Tris (phenanthroline) metal complexes: probes for DNA helicity

DNA Interaction with Coordination Compounds of Cd(II)containing 1,10-Phenanthroline

The experimental study of the DNA interaction with three cadmium coordination compounds [Cd(phen)3](CH3CO2)2, [Cd(phen)2(H2O)2](CH3CO2)2, and [Cd2(phen)4(H2O)2](CH3CO2)4 was carried out using spectrophotometry, viscosity, and dynamic light scattering methods. The role of the solution ionic strength (concentration of NaCl) was analyzed. All compounds can penetrate (fully or partly) to the major or minor DNA grooves. It was shown that, in addition to the important role of electrostatic interactions in the formation of the complex, intercalation of the 1,10-phenanthroline ligand occurs for compounds [Cd(phen)2(H2O)2](CH3CO2)2 and [Cd2(phen)4(H2O)2](CH3CO2)4. Compound [Cd(phen)3](CH3CO2)2 binds to DNA externally. The coordination bond between cadmium and DNA was formed in DNA complexes with [Cd2(phen)4(H2O)2](CH3CO2)4. Preliminary computer modeling of the DNA interaction with the compounds used was performed.

Modulation of DNA structure formation using small molecules

Genome integrity is essential for proper cell function such that genetic instability can result in cellular dysfunction and disease. Mutations in the human genome are not random, and occur more frequently at "hotspot" regions that often co-localize with sequences that have the capacity to adopt alternative (i.e. non-B) DNA structures. Non-B DNA-forming sequences are mutagenic, can stimulate the formation of DNA double-strand breaks, and are highly enriched at mutation hotspots in human cancer genomes. Thus, small molecules that can modulate the conformations of these structure-forming sequences may prove beneficial in the prevention and/or treatment of genetic diseases. Further, the development of molecular probes to interrogate the roles of non-B DNA structures in modulating DNA function, such as genetic instability in cancer etiology are warranted. Here, we discuss reported non-B DNA stabilizers, destabilizers, and probes, recent assays to identify ligands, and the potential biological applications of these DNA structure-modulating molecules.

Сhiral and Racemic Fields Concept for Understanding of the Homochirality Origin, Asymmetric Catalysis, Chiral Superstructure Formation from Achiral Molecules, and B-Z DNA Conformational Transition

The four most important and well-studied phenomena of mirror symmetry breaking of molecules were analyzed for the first time in terms of available common features and regularities. Mirror symmetry breaking of the primary origin of biological homochirality requires the involvement of an external chiral inductor (environmental chirality). All reviewed mirror symmetry breaking phenomena were considered from that standpoint. A concept of chiral and racemic fields was highly helpful in this analysis. A chiral gravitational field in combination with a static magnetic field (Earth’s environmental conditions) may be regarded as a hypothetical long-term chiral inductor. Experimental evidences suggest a possible effect of the environmental chiral inductor as a chiral trigger on the mirror symmetry breaking effect. Also, this effect explains a conformational transition of the right-handed double DNA helix to the left-handed double DNA helix (B-Z DNA transition) as possible DNA damage.

Enantioselective targeting left-handed Z-G-quadruplex

Herein, we report the first example where an M-enantiomer of a chiral metal complex can selectively stabilize a left-handed G-quadruplex, but its P-enantiomer cannot. The interactions between the chiral metal complexes and the left-handed G-quadruplex were evaluated by UV melting, circular dichroism, isothermal titration calorimetry, gel electrophoresis and NMR titrations.

Interaction of an anti-cancer photosensitizer with a genomic DNA: From base pair specificity and thermodynamic landscape to tuning the rate of detergent-sequestered dissociation

