ABSTRACT
Nucleic acids represent remarkable host systems that may associate with a large variety of different guest molecules (Haq 2006; Hannon 2007; Strekowski and Wilson 2007; Xie et al. 2010). In principle, external ligands may bind to DNA by three signi—cantly different binding modes, namely, electrostatic association to the phosphate backbone (also referred to as outside-edge binding), groove binding, and intercalation. The outside binding is mainly governed by the electrostatic interactions, whereas groove binding and intercalation are based on several supramolecular interactions simultaneously operating between the ligand and particular regions of the DNA through, such as π stacking or hydrogen bonding and van der Waals or hydrophobic interactions. In the process of groove binding, an appropriately substituted ligand with crescent-type shape is accommodated in the minor or major groove of double-stranded DNA (Reddy et al. 1999; Nelson et al. 2007). Large molecules such as proteins or oligonucleotides bind to the major groove of DNA by the formation of hydrogen bonds with the functionalities of the DNA bases that point inside the groove. This complex formation is physiologically relevant as it is the basis of the highly selective recognition of DNA sequences by proteins (Rice and Correll 2008) or the speci—c formation of triplex DNA (Escudé and Sun 2005). On the other hand, the minor groove is the preferred binding site for smaller ligands (Neidle 2001;
3.1 Introduction .................................................................................................... 49 3.2 Intercalation-General Principles ..................................................................54
