X-ray Crystal Structure of rac-[Ru(phen)₂dppz]²⁺ with d(ATGCAT)₂ Shows Enantiomer Orientations and Water Ordering

Abstract

We report an atomic resolution X-ray crystal structure containing both enantiomers of rac-[Ru(phen)2dppz](2+) with the d(ATGCAT)2 DNA duplex (phen = phenanthroline; dppz = dipyridophenazine). The first example of any enantiomeric pair crystallized with a DNA duplex shows different orientations of the Λ and Δ binding sites, separated by a clearly defined structured water monolayer. Job plots show that the same species is present in solution. Each enantiomer is bound at a TG/CA step and shows intercalation from the minor groove. One water molecule is directly located on one phenazine N atom in the Δ-enantiomer only.

Reversal of a Single Base‐Pair Step Controls Guanine Photo‐Oxidation by an Intercalating Ruthenium(II) Dipyridophenazine Complex

“…A significant development is the access to detailed information on the binding modes of non‐covalently bound [RuL 2 (dppz)] 2+ (dppz=dipyrido[3,2‐ a :2′,3′‐ c ]phenazine) intercalators provided by crystal structures of Λ‐[Ru(TAP) 2 (dppz)] 2+ (Λ‐ 1 , Figure 1 a),5a Λ and Δ‐[Ru(phen) 2 (dppz)] 2+ ,5b,c and Δ‐[Ru(bpy) 2 (dppz)] 2+   5d in ODNs (TAP=1,4,5,8‐tetraazaphenanthrene, phen=1,10‐phenanthroline, bpy=2,2′‐bipyridyl). Nevertheless, it can be unclear whether these crystal structures reflect what occurs under more dilute conditions in solution, where the majority of experiments on ligand–DNA interactions are performed.…”

Unique Optical Oxygen-Sensing Performance of [Ru(IP)2(HNAIP)]2+ during the Groove-Binding-Induced B-to-Z DNA Conformational Transition

“…8,9 Recently, Cardin and co-workers have reported an atomic resolution X-ray crystal structure of rac-[Ru(phen) 2 (dppz)] 2+ (1,10-phenanthroline and dppz (dipyrido[3,2,-a:2′,3′-c]phenazine) with d(ATGCAT) 2 , showing different orientations of the Λ and Δ binding sites. 10 Among the DNA-binding modes, the groove binding of Ru(II) complexes to DNA has been known to possibly induce the DNA conformational transition, resulting in the Z-DNA stabilized by Ru(II) complexes. 11,12 As we know, the DNA always exists in an oxygen-containing environment.…”

“…24,25 Despite the fact that polypyridyl Ru(II) complexes have been extensively used as luminescent probes of both oxygen sensing and DNA structure, 26,27 there is no report on the oxygen-sensing characteristics of Ru(II) complexes bound to the groove surface of a DNA duplex with the B-to-Z conformational transition. In our previous studies, a di-Ru(II) complex [Ru(bpy) 2 -(mbpibH 2 )(bpy) 2 Ru] 4+ bearing a flexible V-shaped bridging ligand (mbpib = 1,3-bis( [1,10]phenanthroline [5,6-d]imidazol-2-yl)benzene) has been demonstrated to induce the condensation of DNA with the B-to-Z conformation transition via a groove-binding mode. 28 Two intramolecular hydrogen-bondcontaining mono-Ru(II) complexes [Ru(bpy) 2 (HNAIP)] 2+ and [Ru(bpy) 2 (HPIP)] 2+ (HNAIP = 2-(2-hydroxy-1-naphthyl)-imidazo [4,5-f ] [1,10]phenanthroline and HPIP = (2-(2,4-dihydroxyphenyl)imidazo [4,5-f ] [1,10]phenanthroline) have been known to bind DNA by two binding modes.…”

“…In our previous studies, a di-Ru(II) complex [Ru(bpy) 2 -(mbpibH 2 )(bpy) 2 Ru] 4+ bearing a flexible V-shaped bridging ligand (mbpib = 1,3-bis( [1,10]phenanthroline [5,6-d]imidazol-2-yl)benzene) has been demonstrated to induce the condensation of DNA with the B-to-Z conformation transition via a groove-binding mode. 28 Two intramolecular hydrogen-bondcontaining mono-Ru(II) complexes [Ru(bpy) 2 (HNAIP)] 2+ and [Ru(bpy) 2 (HPIP)] 2+ (HNAIP = 2-(2-hydroxy-1-naphthyl)-imidazo [4,5-f ] [1,10]phenanthroline and HPIP = (2-(2,4-dihydroxyphenyl)imidazo [4,5-f ] [1,10]phenanthroline) have been known to bind DNA by two binding modes. 29 Compared with the HPIP ligand, the HNAIP ligand has a unique naphthyl ring and a rotatable C−C single bond between 2-hydroxynaphthalene and imidazo [4,5-f ] [1,10]phenanthroline (IP), leading to a very different DNA-binding mode.…”

“…28 Two intramolecular hydrogen-bondcontaining mono-Ru(II) complexes [Ru(bpy) 2 (HNAIP)] 2+ and [Ru(bpy) 2 (HPIP)] 2+ (HNAIP = 2-(2-hydroxy-1-naphthyl)-imidazo [4,5-f ] [1,10]phenanthroline and HPIP = (2-(2,4-dihydroxyphenyl)imidazo [4,5-f ] [1,10]phenanthroline) have been known to bind DNA by two binding modes. 29 Compared with the HPIP ligand, the HNAIP ligand has a unique naphthyl ring and a rotatable C−C single bond between 2-hydroxynaphthalene and imidazo [4,5-f ] [1,10]phenanthroline (IP), leading to a very different DNA-binding mode. In addition, if the IP ligand was used to replace the two bpy ancillary ligands, the binding interaction of [Ru(IP) 2 (dppz)] 2+ with DNA was enhanced.…”