The Thermodynamic Effects of Ligand Structure on the Molecular Recognition of Mono- and Bi-Ruthenium Polypyridyl Complexes with G-quadruplex DNA

ITC and CD were used to study the thermodynamics of RPC*G-quadruplex DNA (G4) complex formation. RPCs were [Ru(phen)₃]²+ (1²+), [Ru(phen)₂(dppz)]²+ (2²+), [Ru(phen)₂(tatpp)]²+ (3²+), and [Ru(phen)₂(tatpp)(phen)₂Ru]⁴+ (4⁴+) and target DNAs were c-MYC NHE-III1 promoter sequence mutants forming 1-2-1 and 1-6-1 G-quadruplexes. Formation of the 2:1 RPC*G4 complexes is characterized by entropy driven RPC binding to the top and bottom of G-tetrad faces. 1²+ appears to bind very weakly or not at all to G4 DNA. 2²+ having a dipyridophenazine group to stack on the top and bottom of the G4 core, exhibits an average Ka = 6.7 x 10⁴ M-¹. 3²+, with a larger G4 interactive tetraazatetrapyrido-pentacene group, binds with significantly higher affinity, Ka = 1.1 x 10⁶ M-¹. 2²+ and 3²+ appear to bind independently of G4 folding topology and RPC conformation. The thermograms for the titration of G4 DNA with rac-4⁴+ are characterized by two binding modes exhibiting higher and lower affinity (Ka,1 = 3.6 x 10⁷ M-1 and Ka,2 = 3.2 x 10⁵ M-1). The two binding modes are attributed to preferential binding of one of the 4⁴+ enantiomers (e.g. ΛΛ) over the other isomers (e.g. ΔΔ or ΔΛ). Tighter binding of the preferred 4⁴+ enantiomer, in comparison to 3²+, is due to additional favorable entropy for locating a second [(phen)₃Ru-]²+ moiety in a G4 groove. Weaker binding of the disfavored 4⁴+ isomers must be due to a poorer fit of these isomers with the G4 faces.