Synthesis and characterization of a metal salen base pair for the assembly of programmed metal arrays inside the DNA double helix [Elektronische Ressource] / Guido Clever

Guido H. Clever

Informations

• Publié par: ludwig-maximilians-universitat_munchen
• Publié le: 01 janvier 2006
• Nombre de lectures: 33
• Langue: Deutsch
• Poids de l'ouvrage: 6 Mo

Extrait

Dissertation zur Erlangung des Doktorgrades
der Fakultät für Chemie und Pharmazie
der Ludwig-Maximilians Universität München






Synthesis and Characterization of a Metal-Salen Base Pair for the Assembly of
Programmed Metal Arrays inside the DNA Double Helix





Synthese und Charakterisierung eines Metall-Salen Basenpaars für den Aufbau von
programmierten Metallanordnungen im Inneren von DNA-Doppelhelices





Guido Clever

aus

Bad Neuenahr
2006

1 2 Erklärung

Diese Dissertation wurde im Sinne von § 13 Abs. 3 bzw. 4 der Promotionsordnung
der LMU München vom 29. Januar 1998 von Prof. Dr. T. Carell betreut.



Ehrenwörtliche Versicherung

Diese Dissertation wurde selbstständig, ohne unerlaubte Hilfe erarbeitet.



München, den 23.11.06


Guido Clever










Dissertation eingereicht am 24.11.06

1. Gutachter: Prof. Dr. T. Carell
2. Gutachter: Prof. Dr. P. Klüfers

Mündliche Prüfung am 19.12.06

3
4
Ltd. Doolittle: „Wenn Zusammenhänge logisch sind, dann sind sie das
unabhängig von ihrem Ursprung.“
Bombe # 20: „Hmmm…“
Dark Star (John Carpenter, 1974)



























Meiner Familie und Michi gewidmet.
5 Parts of this work were published or presented on conferences

G. H. Clever, K. Polborn, T. Carell, Angew. Chem. Int. Ed. 2005, 44, 7204 - 7208.
“A Highly DNA-Duplex-Stabilizing Metal-Salen Base Pair”

G. H. Clever, Y. Söltl, H. Burks, W. Spahl, T. Carell, Chem. Eu. J. 2006, 12,
8708 - 8718.
“Metal-Salen-Base-Pair Complexes Inside DNA: Complexation Overrides Sequence
Information“

G. H. Clever, T. Carell, Angew. Chem. 2006, in press (DOI: anie.200603099).
“Controlled Stacking of 10 Transition Metal Ions inside a DNA Duplex”

K. Tanaka*, G. H. Clever*, Y. Takezawa, Y. Yamada, C. Kaul, M. Shionoya, T. Carell,
Nature Nanotech. 2006, in press (DOI: 10.1038/nnano.2006.141).
„Programmable Self-Assembly of Metal Ions inside Artificial DNA Duplexes“

G. H. Clever, T. Carell, Coll. Symp. Ser. (M. Hocek, Ed), Vol 7, p. 389 - 391. Institute
of Org. Chem and Biochem., Academy Of Sciences of the Czech Rep., Prague 2005.
“Assembly of a Highly DNA-Duplex-Stabilizing Metal-Salen Base Pair”

Poster presentations on JCF meeting, Heidelberg 2004 (poster prize); ORCHEM,
Bad Nauheim 2004; Nanobionics III, Marburg 2005; NAC XIII, Prague 2005; Summer
School FrontChem, Tokyo 2006; Int. COE Symposium, Tokyo 2006.