A detailed characterization of the binding interaction of a potent cancer cell photosensitizer, norharmane (NHM) with a genomic DNA (herring sperm; hsDNA) is undertaken with particular emphasis on deciphering the strength, mode, dynamics, energetics and kinetics of binding. A major focus of the study underlies a successful exploration of the concept of detergent-sequestered dissociation of drug from the drug-DNA complex. Biophysical techniques such as absorption, steady-state and time-resolved fluorescence spectroscopy, circular dichroism, DNA helix melting, stopped-flow fluorescence kinetics and calorimetry have been used. A primarily intercalative mode of binding of NHM with DNA is shown. However, the overall interaction is governed by more than one type of binding forces. We demonstrate that the essential prerequisite of a slower dissociation rate of drug from DNA helix is achieved by tenable choice surfactants. Our results also highlight an effective tunability of the rate of dissociation of the DNA-intercalated drug via detergent-sequestration. A detailed isothermal titration calorimetric study unveils the key role of hydrophobic force underlying NHM-hsDNA association. This is further substantiated by the enthalpy-entropy compensation behavior. The major entropic contribution in detergent-induced dissociation of NHM from NHM-hsDNA complex is also demonstrated. Our results present not only a comprehensive structural and thermodynamic profile, base pair specificity, association kinetics for binding of NHM with DNA but also explore the thermodynamic and kinetic aspects of dissociation of bound drug. Characterization and tuning of the essential prerequisites for a drug to be efficient in anti-cancer functionality bear direct and widespread significance in contemporary global research.

Fluorescent active ruthenium(ii) complex units containing bpy or phen or dmp ligands anchored on branched poly(ethylenimine): DNA binding and in vitro biological assessment

UV light irradiation visible responses of polymer ruthenium complexes.

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.

Synthesis, DNA binding and cleavage activities of copper (II) thiocyanate complex with 4-(N,N-dimethylamino)pyridine and N,N-dimethylformamide

Two novel copper(II) thiocyanate complexes with 4-(N,N-dimethylamino) pyridine and N,N-dimethylformamide (1) and with 4-(N,N-dimethylamino) pyridine (2) have been synthesized and characterized. The crystal and molecular structures of complexes 1 and 2 were determined by single-crystal X-ray diffraction. Antioxidative activity tests in vitro showed that complex 1 has significant antioxidative activity against hydroxyl free radicals from the Fenton reaction and also oxygen free radicals, which is better than standard antioxidants like vitamin C and mannitol. The interaction of complex 1 with calf thymus DNA was investigated by spectroscopic, cyclic voltammetry, and viscosity measurements. Results suggest that complex 1 can bind to DNA via partial intercalation mode. Moreover, complex 1 has been found to cleavage of plasmid DNA pBR322.

Synthesis, spectroscopic, crystal structure and DNA binding of Ru(II) complexes with 2-hydroxy-benzoic acid [1-(4-hydroxy-6-methyl-2-oxo-2H-pyran-3-yl)-ethylidene]-hydrazide

Reactions of 2-hydroxy-benzoic acid [1-(4-hydroxy-6-methyl-2-oxo-2H-pyran-3-yl)-ethylidene]-hydrazide (H(2)L) with [RuHCl(CO)(EPh(3))(3)] (E = P or As) were carried out and the new complexes obtained were characterized by elemental analysis, electronic, IR, (1)H NMR and (13)C NMR spectroscopic techniques and single crystal X-ray diffraction studies. Complex (1) crystallizes in the monoclinic space group P2(1)/c with unit cell dimensions a=18.6236(17) Å, b=12.8627(12) Å, c=21.683(2) Å, α=90.00, β=114.626(2), γ=90.00 V=4721.8(8) Å, Z=4. The crystal structure of the complex shows Ru(II) atom is six-coordinated, forming a slightly distorted octahedral geometry with two P atoms in axial positions, and three chelating donor atoms of the tridentate Schiff base ligand and one carbonyl group located in the equatorial plane. The molecular structure is stabilized by intramolecular O-H···N interactions. No intermolecular hydrogen bond was observed. The intramolecular hydrogen bond exists between the oxygen atom from salicylic acid moiety and nitrogen from the same moiety. A variety of solution studies were carried out for the determination of DNA binding mode of the complexes. The results suggest that both complexes bind to Herring sperm DNA via non intercalative mode.

