Sc. Chem.

Title: DNA-Based Ligands for Use in Asymmetric Catalysis and Development of
Metallo-(deoxy)Ribozymes

1. Gutachter: Prof. Dr. Andres Jäschke
2. Gutachter: Prof. Dr. Nils Metzler-Nolte

The fascinating way nature relies on biomolecules, mostly proteins and sometimes RNA, to
carry out sophisticated chemical processes led to more and more efforts to use the concepts of
biology for preparing efficient chiral catalysts. The “hybrid catalyst” approach that combines
the steric information derived from a protein scaffold with the catalytic activity of transition
metal complexes offers a resourceful means of developing semisynthetic metalloenzymes for
enantioselective applications. Since the discovery of nucleic acids with enzyme-like functions,
the catalytic potential of nucleic acids is being revealed by in vitro selection and evolution of
novel ribozymes and DNAzymes. Nucleic acids, especially RNA, appear to be versatile
catalysts capable of accelerating a broad range of reactions and exquisitely discriminating
between chiral targets. However, while proteins dominated the construction of hybrid catalysts,
the application of DNA and RNA in asymmetric catalysis has hardly been explored.
This work aimed at exploring the chirality of nucleic acids and generating hybrid catalysts
based on DNA and RNA. Towards the development of metallo-(deoxy)ribozymes assisted by
combinatorial strategies (e.g., SELEX), a straightforward synthetic way of embedding transition
metal complexes in nucleic acids folds was established. DNA sequences carrying mono- and
bidentate phosphine ligands as well as P,N-ligands were successfully prepared starting from
amino-modified oligonucleotide precursors. The optimized “convertible nucleoside” approach
allowed the parallel, high-yielding synthesis of various alkylamino-DNA conjugates differing in
length and structure of the spacer. Coupling of amino-oligonucleotides with PYRPHOS, BINAP
and PHOX ligands equipped with a carboxyl group led to the incorporation of phosphine
moieties at predetermined internal sites. Moreover, the stability of the DNA-tethered BINAP
and PHOX was reasonably high, which makes them attractive candidates for the development
of transition metal-containing oligonucleotides. To this end, systematic studies on the behavior
of phosphine- and PHOX-metal complexes in aqueous medium - a prerequisite of nucleic acid
catalysts - were carried out. Two model organometallic transformations were selected that were
compatible with the structure and chemistry of nucleic acids. The rhodium(I)-catalyzed 1,4-
addition of phenyl boronic acid to 2-cyclohexen-1-one and iridium(I)-catalyzed allylic
amination of the branched phenyl allyl acetate, respectively, proceeded efficiently in the
presence of phosphorus-based ligands, in aqueous medium, at room temperature and low
catalyst concentration. For the first model reaction, the best conversion (80%) was achieved
with the isolated [Rh(nbd)BINAP]BF complex, in 6:1 dioxane/water, and TEA additive. On the 4
basis of these data, a suitable system for assessing the catalytic potential of the DNA-BINAP
ligand was implemented. In the second chosen reaction the in situ formed Ir(I)-PHOX
complexes (0.05-0.1 mM) gave rise to racemic, branched allylic amination products in good
yields (33-75%), in 3:7 dioxane/water. Kinetic resolution of the racemic substrate was then
attempted by employing catalysts generated from the [Ir(cod)Cl] precursor and single- and 2
double-stranded DNA-PHOX conjugates. Good conversions were obtained in the presence of
G-poor DNA/DNA and RNA/DNA hybrids bearing the PHOX moiety, indicating a potential
role of the G-N7 site in the first coordination sphere. With all tested DNA-PHOX conjugates,
the levels of enantioselectivity remained modest. The results described in this work provide
useful information for understanding the influence of nucleic acid sequence and covalent
tethering on the reaction outcome. These are the first reported applications of DNA-based
ligands in organometallic catalysis and they build the fundamentals for further development of
selective nucleic acid catalysts, by means of rational design and in vitro selection approaches.