DNA photocleavage by phenanthrenequinone diimine complexes of rhodium(III): shape-selective recognition and reaction

Abstract

Rh(phen)_2phi^(3+) and Rh(phi)_2bpy^(3+) (phi = 9,10-phenanthrenequinone diimine, phen = 1, 10-phenanthroline, bpy = 2,2’-bipyridyl) bind double helical DNA avidly (K ≥ 10^7 M^(-1)) by intercalation and with photoactivation promote strand cleavage. Rh(phen)_2phi^(3+) and Rh(phi)_2bpy^(3+) unwind double helical DNA by 21° and 18°, respectively, per bound complex. The quantum yields for nucleic acid base release at 313 nm are 0.0012 for Rh(phen)_2phi^(3+) and 0.0003 for Rh(phi)_2bpy^(3+). While both complexes have similar photochemical properties, overall binding modes and affinities, their cleavage patterns, observed on ^(32)P-end-labeled DNA restriction fragments and oligonucleotide substrates, indicate substantially different recognition characteristics. Rh(phen)_2phi^(3+) binds DNA with some sequence selectivity, preferring 5’-pyrimidine-pyrimidine-purine-3’ sites and cleaving with 5’-asymmetry, while Rh(phi)_2bpy^(3+) binds in a predominantly sequence-neutral fashion. These differences in recognition characteristics may be understood based upon the different shapes of the complexes. Owing to steric interactions of the ancillary phenanthroline ligands, Rh(phen)_2phi^(3+) appears to bind preferentially to sites which are more open in the major groove; since no similar steric constraints arise with an ancillary phi ligand, Rh(phi)_2bpy^(3+) binds all sites with similar affinities. The shapes of these complexes also govern their chemistry of strand scission. Chemical modification studies and HPLC analyses of the DNA termini and monomeric products formed in the Rh(phi)^(3+) induced DNA cleavage reactions have been conducted to characterize the products formed upon photoreaction of the rhodium complexes with 5’-CTGGCATGCCAG-3’. For Rh(phen)_2phi^(3+), the primary products are oligomers containing 3’- and 5’-phosphate termini and nucleic acid bases (in stoichiometric proportion). For Rh(phi)_2bpy^(3+), these same products account for approximately 70% of the reaction, but in addition base propenoic acids and a terminus assigned as a 3’-phosphoglycaldehyde are obtained in a correlated amount (30% of reaction). The formation of base propenoic acids and 3’-phosphoglycaldehydes are found furthermore to depend upon oxygen concentration, while other products are oxygen-independent. The products obtained are consistent with photoreaction of Rh(phi)^(3+), intercalated in the major groove of DNA, via abstraction of a C3’-H atom of the deoxyribose. Subsequent addition of dioxygen to the C3’-H radical or solvation would lead to the degradation products obtained. The partitioning between the oxygen dependent and independent pathways of DNA strand scission is found to correlate best with how the shape of the complex limits access of dioxygen to the C-3’ position. While Rh(phi)_2bpy^(3+) was found to promote the oxygen-dependent pathway to an extent of approximately 30%, Rh(phen)_2phi^(3+), with ancillary phenanthrolines that overhang and shelter the C3’-position, appears to disfavor this pathway of DNA degradation. These studies underscore the importance of shape-selection in governing not only recognition but also reaction of molecules on the helix. Such an intimate relationship between recognition and reaction of molecules bound selectively to DNA requires consideration in understanding the reactions of DNA-binding proteins and small molecules.