Exploring the strength, mode, dynamics, and kinetics of binding interaction of a cationic biological photosensitizer with DNA: implication on dissociation of the drug-DNA complex via detergent sequestration

The present study aims at exploring a detailed characterization of the binding interaction of a promising cancer cell photosensitizer, harmane (HM), with DNA extracted from herring sperm. The polarity-sensitive prototropic transformation of HM, a naturally occurring, fluorescent, drug-binding alkaloid, β-carboline, is remarkably modified upon interaction with DNA and is manifested through significant modulations on the absorption and emission profiles of HM. From the series of studies undertaken in the present program, for example, absorption; steady-state emission; the effect of chaotrope (urea); iodide ion-induced steady-state fluorescence quenching; circular dichroism (CD); and helix melting from absorption spectroscopy; the mode of binding of HM into the DNA helix has been substantiated to be principally intercalative. Concomitantly, a discernible dependence of the photophysics of the DNA-bound drug on the medium ionic strength indicates that electrostatic attraction should not be ignored in the interaction. Efforts have also been delivered to delineate the dynamical aspects of the interaction, such as modulation in time-resolved fluorescence decay and rotational relaxation dynamics of the drug within the DNA environment. In view of the prospective biological applications of HM, the issue of facile dissociation of intercalated HM from the DNA helix also comprises a crucial prerequisite for the functioning as an effective therapeutic agent. In this context, our results imply that the concept of detergent-sequestered dissociation of the drug from the drug-DNA complex can be a prospective strategy through an appropriate choice of the detergent molecule. The utility of the present work resides in exploring the potential applicability of the fluorescence property of HM for studying its interactions with a relevant biological target, for example, DNA. In addition, the methods and techniques used in the present work can also be exploited to study the interaction of HM with other biological, biomimicking assemblies and drug delivery vehicles, and so forth.

DNA binding and photocleavage studies of cobalt(III) polypyridine complexes: [Co(en)2PIP]3+, [Co(en)2IP]3+, and [Co(en)2phen-dione]3+

In this paper, three complexes of type [Co(en)₂PIP]³⁺(PIP=2-phenylimidazo[4,5-f][1,10,] phenanthroline)(1), [Co(en)₂IP]³⁺ (IP = imidazo[4,5-f][1,10,] phenanthroline)(2), and [Co(en)₂phen-dione]³⁺(1,10 phenanthroline 5,6,dione)(3) have been synthesized and characterized by UV/VIS, IR, ¹H NMR spectral methods. Absorption spectroscopy, emission spectroscopy, viscosity measurements, and DNA melting techniques have been used for investigating the binding of these two complexes with calf thymus DNA, and photocleavage studies were used for investigating these binding of these complexes with plasmid DNA. The spectroscopic studies together with viscosity measurements and DNA melting studies support that complexes 1 and 2 bind to CT DNA (= calf thymus DNA) by intercalation mode via IP or PIP into the base pairs of DNA, and complex 3 is binding as groove mode. Complex 1 binds more avidly to CT DNA than 2 and 3 which is consistent with the extended planar ring π system of PIP. Noticeably, the two complexes have been found to be efficient photosensitisers for strand scissions in plasmid DNA.

DNA Binding and Photocleavage Studies of Cobalt(III) Ethylenediamine Pyridine Complexes: [Co(en)2(py)2]3+ and [Co(en)2(mepy)2]3+

Two novel cobalt(III) pyridine complexes (1)[Co(en)2(py)2]3+ and (2)[Co(en)2(mepy)2]3+ (en=ethylenediamine, py=pyridine, and mepy=methylpyridine) have been synthesized and characterized. The interaction of these complexes with calf thymus DNA was investigated by absorption, emission spectroscopy, viscosity measurements, DNA melting, and DNA photocleavage. Results suggest that the two complexes bind to DNA via groove mode and complex 2 binds more strongly to CT DNA than complex 1. Moreover, these Co(III) complexes have been found to promote the photocleavage of plasmid DNA pBR322 under irradiation at 365 nm, cytotoxicity results of complexes are also showing anticancer activity.

