NMR Study of the Sequence-Specific Binding of the Delta-Tris(ethylenediamine)cobalt(III) Cation with d(TCGGGATCCCGA)(2)

Metal complex interactions with DNA

Increasing numbers of DNA structures are being revealed using a diverse range of transition metal complexes and biophysical spectroscopic techniques. Here we present a review of metal complex-DNA interactions in which several binding modes and DNA structural forms are explored.

DNA-based asymmetric catalysis: sequence-dependent rate acceleration and enantioselectivity

This study shows that the role of DNA in the DNA-based enantioselective Diels-Alder reaction of azachalcone with cyclopentadiene is not limited to that of a chiral scaffold. DNA in combination with the copper complex of 4,4'-dimethyl-2,2'-bipyridine (Cu-L1) gives rise to a rate acceleration of up to 2 orders of magnitude compared to Cu-L1 catalysis alone. Furthermore, both the enantioselectivity and the rate enhancement prove to be dependent on the DNA-sequence. These features are the main reasons for the efficient and enantioselective catalysis observed with salmon testes DNA/Cu-L1 in the Diels-Alder reaction. The fact that absolute levels of stereocontrol can be achieved with a simple and weak DNA-binding complex like Cu-L1 is a clear demonstration of the power of the supramolecular approach to hybrid catalysis.

Metallo-intercalators and metallo-insertors

Since the elucidation of the structure of double helical DNA, the construction of small molecules that recognize and react at specific DNA sites has been an area of considerable interest. In particular, the study of transition metal complexes that bind DNA with specificity has been a burgeoning field. This growth has been due in large part to the useful properties of metal complexes, which possess a wide array of photophysical attributes and allow for the modular assembly of an ensemble of recognition elements. Here we review recent experiments in our laboratory aimed at the design and study of octahedral metal complexes that bind DNA non-covalently and target reactions to specific sites. Emphasis is placed both on the variety of methods employed to confer site-specificity and upon the many applications for these complexes. Particular attention is given to the family of complexes recently designed that target single base mismatches in duplex DNA through metallo-insertion.

Crystal Structure and DNA Interaction of the Facial-Type rac-Tris[2-(aminomethyl)benzimidazole]cobalt(III) Complex

rac-[Co(ambi)3]Cl3.3H2O corresponds to a tris-chelate complex bearing 2-(aminomethyl)benzimidazole (ambi) ligands bound to the Co(III) ion in a facial-type fashion. The high metal q/r ratio and electronic delocalization between coordination heterocyclic functionalities can provide powerful tools to minimize DNA condensation, which arises from the neutralization of the negatively charged sugar phosphate backbone in the presence of multivalent [Co(ambi)3]3+.

NMR analysis of duplex d(CGCGATCGCG)2 modified by Λ- and Δ-[Ru(bpy)2(m-GHK)]Cl2 and DNA photocleavage study

The interaction of the diastereomeric complexes Lambda-[Ru(bpy)2(m-GHK)]Cl2 and Delta-[Ru(bpy)2(m-GHK)]Cl2 (bpy is 2,2'-bipyridine, GHK is glycine-L-histidine-L-lysine) with the deoxynucleotide duplex d(5'-CGCGATCGCG)2 was studied by means of 1H NMR spectroscopy. At a Delta-isomer to DNA ratio of 1:1, significant shifts for the metal complex are observed, whereas there is negligible effect on the oligonucleotide protons and only one intermolecular nuclear Overhauser effect (NOE) is present at the 2D nuclear Overhauser enhancement spectroscopy spectrum. The 1Eta NMR spectrum at ratio 2:1 is characterized by a slight shift for the Delta-isomer's bpy aromatic protons as well as significant shifts for the decanucleotide G4 H1' and Eta2'', A5 H2, G10 H1', T6 NH and G2 NH protons. Furthermore, at ratio 2:1, 11 intermolecular NOEs are observed. The majority of the NOEs involve the sugar Eta2' and Eta2'' protons sited in the major groove of the decanucleotide. Increasing the Delta-isomer to d(CGCGATCGCG)2 ratio to 5:1 results in noteworthy spectral changes. The Delta-isomer's proton shifts are reduced, whereas significant shifts are observed for the decanucleotide protons, especially the sugar protons, as well as for the exchangeable protons. Interaction is characterized by the presence of only one intermolecular NOE. Furthermore, there is significant broadening of the imino proton signals as the ratio of the Delta-isomer to DNuAlpha increases, which is attributed to the opening of the two strands of the duplex. The Lambda-isomer, on the other hand, approaches the minor groove of the oligonucleotide and interacts only weakly, possibly by electrostatic interactions. Photocleavage studies were also conducted with the plasmid pUC19 and a 158-bp restriction fragment, showing that both diastereomers cleave DNA with similar efficiency, attacking mainly the guanines of the sequence probably by generating active oxygen species.

