Time-resolved and Static NMR
Characterization of the Structure and
Folding Kinetics of the Diels-Alder

zur Erlangung des Doktorgrades
der Naturwissenschaften

vorgelegt beim Fachbereich Biochemie, Chemie und Pharmazie
der Johann Wolfgang Goethe-Universität
in Frankfurt am Main


Vijayalaxmi Manoharan


Chennai, Indien

Frankfurt am Main

Dem Fachbereich Biochemie, Chemie und Pharmazie der
Johann Wolfgang Goethe-Universität als Dissertation vorgelegt.

Dekan: Prof. Dr. Dieter Steinhilber
1. Gutachter: Prof. Dr. Harald Schwalbe
2. Gutachter: Prof. Dr. Beatrix Süß

Datum der Disputation: 2009
iii iv

This thesis was prepared under the supervision of Prof. Dr. Harald Schwalbe
between June 2005 and June 2009 at the Institute for Organic Chemistry and
Chemical Biology of the Johann-Wolfgang Goethe-University of Frankfurt.
vi Acknowledgement

Many people have made this work possible. I dedicate this thesis to
those who have been directly and indirectly behind it and who have made an
impact in my life through their contributions.

To my advisor Prof. Dr. Harald Schwalbe
Thank you for your support and guidance. Your constant feedback and
encouragement and ability to provide a macro perspective to my work have
been invaluable.

To Dr. Jens Wöhnert, Dr. Boris Fürtig, Dr. Jonas Noeske - the RNA guys
I was lucky to have the smartest guys I have known with me in my
graduate career. Your tremendous support definitely made my initiation into
this world much smoother. Jens - the trouble shooter- who I have constantly
consulted with even when he was 1000s of miles away! Your pithy
explanations have saved me hours in the laboratory. Somehow you made it all
sound so simple! I can't thank you enough for your support. Boris -who worked
with me on this project from the very beginning - You have shown me how
constant diligence definitely pays off. Thank you for tirelessly and patiently
sharing your expertise. Jonas - I and my RNA are grateful to you for your
patience and support in the lab. My RNA have definitely had it easy because of

Prof. Dr. Andres Jäschke and his group
For providing this fruitful collaboration on the Diels-Alder ribozyme.
Thank you for your time and input on this project and for the numerous
perusals and insightful remarks that finally made the publication of the work
possible. I would also like to acknowledge his generosity in sharing RNA and
ligand with me.

Dr. Judith Klein-Seetharaman and her group
For the nurturing in your laboratory during my programmer days and
your encouragement and support that have got me where I am today. Thank
you for generously hosting me in Pittsburgh for a year.

Dr. Johannes Gottfried Zimmermann - A perfect world will be filled with
Zims! Zim, your good spirits are amazing. Your patience and support at the
spectrometers were invaluable. Dr. Christian Richter - with his impressive
technical expertise. Thank you for your excellent support at the spectrometers.
Elke Stirnal, who has a way with RNA, thank you for the innumerable HPLC

Anna Paulus and Elena Hartmann - Many a late nights at the lab were made
cozy only because of Anna's presence in her office. Thanks so much for being
there when we needed you - for finding the 'rat hole' which I really really
adored. :) - for clarifying the numerous bureaucratic procedures and making
our lives easier and for lots and lots of good conversations. Elena, your
viienthusiasm is infectious. It was always good fun to be around you. I thank you
two for being such good supports in our life.

Gerd Nielsen and Dr. Henry Jonker. I can not imagine my four years there
without you guys in it. The coffee breaks - the lunch breaks - the laughs - the
beer hour - the Alte Papier Mühle - the walks in the Taunus - Bad Soden
barbecues - the stroopwaffels. I hope we stay connected. Henry, thanks for
always having an open door – be it help with spectrometers, critical discussions
or for just bouncing ideas.

Sridhar Sreeramulu and Dr. Santhosh Gande. For providing the home away
from home. Countless couch crashes, cookouts in coffee room, movie nights,
lab nights, weekends in lab. You guys made it so much fun. I have learnt so
much from you two. Sridhar, your drive and commitment to your work is
amazing. Thank you for always having the time and good ideas when I turned
to you with mini crises. Dr. Raja K. Muruga Poopathi and Jitendra Kumar
- I appreciate the interest you have always shown in my work and your
invaluable inputs and encouragement. Also memorable are the days spent at
your homes. Thanks for making me so welcome.

Dr. Kai Schlepckow – for stimulating discussions and of course for saving me
from lab work by generously sharing his hoard of DMN. Dr. Jürgen & Iris
Graf – my time in Frankfurt was definitely enriched by your presence. Thanks
for the good conversations, awesome food and wine. Jan-Peter Ferner - your
enthusiasm in everything to do with RNA and relaxation is cool.

Dr. Nicole Schmut and Max Stadler – who have contributed so much of their
valuable time for the smooth running of the lab. Dr. Christian Schlörb and
Martin Hähnke, Daniel Mathieu and Fabian Hiller for being such
competent and cheerful computer administrators in addition to being good
researchers. Dr. Elke Duchardt, Dr. Julia Wirmer, Dr. Steffen Grimm, Dr.
Karla Werner, Neda Bahktiari, Janina Buck, Christian Gerum, Dr.
Hamid Nasiri and Jörg Rinnenthal, the original guys and fellow colleagues.
Anna Wacker, Senada Nozinovic, Anke Reining, Katja Barthelmes,
Melanie Koschinat, Friederike Heinicke, Tanja Machnik, Anna Lena
Lieblein, Florian Buhr, Jochen Stehle and Robert Silvers – the youngsters
leading the show now.

Dr. Karin A Heidemann, Teresa Jimenez, Stephan Rehm, Carlos &
Stefanie Mauricio. for the Clubkeller nights (and mornings!) the
Lokalbahnhof and parties. Your warmth and hospitality definitely helped me
find my footing there. Dr. Jesse & Ralf Bidinger– for opening your home to
us and for the many a good evenings around your kitchen table. Sofia and Dr.
Radhan Ramadass – for the many late nights and many many debates about
everything under the sun.

To my loved ones in Pittsburgh – my crazy nephews who bring perspective
into my life. My family there and in India, who are happy that the end is in
sight at last. Oznur Tastan, for the numerous brunches, the sleep-overs, the
viiiworkathons and most of all, for the constant companionship, encouragement
and support.

And to Andreas Christoph Zollmann – my husband - for being a pillar by my

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