Exploring the Direct and Indirect Readout of DNA with Phenanthrenequinone Diimine Complexes of Rhodium(III)

Phenanthrenequinone diimine (phi) complexes of rhodium(III) have been designed and characterized in order to investigate the principles of direct and indirect readout of double helical DNA The metallointercalator l-Rh(MGP)2phi5+ (MGP = 4-guanidylmethyl-1,10-phenanthroline) binds via intercalation in the major groove of DNA and upon irradiation promotes DNA strand scission. The Λ-enantiomer, Λ-1-Rh(MGP)2phi5+, binds at subnanomolar concentrations to the 6 base pair sequence, 5'-CATATG-3', with enantiospecificity. An essential feature of this recognition is the sequence-specific unwinding of the DNA helix which permits direct contacts between guanidinium functionalities on the metal complex and guanine residues. Deazaguanine substitutions were used to establish direct contacts between the N7 nitrogen atoms of guanine and the guanidinium moiety on the metal complex. Through an assay developed to test for sequence-specific DNA unwinding, a 70 ± 10 degrees unwinding of the sequence 5'-CATATG-3' upon binding by Λ-1-Rh(MGP)2phi5+ was established. Thus, the sequence-dependent twistability of DNA plays an important role in determining the sequence specificity of the complex. The Δ-enantiomer, Δ-1-Rh(MGP)2phi5+, binds preferentially to the 6 base pair sequence, 5'-CATCTG-3'. The hierarchy of recognition sites determined in photocleavage studies on oligonucleotides suggests that DNA recognition by this complex also involves sequence specific contacts by the guanidinium functionalities. Photocleavage studies indicate additional similarities in the recognition of Δ and Λ-1-Rh(MGP)2phi5+. Both enantiomers of 1- Rh(MGP)2phi5+ display increased binding specificity relative to the parent complex, Rh(phen)2phi3+. The exchange rates of both enantiomers are also decreased at least a 1000-fold relative to Rh(phen)2phi3+. Studies in which the length of the linker arm between the core of the metal complex and the guanidinium moiety was varied demonstrate that proper orientation of the guanidinium moiety is an essential feature of complex specificity. As the length of the linker arm increases, the binding specificity of the complex decreases. DNA recognition studies with Rh(APB)2phi5+ (APB= 4-(3-aminopropyl)-4'-2,2'-bipyridine) have demonstrated that the amino moiety can also be used to alter the sequence specificity of phi complexes of rhodium(III), although the sequence specificity of this complex is reduced greatly as compared with Δ- and Λ-1-Rh(MGP)2phi5+. This work therefore demonstrates that the guanidinium moiety may be used to enhance both the binding affinity and specificity of phi complexes of rhodium(III). In mimicking DNA binding proteins, molecules which recognize their binding sites through direct and indirect readout of the DNA can be designed. Importantly, this study highlights a new structural element of DNA recognition, the sequence-dependent twistability of the DNA helix. This sequence-dependent twistability may be an essential feature of the recognition of sequences by DNA-binding proteins and may be powerfully exploited in future design.