Oral presentations on Volkswagen Foundation meeting, Aachen 2005; “Roche
Symposium for Leading Scientists of the next decade”; Basel 2005, FCI stipend
meeting, Munich 2006.
6 Table of contents

1 Summary............................................................................................................. 9
2 Zusammenfassung............................................................................................ 13
3 Introduction........................................................................................................ 16
3.1 Bionanotechnology..................................................................................... 16
3.1.1 Structure and function of biopolymers................................................. 16
3.1.2 Nature as paragon for nanotechnology ............................................... 18
3.1.3 Examples of oligonucleotide-based nanoscale objects....................... 20
3.2 Hypermodification of the DNA backbone and bases .................................. 27
3.3 Metal coordination inside/to nucleic acids .................................................. 28
3.3.1 Metal coordination to unmodified DNA................................................ 28
3.3.2 The metal-base pair concept and examples........................................ 30
3.4 Coordination chemistry: salen complexes and metal stacking ................... 37
3.4.1 Monomeric and oligomeric salen complexes....................................... 37
3.4.2 Interaction of metal-salen complexes with DNA.................................. 39
3.4.3 Metal stacks and arrays in solid state structures and in solution......... 39
4 Part I: Coordination of metals inside the DNA duplex........................................ 43
4.1 Aims of project (part I)................................................................................ 43
4.2 Synthesis of ligand nucleosides ................................................................. 44
4.2.1 Synthesis of the salicylic aldehyde nucleobase................................... 44
2+4.2.2 Synthesis and X-ray structure of a monomeric Cu -salen-base pair.. 54
4.2.3 Attempts to prepare a hydroxyphenyl-oxazoline nucleoside ............... 58
4.2.4 Incorporation of an oxazolinylidene-indolone nucleoside into DNA..... 60
4.2.5 Synthesis of 3’-O-methylxylose-based C-nucleosides ........................ 64
4.3 Incorporation of the salicylic aldehyde nucleoside into oligonucleotides .... 70
4.3.1 Automated DNA synthesis .................................................................. 70
4.3.2 Deprotection of the incorporated nucleosides ..................................... 73
4.3.3 Chromatographic purification of aldehyde carrying oligonucleotides... 74
4.4 Assembly of the metal-salen base pair....................................................... 77
4.4.1 Hybridization and reaction with amines and metal ions....................... 77
4.4.2 Melting point studies ........................................................................... 80
4.4.3 UV-Vis and CD spectroscopy.............................................................. 92
4.4.4 ESI mass spectrometry ....................................................................... 98
4.4.5 Liquid chromatography-mass spectrometry (LC-MS).........................103
4.4.6 EPR spectroscopy..............................................................................104
7 4.5 Interplay of salen complex formation and DNA sequence.........................107
4.5.1 Complex formation in different sequence context ..............................107
4.5.2 Brick-wise elongation of overlapping sequences................................110
4.5.3 (Unspecific) hairpin formation and dynamics......................................111
4.5.4 Reaction of single strands..................................................................115
4.6 Metal stacks and arrays ............................................................................116
4.6.1 Two metal-salen complexes inside one duplex..................................116
4.6.2 Homo-polynuclear metal stacks inside DNA ......................................117
4.6.3 Hetero-polynuclear stacks: controlled mixing of metals inside DNA...121
4.7 Conclusion and outlook (part I) .................................................................130
5 Part II: Coordinating metals on the exterior of the DNA double helix................132
5.1 Aims of project (part II) ..............................................................................132
5.2 Synthesis of ligand-modified uridine compounds ......................................132
5.3 “Clicking” of gold clusters to DNA via glutathione-bisazide .......................139
5.4 Conclusion and outlook (part II).................................................................141
6 Experimental part .............................................................................................142
6.1 Materials and methods ..............................................................................142
6.2 DNA synthesis, cleavage and purification .................................................142
6.3 Melting point experiments .........................................................................143
6.4 UV and CD spectra and titrations..............................................................143
6.5 ESI mass spectrometry .............................................................................144
6.6 Synthesis of the salicylic aldehyde nucleobase.........................................145
6.7 Synthesis of a monomeric copper salen complex .....................................151
6.8 Synthesis of a 3-(2-oxazolidinylidene-)indol-2-one nucleoside..................154
6.9 Synthesis of 3’-O-methyl-xylopyranosyl nucleosides.................................159
6.10 Synthesis of a hydroxyphenyl-oxazoline-uridine nucleoside .....................165
6.11 Synthesis of a benzotriazole-uridine nucleoside .......................................169
6.12 Synthesis of a glutathione-bisazide...........................................................175
7 Appendix ..........................................................................................................177
7.1 Further selected ESI spectra.....................................................................177
7.2 Crystallographic data