Novel multistranded, alternative, plasmid and helical transitional DNA and RNA microarrays: implications for therapeutics

Novel multistranded and alternative DNA, RNA and plasmid microarrays (transitional structural nucleic acid microarrays) have been developed that allows for the immobilization of intact, nondenatured, double-stranded DNA, double-stranded RNA, and alternative and multistranded nucleic acids. It also allows for the study of transitional changes that occur in the structure of DNA and RNA. Alternative types of DNA, RNA and multistranded nucleic acids are immobilized by a variety of different surface chemistries (i.e., noncovalent or covalent) onto a novel substrate surface. This technology represents the next generation of microarrays, which will aid in the characterization of nucleic acid structure and function, and accelerate the discovery of drugs that bind to nucleic acids. In addition, we demonstrate four novel techniques that are the first practical applications of the microarray, that is, transitional structural chemogenomics, transitional structural chemoproteomics, transitional structural pharmacogenomics and transitional structural pharmacoproteomics. These novel nucleic acid microarrays, together with pharmacogenomics, can be used to improve the study of DNA and RNA structure, gene expression, drug development and treatment of various diseases.

Oxidation of Guanine in Double-Stranded DNA by [Ru(bpy)2dppz]Cl2in Cationic Reverse Micelles

DNA oxidation has been investigated in the medium of cationic reverse micelles (RMs). The oxidative chemistry is photochemically initiated using the DNA intercalator bis(bipyridine)dipyridophenazine ruthenium(II) chloride ([Ru(bpy)2dppz]Cl2) bound to duplex DNA in the RMs. High-resolution polyacrylamide gel electrophoresis (PAGE) is used to reveal and quantify guanine (G) oxidation products, including 8-oxo-7,8-dihydroguanine (8OG). In buffer solution, the addition of the oxidative quenchers potassium ferricyanide or pentaamminechlorocobalt(III) dichloride leads to an increase in the amount of piperidine-labile G oxidation products generated via one-electron oxidation. In RMs, however, the yield of oxidatively generated damage is attenuated. With or without ferricyanide quencher in the RMs, the yield of oxidatively generated products is approximately the same. Inclusion of the cationic quencher [CoCl(NH3)5]2+ in the RMs increases the amount of oxidation products generated but not to the extent that it does in buffer solution. Under anaerobic conditions, all of the samples in RMs, with or without added oxidative quenchers, show decreased levels of piperidine-labile oxidation products, suggesting that the primary oxidant in RMs is singlet oxygen. G oxidation is enhanced in D2O and deuterated heptane and is diminished in the presence of sodium azide in RMs, also supporting 1O2 as the main G oxidant in RMs. Isotopic labeling experiments show that the oxygen atom in 8OG produced in RMs is not from water. The observed change in the G oxidation mechanism from a one-electron process in buffer to mostly 1O2 in RMs illustrates the importance of both DNA structure and DNA environment on the chemistry of G oxidation.

Characterization of enantioselective binding of racemic natural tetrahydropalmatine to DNA by chromatographic methods

A racemate from natural product, tetrahydropalmatine (THP), was characterized on its enantioselective binding to DNA by the chromatographic methods including microdialysis/HPLC, centrifugal ultrifiltration/HPLC and immobilized DNA affinity chromatography. It was found that its (+)-enantiomer was preferential to binding on B-form duplex DNA including calf thymus DNA, AT and GC sequence oligo DNA, as well as triplex oligo DNA. The binding constants of the THP enantiomers to ct-DNA were determined with the methods of microdialysis/HPLC and frontal affinity chromatography. In addition, the DNA structural preference of either enantiomer was evaluated with the chromatographic methods.

Synchronous fluorescence, UV–visible spectrophotometric, and voltammetric studies of the competitive interaction of bis(1,10-phenanthroline)copper(II) complex and neutral red with DNA

