I-Modified Nucleosides as DNA-Sugar Centered Radical Precursors II-DNA Excess Electron Transfer Studies III-A new Direct DNA Detection Method: DNA-Photography (Tienda española)

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During cellular metabolism of oxygen to water in the mithocondria, a small fraction of the oxygen is reductively converted into superoxide (O2•-) as a by product. Through complex biochemical processes, superoxide may be converted into various reactive oxygen species (ROS), e.g. hydroxyl radicals (•OH), H2O2, 1O2, etc. These ROS and in particular the highly diffusible •OH are known to cause chemical modifications on DNA through the formation of strand breaks and nucleobase modifications. DNA damage and strand breaks may also be induced through other environmental influences such as ionizing radiation, photooxidation and naturally occurring or synthetic chemical mutagens. Oxidative DNA damage can be produced by the oxidation of the nucleobases or of the sugar units. In the last case carbon centered radicals are formed by direct or indirect hydrogen abstraction. In the first part of this thesis (Chapter 1), the fate of the carbon centered radicals C5’ and pseudo C4’ of the sugar was investigated at the nucleoside level. The syntheses of new thermal or photolabile C5’ and pseudo C4’ radical precursors were achieved to this end and the mechanistic aspects were studied under various conditions. Kinetic data were obtained as well and the access to biological lesions was possible through these studies. In section 1.2.1, the synthesis of a novel perester radical precursor was achieved. The unprecedented selective generation of the pseudo C4’ radical was established as well. The radical was studied in solution under various conditions and the pathways of base releasing and degradation were proved and described.
In section 1.2.2 a short and efficient synthetic sequence for the preparation of cyclonucleosides has been disclosed, based on consecutive radical reactions followed by a photochemical desilylation. The C5’ radicals, generated by the addition of a (TMS)3Si• radical to the corresponding 5’ carboxaldehyde, are the key intermediates in these transformations. The rate constant kC of the subsequent cyclisation reaction was estimated for the first time in such systems through a radical clock reaction setup. The value of kC = 7 × 103 s 1 at 25 °C found here is strictly correlated with the C5’ radical repair reaction.
In section 1.2.3 a new synthetic route for the preparation of (5’R) tert butyl ketones was disclosed. Photolysis experiments selectively afforded the corresponding C5’ radical. In the presence of a physiological concentration of alkanethiol, the thymidin 5’ yl radical is efficiently reduced. Under these conditions the half life of the thymidin 5’ yl radical was calculated to be t1/2 = 6.6 min. without any cyclisation product being observed. The resulting C5’ radical could be obtained either by Norrish Type I photocleavage or by initial formation of an acyl radical that decarbonylates with a rate constant in the range of 105–106 s–1. The presence of a thiol prevents subsequent reactions such as the intramolecular attack onto the C6–C5 double bond of thymine.

When an electron donor injects electrons into a duplex, negative charges move to an acceptor site in DNA. Investigations on how charges move through DNA and studies of how the electron transfer can be accelerated and controlled is an active field of research. In the second part of the thesis (Chapter 2) the study of the excess electron transfer (EET) through the DNA was undertaken. A flavin used as electron donor was alternated with a single electron injector in order to establish diverse EET features. A CPD lesion (T=T dimer) and one of three bromo nucleosides were used as electron acceptors enabling the evaluation of the sequence dependence and the donor/acceptor system influence on the EET. Three series of five flavin containing hairpins were prepared. They contained the flavin electron injector placed in the loop region of the hairpin and one of the three electron acceptors positioned in the stem region at a distance of about 17 Å to the flavin. The nature of the acceptor influences the debromination yield and therefore the EET process analysis. Moreover, the differences shown by the traps indicate that the reduction of the acceptor can indeed be the rate determining step. Thus, in the process of electron migration through DNA, which involves electron injection, migration and capture, the latter step might determine the final efficiency of the whole process. As a result of these studies, a G:C bp between the donor and the acceptor reduces the excess electron transfer efficiency approximately by a factor of two. More important is the unprecedented observation that the position of G:C base pairs between the donor and the acceptor strongly influences the efficiency of the process. Although every G:C bp reduces the EET efficiency by about 50 %, the position of a single G:C bp in proximity to the trap can decrease the efficiency by more than 85 %.
To further investigate the EET through DNA, it was chosen to initiate the process by the injection of one single electron per strand using a single electron donor (SED). In section 2.2.2 the use of SED was alternated with the use of the flavin donor in systems containing two electron acceptors in a row. The irradiation at 320 nm of SED containing double strands initiates a cascade of homolysis, charge translocation and deprotonation enabling the final electron injection into the DNA base stack. This process is initiated by a Norrish type I photolysis of the tert butyl α hydroxy ketone of the SED moiety. On the other hand, the results observed upon irradiation of a flavin containing hairpin, provide an astonishing outcome. The chemistry that is triggered by a charge in DNA depends on how the charge was initially injected. In excited state systems, the injected electron feels the efficient charge recombination process, which seems to limit and bias charge propagation. If, however, ground state chemistry is employed to inject the charge, no recombination trap is present. In this case, the charge can move freely. Excess electrons injected by such a system can trigger more than one reaction, establishing a catalytic electron, and they can hop over acceptors if their triggering mechanism is slower than the hopping step.
Strong efforts are under way to create DNA based nanoelectronic materials with self organizing properties. The long term goal is that such a novel material may self assemble into complex conductive nano wire networks with computing or diagnostic potential. Recently, a controlled assembly of metallised DNA in which one or more natural base pairs are replaced by nucleosides carrying flat metal complexes was reported. The design and the synthesis of DNA structures containing an internal metal complex between an electron donor and an acceptor opened the access to the study of EET through metal base pairs (metal mediated EET, M MEET). A series of DNA hairpins containing the light dependent flavin electron donor and the fast electron acceptor BrdU were designed. A salen metal complex between the donor and the electron acceptor was introduced via the oligonucleotide solid phase synthesis in order to establish the influence of one metal in the electron transfer process. The hairpins design was aimed at exploring the electron transfer through the salen metal complexes in the context of mixed sequences. The effect of only one metal per DNA was investigated in this proof of concept study, in which only the nature of the metal and the irradiation conditions were systematically changed.

In the third part of the thesis (Chapter 3) a new direct DNA detection method was established based on the principle of the black and white photography, called DNA photography, DP. A detection limit lower than 300 attomoles of DNA (10-18 mol) was achieved with a simple setup in a photography dark room. Moreover the detection of 600 femtomoles (10-15mol) of a sequence associated with a gene of Y. pestis, which causes the mortal disease plague, was achieved. In the latter case, molecular beacons (MBs) were used in order to use the FRET principle together with the DP method.