# Ru(II)-Dppz Derivatives and Their Interactions with DNA: Thirty Years and Counting
## 3 DNA Binding  
### Interaction of Small Molecules with DNA  
It is possible to distinguish two kinds of interactions with DNA--reversible and irreversible ones [20; 21]. Irreversible interactions involve the formation of a covalent or coordination bond between a species and an atom site of the helix; such a linkage implicates the total inhibition of DNA processes (and the cell death as a consequence), if DNA repair systems, such as the NER (nucleotide excision repair) fail. Very often, the steric hindrance of species bound irreversibly might cause a distortion of the phosphate groups, which leads to negative effects on DNA transcription and replication, such as preventing the protein-complex identification [2; 3; 4]. Reversible interactions are usually less toxic than the irreversible ones. These can be classified into four types (see Scheme 2)--(i) external electrostatic interaction, (ii) groove binding, (iii) external self-aggregation, and (iv) intercalation. The external electrostatic interaction (i) is due to the presence of the phosphate groups in the chain, because their negative charge might attractively interact above any positive ion. In particular, simple cations like alkaline ones associate with nucleic acids in the base of the density charge generated by the phosphate groups, resulting in a stabilization of the DNA itself. This association is called 'condensation', because the ions are associated to the overall charge of the biomolecule and not to specific sites, which remain capable of moving along the double helix. The typical DNA counterions are Na\({}^{+}\) ions, which compensate most of the phosphate groups' negative charge. The remaining charges are neutralized by other cations through the classic Debye-Huckel mechanism. The groove binding (ii) occurs for species that have the right dimension and conformation to \"lay down\" in one of the grooves, which interact via electrostatic interactions, Van der Waals forces, and especially, hydrogen bonds [22; 23]. The typical molecules that are able to make this kind of interaction have an appropriate length and flexibility, which might assume an optimal conformation. Usually, these molecules have several aromatic rings(like pyrroles, furans, or benzenes) that are bound to substituents that are capable of rotating around the bonds, letting them adapt to the double helix shape without significantly perturbing the DNA structure. External self-aggregation (iii) occurs when molecules, especially aromatic planar species, stack along the external part of the double helix, forming dimers or even huge aggregates through a non-specific bond called external stacking. It is known that interactions of porphyrin and metal-porphyrin with DNA, lead to the formation of chiral supramolecular structures [24; 25; 26; 27; 28], Pt(II) organometal complexes coordinated by terpyridine [29; 30] or Pt(II) complexes with extended aromatic ligands like dipyrido[3,2-a-2\({}^{\prime}\),3\({}^{\prime}\)-c]phenazine or benzodipyrido[b:3,2-h:2\({}^{\prime}\),3\({}^{\prime}\)-j]phenazine, in the case of low [DNA]/[complex] ratio, and consequently, the presence of few intercalative sites [31]. [PERSON] et al. highlighted that the structure of intercalators influences the interaction type with DNA and might lead an external interaction to be preferred to an intercalation [32; 33]. Intercalation (iv) is essentially a stacking interaction resulting from the insertion of a planar aromatic system between the base pairs of the DNA double helix, and is permitted by a significant overlap between \(\pi\) orbitals of the intercalative species and those of nitrogenous bases, forming a system stabilized by Van der Waals forces, hydrophobic interaction, and especially, \(\pi\)-\(\pi\) stacking [34; 35]. This type of interaction was first proposed by [PERSON] [34] in order to rationalize his results on the high affinity for DNA of certain arcidine derivatives.