Molecular recognition within the minor groove of the DNA double helix

This thesis describes the synthesis of two nucleoside analogues with potential hydrogen bond acceptor sites removed. The effect that these compounds have on the sequence specific binding of distamycin to (AT) sequences and the stability of DNA double helices has been investigated. The approach taken to synthesise 3-deaza-2/-deoxyadenosine with the adenine N3 atom removed utilised 4,6-dichloroimidazo 4,5-c pyridine as the heterocyclic synthon which underwent stereoselective glycosylation to the /3-anomer of the corresponding 2'-deoxynucleoside. The synthesis of 2-thiothymidine with the thymine 02 atom removed started with the commercially available thymidine. The nucleoside analogues were incorporated into a series of self- and non-self- complementary oligonucleotides using the corresponding phosphoramidite monomers and automated oligonucleotide synthesis. Only the oligonucleotides with the adenine N3 atoms removed from the minor groove of the double helices could be used during the course of the thermal melting, differential scanning calorimetry and NMR studies. Studying the effect of incorporating 3-deaza-2/-deoxyadenosine into the recognition sequence of distamycin in the minor groove of the DNA double helices identified that: (1) Removing adenine N3 atoms from the minor groove decreases the stability of the DNA sequences. (2) The stabilising effect of distamycin is not affected by the removal of the potential hydrogen bond acceptor sites from the minor groove. (3) Replacing the dA residues leads to little disruption of the basic structure of the double helices. This thesis also describes the synthesis of the nucleoside analogue 6- 2Hi thymidine and how it has enabled the primary sites of electron addition to DNA to be investigated. The use of electron paramagnetic resonance spectroscopy of selectively deuteriated DNA has shown that one-electron reduced DNA comprises 85% cytosine and 15% thymine radical anions. The distribution of radical anions reflects the relative electron affinities of the various trapping sites.