# Ru(II)-Dppz Derivatives and Their Interactions with DNA: Thirty Years and Counting
## 3 DNA Binding
### Interaction of Small Molecules with DNA
The combination of these structural modifications results in functional changes, and frequently, in the inhibition of DNA transcription and replication and repair processes, thus making the intercalators mutagens. To permit this intercalation process, it is necessary that a \"cavity\" forms between the nucleobases, so they have to distance each other; this process causes the elongation of DNA [36; 37; 38; 39]. Vertical separation between nucleobases (about 3.4 A in the B-DNA) might increase from 1.8 to 4.5 A per intercalated molecule when a huge aromatic molecule intercalates. The angle of rotation might vary from 11\({}^{\circ}\) to 48\({}^{\circ}\), depending on the intercalator structure and the type of nucleotides involved [40]. The process causes distortions in the DNA structure that can be used to study DNA-molecule interactions by, for example, viscosity measurements [41] sedimentation studies [42], circular dichroism (CD) variations [36; 37; 38; 39; 40; 43], and electrophoresis studies on circular DNA supercoil [44]. The intercalation model proposed by [PERSON], however, did not take into account the possibility of the species to insert itself between nucleobases pairs, until a double helix saturation. [PERSON] introduced the neighbor exclusion model: [45; 46] in case a molecule intercalates into a site, it distorts the vicinal ones, so that they would not be available to permit the intercalation of other molecules. Therefore the intercalation is anti-cooperative at adjacent sites, and therefore, only 50% of DNA sites can undergo an intercalative interaction. Moreover, it is also (highly) possible that the molecules do not occupy every other site, obstructing more than two of them; also, huge molecules might prevent this kind of interaction due their steric hindrance. Several studies were conducted to understand whether there exists a specificity in the intercalative interactions related to the type or the sequence of the nucleobases involved. Some intercalators showed preferential interactions, but almost all of them interact aspecifically with the nucleobases. At first it was believed that only small molecules, with a planar structure, could intercalate, but after several studies during the years a distinction between 'classical' and 'non-classical' intercalators was made. Classical intercalators are characterised by aromatic condensed rings and have positive charge(s) on the rings themselves or on the side chains. Among non-classical intercalators there are compounds that have huge or polar (or charged) substituents on the opposite sites of the intercalating aromatic system [47]. These compounds need to insert at least one of the substituents between the nucleobases pairs to intercalate. Among these species there are known compounds like naphthalene bisimide and cationic porphyrins, which, although they are not supposed to intercalate, might interact efficiently with DNA through such an interaction [48]. Even if thermodynamically favorable, this interaction is kinetically unfavorable, and needs opening of the double helix (causing distortion or breaking of hydrogen bonds); such effect makes the DNA-molecule interaction slow. The initial studies of the intercalative process involved simple organic molecules, but they were followed by studies focused on the interaction between DNA and metal complexes. The presence of a transition metal indeed provides several advantages, as described below [49; 50; 51; 52; 53; 54]. * The presence of \(d\) orbitals grants more ways (bonds and geometries) such that the species might interact with DNA other than those of organic molecules. * Steric and electronic properties can be modulated choosing opportune ancillary ligands. * Bridging ligands of certain dimensions might modify the size of the intercalator. * It is possible to take advantages from their spectroscopic, magnetic, redox, photophysical, and photochemical properties. Since the antimuoral properties of cisplatin, square planar Pt(II) complexes were the first inorganic species whose interaction with DNA was studied.