Structural Examination of Enantioselective Intercalation: ^1H NMR of Rh(en)_2phi^(3+) Isomers Bound to d(GTGCAC)_2

Abstract

The enantioselective recognition of d(GTGCAC)_2 by Δ- and Λ-Rh(en)_2phi^(3+) (en= ethylenediarnine; phi = 9, 10-phenanthrenequinone diimine) has been examined in a series of one-dimensional (ID) and two-dimensional (2D) 500 MHz ^1H NMR experiments both to extend our understanding of the basis for the enantioselective DNA binding and to gain structural information concerning intercalation by the octahedral metal complexes. Δ-Rh(en)_2phi^(3+) forms a symmetric 1:1 complex with d(GTGCAC)_2, and the metal complex is in slow exchange with the oligodeoxynucleotide bound form at 295 K. The strong upfield shifts of the phi ligand's aromatic protons (0.6-1.3 ppm) are consistent with full intercalation of the phi ligand into the DNA base stack. 2D-NOESY experiments reveal a loss in internucleotide connectivity between G_3 and C_4 bases, while new NOE cross peaks are observed between the phi ligand and the G_3 deoxyribose sugar. In contrast to binding by Δ-Rh(en)_2phi^(3+), the 1:1 Δ-Rh(en)_2phi^(3+)-d(GTGAC)_2 complex shows much broader resonances, and both metal complex and DNA protons appear to be in the intermediate exchange regime. The loss of C_2 symmetry in the 1:1 complex is consistent with binding by Λ-Rh(en)_2phi^(3+) at the T_2G_3 step. Although the enantiomeric metal complexes display different sequence selectivities and exchange characteristics, Λ- and Δ-Rh(en)_2phi^(3+) interact with the oligonucleotide duplex in a fundamentally similar manner, through the full intercalation of the phi ligand. Upfield movements in chemical shifts of phi protons are nearly identical for the two enantiomers, and both Λ- and Δ-Rh(en)_2phi^(3+) stabilize the duplex to melting by 5-10 °C. Given the common binding mode of the two enantiomers, the differences in their binding characteristics emanate from interactions with the ancillary nonintercalating ligands. Thus, as a general strategy, intercalation may provide an anchor for sequence-selective interactions of octahedral metal complexes in the groove of duplex DNA.