Constant wavelength synchronous fluorescence spectroscopy (CW-SFS), UV-visible absorption spectroscopy, and cyclic and differential pulse voltammetry were applied to investigate the competitive interaction of DNA with the bis(1,10-phenanthroline)copper(II) complex cation ([Cu(phen)(2)](2+)) and a fluorescence probe, neutral red dye (NR), in a tris-hydrogen chloride buffer (pH 7.4). The results show that both the [Cu(phen)(2)](2+)and the NR molecules can intercalate competitively into the DNA double-helix structure. The cyclic voltammetry method showed that both anodic and cathodic currents of [Cu(phen)(2)](2+) decreased on addition of the DNA and the intercalated [Cu(phen)(2)](2+)-DNA complex formed (beta = (4.14 +/- 0.24) x 10(3)). CW-SFS measurements were facilitated by the use of the three-way resolution of the CW-SFS for NR, [Cu(phen)(2)](2+), and NR-DNA. The important constant wavelength (CW) interval, Deltalambda, was shown to vary considerably when optimized (135, 58, and 98 nm for NR, NR-DNA, and [Cu(phen)(2)](2+), respectively). This approach clearly avoided the errors that otherwise would have arisen from the common assumption that Deltalambda is constant. Furthermore, a chemometrics approach, parallel factor analysis (PARAFAC), was applied to resolve the measured three-way CW-SFS data, and the results provided simultaneously the concentration information for the three reaction components, NR, [Cu(phen)(2)](2+), and NR-DNA, for the system at each equilibrium point. The PARAFAC analysis indicated that the intercalation of the [Cu(phen)(2)](2+) molecule into the DNA proceeds by exchanging with the NR probe and can be attributed to two parallel reactions. Comprehensive information was readily obtained; the replacement of the intercalated NR commenced immediately on introduction of [Cu(phen)(2)](2+), approximately 50% of NR was replaced by [Cu(phen)(2)](2+) at a concentration of 0.45 x 10(-5) mol L(-1), and nearly all of the NR was replaced at a [Cu(phen)(2)](2+) concentration of 2.50 x 10(-5) mol L(-1). This work has the potential to improve extraction of information from the fluorescence intercalator displacement (FID) assay.

Spectral and redox studies on mixed ligand complexes of cobalt(III) phenanthroline/bipyridyl and benzoylhydrazones, their DNA binding and antimicrobial activity

Cobalt(III) complexes of the type [Co(N-N)2L](ClO4)2.H2O [where L=anionic form of para-substituted benzaldehyde-benzoylhydrazone (BHBX-); X=H, Me, OMe, OH, Cl or NO2; N-N=2,2'-bipyridine (bpy) or 1,10-phenanthroline (phen)] have been synthesized and characterized through UV-Vis, IR, NMR and electrochemical studies. The IR spectral frequencies support the mode of coordination of BHBX to the metal through the imino nitrogen and enolic oxygen atoms. The electronic absorption spectra exhibit metal to ligand charge transfer (MLCT) transition around 450 nm together with intraligand (IL) bands that are comparable to that of [Co(phen/bpy)3]3+. In acetonitrile solution these complexes show two well defined redox couples corresponding to Co(III/II) and Co(II/I) processes. Binding of these complexes with herring sperm DNA have been investigated by spectroscopic and voltammetric methods. The lower binding constant values of these complexes with respect to the [Co(phen/bpy)3]3+ are ascribed to the polar interaction of the substituted benzoylhydrazone moiety with the sugar-phosphate backbone of the DNA. The UV spectrum shows reasonable hypochromism with slight (2-4 nm) red shift, while the cyclic voltammogram shows decrease in current intensity along with a very small shift in the formal potential of the Co(III/II) redox couple. These experimental results indicate that phen mixed ligand complexes bind to DNA through an intercalative mode more effectively than their bpy counterparts. These complexes are also found to have good antimicrobial activity.

Mixed ligand copper(II) complexes of phenanthroline/bipyridyl and curcumin diketimines as DNA intercalators and their electrochemical behavior under Nafion® and clay modified electrodes

The mode of binding of copper(II) mixed ligand complexes of phen/bpy and Knoevenagel condensate of curcumin (4-salicylidene-1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dione) and 4-X-anilines with herring sperm DNA has been investigated using spectral and electrochemical techniques in Tris-HCl buffer pH 7.1. On titration with DNA, usual hypochromism and unusual (large) red shift (30-35 nm) for some of these complexes were observed in their absorption spectra of intense intraligand (IL) pi-pi* transition around 420 nm. Variations in the absorbance due to their interaction with DNA on time scale were also investigated, under fixed concentrations of complex and DNA. On interaction with DNA, the quasi-reversible CuII/I redox couple slightly improves its reversibility with considerable decrease in current intensity. The intercalation of these copper complexes into the DNA base pairs was also investigated by gel retardation assay method. All the experimental results indicate that the phen mixed copper(II) complexes intercalate more effectively into the DNA base pairs than their bpy counterparts. Significant differences in the redox behavior of these copper(II) complexes under electrochemically modified GC electrodes with Nafion and K10 Montmorillonite clay have also been investigated and discussed.

