Insertion of a bulky rhodium complex into a DNA cytosine-cytosine mismatch: an NMR solution study.

The bulky octahedral complex Rh(bpy)2chrysi3+ (chrysi = 5,6-chrysenequinonediimine) binds single-base mismatches in a DNA duplex with micromolar binding affinities and high selectivity. Here we present an NMR solution study to characterize the binding mode of this bulky metal complex with its target CC mismatch in the oligonucleotide duplex (5'-CGGACTCCG-3')2. Both NOESY and COSY studies indicate that Rh(bpy)2chrysi3+ inserts deeply in the DNA at the mismatch site via the minor groove and with ejection of both destabilized cytosines into the opposite major groove. The insertion only minimally distorts the conformation of the oligonucleotide local to the binding site. Both flanking, well-matched base pairs remain tightly hydrogen-bonded to each other, and 2D DQF-COSY experiments indicate that all sugars maintain their original C2'-endo conformation. Remarkably, 31P NMR reveals that opening of the phosphate angles from a BI to a BII conformation is sufficient for insertion of the bulky metal complex. These results corroborate those obtained crystallographically and, importantly, provide structural evidence for this specific insertion mode in solution.

Mono- and dicarboxylic polypyridyl-Ru complexes as potential cell DNA dyes and transfection agents.

A ruthenium coordination complex, incorporating two highly extended pi-systems DIP and two carboxylic groups: [Ru(DIP)2(L-L)]2+ where DIP=4,7-diphenyl-1,10-phenanthroline and L-L=4,4'-dicarboxy-2,2'-bipyridine, is found to be of biological interest. It constitutes an effective nuclear DNA dye for living cells: fluorescent, permeant, biocompatible, high Stokes shift. These features are commented in terms of hydrophobicity and DNA binding. In addition, this complex is shown to internalize a plasmid carrying the enhanced green fluorescent protein (EGFP) gene. Positive results are obtained for gene expression, which is related to condensation of the DNA by this ruthenium agent. This opens up an innovative transfection route based on metal complexes.

A new family of mono- and dicarboxylic ruthenium complexes [Ru(DIP)2(L2)]2+ (DIP = 4,7-diphenyl-1,10-phenanthroline): synthesis, solution behavior, and X-ray molecular structure of trans-[Ru(DIP)2(MeOH)2][OTf]2.

A new family of ruthenium complexes of general formula [Ru(DIP)2(L2)]2+, where DIP = 4,7-diphenyl-1,10-phenanthroline, a bidentate ligand with an extended aromatic system, was prepared and fully characterized. When L is a monodentate ligand, the following complexes were obtained: L = CF3SO3(-1) (2), CH3CN (3), and MeOH (4). When L2 is a bidentate ligand, the compounds [Ru(DIP)2(Hcmbpy)][Cl]2 (5) and [Ru(DIP)2(H2dcbpy)][Cl]2 (6) were prepared (Hcmbpy = 4-carboxy-4'-methyl-2,2-bipyridine, H2dcbpy = 4,4'-dicarboxy-2,2'-bipyridine). Complex [Ru(DIP)2(MeOH)2][OTf]2 (4) displayed a trans configuration of the DIP ligands, which is rare for octahedral complexes featuring DIP bidentate ligands. DFT calculations carried out on 4 showed that the cis isomer is more stable by 12.2 kcal/mol relative to the trans species. The solution behaviors of monocarboxylic complex [Ru(DIP)2(Hcmbpy)][Cl]2 (5) and dicarboxylic complex [Ru(DIP)2(H2dcbpy)][Cl]2 (6) were investigated by 1H NMR spectroscopy. VT-NMR, concentration dependence, and reaction with NaOD allowed us to suggest that aggregation of the cationic species in solution, especially for 6, originates mainly from hydrogen bonding interactions.

Spectroscopic and structural impact of a stem base-pair change in DNA hairpins: GTTC-ACA-GAAC versus GTAC-ACA-GTAC.

Successive investigations over the last decade have revealed and confirmed a stable loop closure in a family of d-[GTAC-5Pur6N7N-GTAC] hairpins, where 5Pur6N7N is a AAA, GAG and AXC loop (X being any nucleotide). The trinucleotide loop is characterized by a well defined 5Pur-7N mispairing mode, and by upfield chemical shifts for three sugar protons of the apical nucleotide 6N. The GTTC-ACA-GAAC DNA hairpin, of interest for its likely involvement in Vibrio cholerae genome mutations, has now been investigated. The GTAC-ACA-GTAC DNA hairpin has also been studied because it is intermediate between the other structures, as it contains the loop of the hairpin under consideration and the stem of the above family. The two hairpins with the ACA loop are stable. They show the same mispairing mode and similar upfield shifts as the previous family, but GTTC-ACA-GAAC seems to be slightly less compact than any other. GTTC-ACA-GAAC is remarkable in that it exhibits a B(II) character for the phosphate-ester conformation at 8Gp9A, together with a swing of the upper hairpin into the major groove that, in particular, brings 6CH1' roughly as close to 7AH2 as to 6CH6. These unexpected structural features are qualitatively deduced from (1)H and (31)P NMR spectra, and confirmed by Raman spectroscopy. This comparative study shows that not only the loop sequence but also the stem sequence may control hairpin structures.

Efficient DNA binding by optically Pure Ruthenium Tris(bipyridyl) complexes incorporating carboxylic functionalities. Solution and structural analysis.

Herein, we report on the binding of optically pure ruthenium complexes Delta- or Lambda-[Ru(bpy)(2)(L-L)][PF(6)](2) [L-L = Hcmbpy = 4-carboxy-4'-methyl-2,2'-bipyridine (1), L-L = H(2)dcbpy = 4,4'-dicarboxy-2,2'-bipyridine (2)] to DNA. The binding constants of the two enantiomeric Delta-1 and Lambda-1 complexes to DNA were estimated from titration monitored by (1)H NMR spectroscopy. 2D transferred NOESY (TRNOESY) experiments support the conclusion that Delta-1 and Lambda-1 bind to DNA and that an intermediate-to-fast exchange occurs between bound and free Ru(II) complex. Further, evidence for enantioselective DNA cleavage by Delta-2 is provided by means of gel electrophoresis performed in the presence and in the absence of light; in contrast, the Lambda-2 enantiomer does not. The IR spectrum of enantiomer Delta-2 (or Lambda-2) compared to that of the racemate (rac-2) gives evidence that, in the latter form, the enantiomers are strongly associated. Moreover the X-ray structure of rac-2 was also determined and exhibits as an outstanding feature the formation of a one-dimensional supramolecular species in which the cohesion of the system is maintained by strong hydrogen bonding between carboxylic acid groups of enantiomers Delta-2 and Lambda-2 (cationic parts) with d(O...O) = 2.6 A in agreement with the infrared results. The conclusion that can be drawn from IR and X-ray spectroscopies together is that the self-association in rac-2 is strong.