Studies of metal ion-DNA interactions

This thesis is primarily concerned with the derivation of a detailed structure for the Cu(II)-DNA complex. Cu(II) readily facilitates the denaturation and renaturation of DNA under certain conditions. Such processes occur during biological replication and recombination. Thus, there is considerable importance attached to a detailed knowledge of the Cu(II)-DNA complex. This is especially true when one finds that 'unwindase' (a DNA denaturing protein) which is essential for DNA replication during cell division has very similar solution properties (with DNA) to that of Cu(II). From numerous solution studies, other workers have derived various models of the Cu(II)-DNA complex. However, these models do not provide detailed structural features of the Cu(II)-DNA complex. So, an attempt was made to obtain additional evidence that would give rise to a more detailed structural model of the Cu(II)-DNA complex which in turn would more fully account for its properties. Two main approaches were made: (1) Studies of Cr(II)-DNA chemistry. Cu(II) and Cr(II) very often have similar chemistries due to the axial distortions of its bonding geometry in five and six co-ordinate complexes. By analogy with the studies of Ag(I)-DNA with Hg(II) and Cu(I)-DNA, similarity of properties could mean similarity of geometry of binding of these ions to DNA. (2) Correlation with the electron microscopic studies of 'unwindase'-DNA. The similarities of the properties of Cu(II) and 'unwindase'-DNA complexes could mean the similarity of certain basic structural features of these complexes. These studies result in the derivation of a model of Cu(II)-DNA which readily accounts for the kinetic and equilibrium properties of the Cu(II)-DNA complex. This model involves a square pyramidal (with a long axial bond) co-ordination of Cu(II) to N₇ of adenine or guanine and a phosphate group of the same strand on the next but one nucleotide as shown in Figure 34 (following page 124). The structural features of the 'unwindase'-DNA complex show how difficult it is to transfer twists from neighbouring denaturing regions towards the ends of the DNA molecule during denaturation (as required by the Watson-Crick model of DNA) . Such studies therefore support the contention of Day and Rodley that an essentially non-intertwined structure (SBS) of DNA (which requires minimal twists on denaturation) could more readily account for the requirements associated with the separation of the two strands of DNA. This conclusion is also supported by the Cu(II)-DNA studies. Since Cr(II) solutions are hydrolysed at high pH and are readily oxidized by atmospheric oxygen, special conditions and apparatus had to be devised for its studies. Under the conditions which had to be used (pH ≃ 4.2), the structural features of the DNA molecule could be different from those under 'normal conditions' of pH ≃ 6. So, a systematic study of Cr(III), Co(II) and Cu(II) was carried out to check the applicability of the Cr(II) results. These studies show that the structures of the metal DNA species are not very different from those under 'normal conditions', thus allowing for the application of known properties of other metal ion systems in the interpretation of the results obtained. Also, as predicted the properties of the Cr(II)-DNA complex are similar to those of Cu(II) under these conditions. However, the greater reactivity of Cr(II) with DNA does not allow for a 'straight forward' comparison. The Cr(III)-DNA studies are also of interest. Experimental results show that it behaves differently towards DNA than Cr(II) but there are certain similarities. Other studies of metal-DNA interaction (optical) and studies of X-ray metal-nucleotides were attempted to further support the proposed model of Cu(II)-DNA. Due to various difficulties, very little additional information was obtained. Finally, the indirect biological and medical implications of the Cu(II)-DNA studies are discussed in some detail