Electrochemical DNA sensing using osmium complexes as hybridization indicators

A surface-based method for the study of the interactions of DNA with redox-active osmium complexes is described. The study was carried out using gold electrodes modified with DNA by adsorption and [Os(bpy)3]3+/2+ (bpy=2,2'-bipyridyl) or [Os(phen)3]3+/2+ (phen=1,10-phenantroline) as electrochemical indicators. The method, which is simple and reagent saving, allows the accumulation of osmium complexes on the DNA layer. The amount of osmium complex bound by the layer of double-stranded (dsDNA) or single-stranded DNA (ssDNA) adsorbed at gold electrodes was estimated from the cyclic voltammetric (CV) peak charge of osmium complex reduction. The dissociation constants (K) for the oxidized and reduced forms of a bound species are also estimated. [Os(phen)3]3+/2+ was applied to a probe for electrochemical DNA sensing. A thiol-linked single-stranded DNA probe was immobilized through the S-Au bonding to 70 pmol/cm2 on a gold electrode. Following hybridization with the complementary DNA, the osmium complex was electrochemically accumulated on the double-stranded DNA layer and the differential pulse voltammogram for this electrode gave an electrochemical signal due to the redox reaction of [Os(phen)3]3+/2+ that was bound to the double-stranded DNA on the electrode.

(P)-Helicene Displays Chiral Selection in Binding to Z-DNA

Enantiomeric helicenes of (P)-A and (M)-A were synthesized. The binding of the helicenes to B- and Z-DNA was studied quantitatively by CD, equilibrium dialysis, and fluorescence spectroscopy. Enantiomeric (P)-A not only bound selectively to Z-DNA but also effectively converted the B-DNA conformation to Z-DNA. The enantioselectivity of the helicenes offers a new route for the rational design of inhibitors of biological functions that may depend on Z-DNA.

Aryl substituted ruthenium bis-terpyridine complexes: intercalation and groove binding with DNA

The non-covalent interaction of five novel ruthenium(II) bis-terpyridine complexes with calf thymus DNA and, where appropriate, with poly[d(G-C)](2) and poly[d(A-T)](2) is described. Each complex is functionalised with aryl tail groups in the 4' position of the terpyridine ligands ((i) 9-anthracenyl, (ii) 4,4'-biphenyl, (iii) beta-naphthyl, (iv) 9-phenanthrenyl, and (v) 1-pyrenyl). Circular dichroism and linear dichroism show that the binding of three of the complexes (phenanthrenyl, anthracenyl and pyrenyl) at low metal complex concentration is dominated by intercalation of the aryl tail groups between the DNA bases. The complex with the biphenyl tail predominantly exhibits groove binding with no significant tail intercalation. The naphthyl derivative binds both by intercalation and a non-intercalative mode even at low metal complex concentrations. At high metal complex concentrations, aggregation of the complexes on the DNA is observed. Resonance light scattering indicates that the aggregates are of low nuclearity along the groove.

Structural basis for the binding affinity of xanthines with the DNA intercalator acridine orange

Caffeine (CAF), a methyl-substituted xanthine, interacts with polyaromatic DNA intercalators and has been hypothesized to interfere with their intercalation into DNA. Optical absorption spectroscopy was used to determine the binding affinities (K(assoc)) and structural effects of a series of methyl-substituted xanthines and a series of methyl-substituted uric acids (8-oxoxanthine) with the known DNA intercalator acridine orange (AO). There is evidence that complexation occurred (K(assoc) > or = 150 M(-1); binding curve saturation approximately > or =50%) between AO and 1,7-dimethylxanthine (155 M(-1)), 1,3-dimethylxanthine (theophylline, 157 M(-1)), 1,3,7-trimethylxanthine (CAF, 256 M(-1)), 1,3-dimethyl-8-chloroxanthine (413 M(-1)), 1,3,7,9-tetramethyl-8-oxyxanthine (tetramethyl uric acid or TMU, 552 M(-1)), and theophylline ethylenediamine (aminophylline, 596 M(-1)). No definitive evidence of complexation occurred between AO and 16 other substituted xanthines or purines, although there was some evidence of weak complexation (K(assoc) < 150 M(-1)) between AO and eight of the sixteen. Three common structural similarities were identified among those compounds found to form significant bonding with AO: (i) the N(1) or N(3) on the xanthine structure must be substituted with a methyl group; (ii) oxygen or chlorine substitution at C(8) increases binding affinity to AO when resonate states remain unchanged; and (iii) K(assoc) increases with an increase in number of methyl group substitutions on the 1- or 3-methylxanthine core structure. These results are explained on the basis of complex stabilization due predominately to hydrophobic attraction, with a contribution from charge transfer between donor and acceptor components. This information can be used in the manipulation of the physical or chemical characteristics of biologically active polyaromatic molecules.

