Verhage, Jeroen (2005) Model systems for the replication of genetic information. PhD thesis Institut Européen de Chimie et Biologie, Institut Européen de Chimie et Biologie, EP/X p.192.

Alternative Locations: http://www.imprimerie.polytechnique.fr/Theses/Files/Verhage.pdf

Abstract

The goal of this research project is to develop an artificial replicating model system to ‘repair’ abasic sites within DNA double helices. We will not restore a natural base pair, but introduce a chemical modification that restores duplex stability according to the base facing the abasic site. The opposite base will thus serve to select one “repair reagent” among several possibilities. We amount here to a “information transfer system”, or a “replicating system”, which is an interesting topic by itself.
We would like our system to make use of reactions that are reversible on the time scale of the experiment to allow error correction in the system. We would also like the repair units to react with the DNA backbone without having to cleave it, to make the system more reliable.
For our system we chose the reaction of aldehydes with amine type compounds to form imine type products. We chose this group of reactions because they can be made reversible in water at pH 7.
The work is divided in three main chapters; in chapter two an overview of relevant literature is given. Chapter three involves the work we did on the repair of natural abasic sites. Chapter four involves the work we did on the repair of artificial abasic sites.

Table of content

Summary - 5
Sommaire - 9
Samenvatting - 14
1 Introduction - 19
2 Literature background - 21
2.1 Introduction - 21
2.2 Templates for synthetic purposes - 21
2.2.1 Macrocycles - 23
2.2.2 Enzyme mimics - 24
2.2.3 DNA based systems - 28
2.2.4 Ribozymes - 34
2.3 Dynamic combinatorial chemistry and molecular imprinting - 36
2.3.1 Dynamic combinatorial chemistry - 36
2.3.2 Irreversible reactions - 41
2.3.3 Molecular imprinting - 42
2.4 Replication model systems - 44
2.4.1 Replicating systems - 44
2.4.2 Self replication - 50
2.4.3 Cross catalytic systems - 57
3 Design of a natural abasic site repair system - 60
3.1 Introduction and goal - 60
3.2 Design of the system - 63
3.2.1 Biological relevance - 63
3.2.2 Choice of the reaction - 64
3.3 Possible behavior of the system - 70
3.3.1 Introduction - 70
3.3.2 Conformation of the abasic site - 71
3.3.3 Molecular modeling - 75
3.4 Synthesis of aminobases and hydrazides - 84
3.5 Model reactions with ribose and deoxyribose - 87
3.5.1 Test reactions with ribose - 87
3.5.2 Test reactions with deoxyribose - 98
3.5.3 Conclusion - 107
3.6 Design of an oligonucleotide sequence - 108
3.7 Synthesis - 110
3.7.1 Introduction - 110
3.7.2 Synthesis of the phosphoramidite and the oligonucleotide - 111
3.7.3 Purification of the oligonucleotide - 112
3.8 Conclusion - 117
3.9 Experimental section - 118
4 Design of an artificial abasic site repair system 127
4.1 Introduction and goal - 127
4.2 Design of the amines and the aldehydes - 128
4.2.1 Choice of the reaction - 128
4.2.2 Aldehyde design - 129
4.2.3 Molecular Modeling - 131
4.3 Aldehydes protected as 1,3-dioxolanes - 141
4.3.1 Retro-synthesis - 141
4.3.2 Synthesis - 143
4.3.3 Deprotection tests - 147
4.4 Aldehydes masked as 1,2-diols - 152
4.5 Conclusion - 155
4.6 Experimental section - 155
5 Perspectives - 167
5.1 Short term research on natural abasic site repair systems - 167
5.2 Short term research on artificial abasic site repair systems - 169
5.3 Long term research on artificial abasic site repair systems - 172
6 Glossary - 175
7 Literature references - 177
Word of Thanks / Remerciément / Dankwoord - 190

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