Enantioselective binding of lambda- and delta-[Ru(bpy)(2)(HPIP)]Cl2 (HPIP=2-(2-hydroxyphenyl)imidazo[4,5-f][1,10]phenanthroline) to the hexanucleotide [d(5'-GTCGAC-3')2]

Multidimensional NMR techniques (1D (1)HNMR, 2D DQF (1)H(1)H COSY and 2D (1)H(1)H NOESY), electrospray ionization mass spectrometry (ESI-MS) and electronic spectroscopy, were performed to study the interactions of the enantiomers lambda- and delta-[Ru(bpy)(2)(HPIP)]Cl(2), (HPIP=2-(2-hydroxyphenyl)imidazo[4,5-f][1,10]phenanthro-line) with the self complementary hexanucleotide duplex d(5'-GTCGAC-3')(2). The results show that the delta-[Ru(bpy)(2)(HPIP)]Cl(2) binds tightly to the oligonucleotide, by intercalation of the ligand HPIP, between the A5 and C6 base sequence of the same strand, probably through the minor groove. Lambda-enantiomer binds weakly, suggesting groove interactions with the hexanucleotide duplex. ESI-MS spectrometry and UV-vis spectroscopy also confirmed these observations.

Effect of steric encumbrance of tris(3-phenylpyrazolyl)borate on the structure and properties of ternary copper(II) complexes having N,N-donor heterocyclic bases

Complexes of formulation [Cu(Tp(Ph))(L)](ClO(4)) (1-4), where Tp(Ph) is anionic tris(3-phenylpyrazolyl)borate and L is N,N-donor heterocyclic base, viz. 2,2'-bipyridine (bpy, 1), 1,10-phenanthroline (phen, 2), dipyridoquinoxaline (dpq, 3), and dipyridophenazine (dppz, 4), are prepared from a reaction of copper(II) acetate.hydrate with KTp(Ph) and L in CH(2)Cl(2) and isolated as perchlorate salts. The complexes are characterized by analytical, structural, and spectral methods. The crystal structures of complexes 1-4 show the presence of discrete cationic complexes having the metal, Tp(Ph), and L in a 1:1:1 ratio and a noncoordinating perchlorate anion. The complexes have a square-pyramidal 4 + 1 coordination geometry in which two nitrogens of L and two nitrogens of the Tp(Ph) ligand occupy the basal plane and one nitrogen of Tp(Ph) binds at the axial site. Complexes 3 and 4 display distortion from the square-pyramidal geometry. The Cu-N distances for the equatorial and axial positions are approximately 2.0 and 2.2 A, respectively. The phenyl groups of Tp(Ph) form a bowl-shaped structure that encloses the [CuL] moiety. The steric encumbrance is greater for the bpy and phen ligands compared to that for dpq and dppz. The one-electron paramagnetic complexes (mu approximately equal to 1.8 mu(B)) exhibit axial EPR spectra in CH(2)Cl(2) glass at 77 K giving g(parallel) and g(perpendicular) values of approximately 2.18 (A(parallel) = 128 G) and approximately 2.07. The data suggest a [d(x(2)-y(2))](1) ground state. The complexes are redox-active and display a quasireversible cyclic voltammetric response for the Cu(II)/Cu(I) couple near 0.0 V versus SCE with an i(pc)/i(pa) ratio of unity in CH(2)Cl(2) or DMF-0.1 M TBAP. The E(1/2) values of the couple vary in the order 4 > 3 > 2 > 1. A profound effect of steric encumbrance caused by the Tp(Ph) ligand is observed in the reactivity of 1-4 with the calf thymus (CT) and supercoiled (SC) DNA. Complexes 2-4 show similar binding to CT DNA. The propensity for the SC DNA cleavage varies as 4 > 3 > 2. The bpy complex does not show any significant binding or cleavage of DNA. Mechanistic investigations using distamycin reveal minor groove binding for 2 and 3 and a major groove binding for 4. The scission reactions that are found to be inhibited by hydroxyl radical scavenger DMSO are likely to proceed through sugar hydrogen abstraction pathways.