Synthesis of [Ru(phen)(2)dppz](2+)-tethered oligo-DNA and studies on the metallointercalation mode into the DNA duplex

To explore the binding properties of [Ru(phen)(2)dppz](2+) complex (phen = 1,10-phenanthroline, dppz = dipyrido[3,2-a:2',3'-c]phenazine) in a sequence-specific manner in DNA duplex, it was tethered through the dppz ligand to a central position as well as both at the 3'- and 5'-ends of oligodeoxyribonucleotide (ODN). The middle [Ru(phen)(2)dppz](2+)-ODN tethered was resolved and isolated as four pure diastereomers, while the 3'- or 5'-[Ru(phen)(2)dppz](2+)-ODNs were inseparable on RP-HPLC. Thermal stability of the (Ru(2+)-ODN).DNA duplexes is found to increase considerably (DeltaT(m) = 12.8-23.4 degrees C), depending upon the site of the covalent attachment of the tethered [Ru(phen)(2)dppz](2+) complex, or the chirality of the [Ru(phen)(2)dppz](2+)-linker tethered at the middle of the ODN, compared to the unlabeled counterpart. Gross differences in CD between the [Ru(phen)(2)dppz](2+)-tethered and the native DNA duplexes showed that the global duplex conformation of the former has considerably altered from the B-type, but is still recognized by DNase I. The thermal melting studies, CD measurements, as well as DNase I digestion data, are interpreted as a result of intercalation of the dppz moiety, which is realized by threading of the Ru(phen)(2) complex part through the DNA duplex core. DNase I footprinting with four diastereomerically pure middle ([Ru(phen)(2)dppz](2+)-ODN).DNA duplexes furthermore showed that the tethered [Ru(phen)(2)dppz](2+)-linker chirality dictates the stereochemical accessibility of various phosphodiester moieties (around the intercalation site) toward the cleavage reaction by the enzyme. The diastereomerically pure ruthenium-modified duplexes, with the well-defined pi-stack, will be useful to explore stereochemistry-dependent energy- and electron-transfer chemistry to understand oxidative damage to the DNA double helix as well as the long-range energy- and electron-transfer processes with DNA as a reactant.

Allosteric, chiral-selective drug binding to DNA

The binding interactions of (-)-daunorubicin (WP900), a newly synthesized enantiomer of the anticancer drug (+)-daunorubicin, with right- and left-handed DNA, have been studied quantitatively by equilibrium dialysis, fluorescence spectroscopy, and circular dichroism. (+)-Daunorubicin binds selectively to right-handed DNA, whereas the enantiomeric WP900 ligand binds selectively to left-handed DNA. Further, binding of the enantiomeric pair to DNA is clearly chirally selective, and each of the enantiomers was found to act as an allosteric effector of DNA conformation. Under solution conditions that initially favored the left-handed conformation of [poly(dGdC)](2), (+)-daunorubicin allosterically converted the polynucleotide to a right-handed intercalated form. In contrast, under solution conditions that initially favored the right-handed conformation of [poly(dGdC)](2), WP900 converted the polynucleotide to a left-handed form. Molecular dynamics studies by using the amber force field resulted in a stereochemically feasible model for the intercalation of WP900 into left-handed DNA. The chiral selectivity observed for the DNA binding of the daunorubicin/WP900 enantiomeric pair is far greater than the selectivity previously reported for a variety of chiral metal complexes. These results open a new avenue for the rational design of potential anticancer agents that target left-handed DNA.