Simultaneous Binding of Ruthenium(II) [(1,10-Phenanthroline)2dipyridophenazine]2+ and Minor Groove Binder 4‘,6-Diamidino-2-phenylindole to Poly[d(A−T)2] at High Binding Densities: Observation of Fluorescence Resonance Energy Trasfer Across the DNA Stem

Interaction of Cucurbit[7]uril With Protease Substrates: Application to Nanosecond Time-Resolved Fluorescence Assays

We report the use of the macrocyclic host cucurbit[7]uril (CB7) as a supramolecular additive in nanosecond time-resolved fluorescence (Nano-TRF) assays for proteases to enhance the discrimination of substrates and products and, thereby, the sensitivity. A peptide substrate was labeled with 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as a long-lived (>300 ns) fluorescent probe and 3-nitrotyrosine was established as a non-fluorescent fluorescence resonance energy transfer (FRET) acceptor that acts as a “dark quencher.” The substrate was cleaved by the model proteases trypsin and chymotrypsin and the effects of the addition of CB7 to the enzyme assay mixture were investigated in detail using UV/VIS absorption as well as steady-state and time-resolved fluorescence spectroscopy. This also allowed us to identify the DBO and nitrotyrosine residues as preferential binding sites for CB7 and suggested a hairpin conformation of the peptide, in which the guanidinium side chain of an arginine residue is additionally bound to a vacant ureido rim of one of the CB7 hosts.

Complexation of DNA with ruthenium organometallic compounds: the high complexation ratio limit

Organometallic compounds possess two modes of interaction with DNA: intercalation at low complexation ratios and electrostatic adsorption at high ratios.

Lifetime heterogeneity of DNA-bound dppz complexes originates from distinct intercalation geometries determined by complex-complex interactions

Despite the extensive interest in structurally explaining the photophysics of DNA-bound [Ru(phen)(2)dppz](2+) and [Ru(bpy)(2)dppz](2+), the origin of the two distinct emission lifetimes of the pure enantiomers when intercalated into DNA has remained elusive. In this report, we have combined a photophysical characterization with a detailed isothermal titration calorimetry study to investigate the binding of the pure Δ and Λ enantiomers of both complexes with [poly(dAdT)](2). We find that a binding model with two different binding geometries, proposed to be symmetric and canted intercalation from the minor groove, as recently reported in high-resolution X-ray structures, is required to appropriately explain the data. By assigning the long emission lifetime to the canted binding geometry, we can simultaneously fit both calorimetric data and the binding-density-dependent changes in the relative abundance of the two emission lifetimes using the same binding model. We find that all complex-complex interactions are slightly unfavorable for Δ-[Ru(bpy)(2)dppz](2+), whereas interactions involving a complex canted away from a neighbor are favorable for the other three complexes. We also conclude that Δ-[Ru(bpy)(2)dppz](2+) preferably binds isolated, Δ-[Ru(phen)(2)dppz](2+) preferably binds as duplets of canted complexes, and that all complexes are reluctant to form longer consecutive sequences than triplets. We propose that this is due to an interplay of repulsive complex-complex and attractive complex-DNA interactions modulated by allosteric DNA conformation changes that are largely affected by the nature of the ancillary ligands.

Synthesis, DNA binding, and cleavage studies of Co(III) complexes with fused aromatic NO/NN-containing ligands

Four new Co(III) complexes, namely [Co(cq)(3)](PF(6))(3), [Co(phen)(2)(cq)](PF(6))(3), [Co(bnp)(3)] (PF(6))(3), and [Co(phen)(2)(bnp)](PF(6))(3) (where cq = chromeno[2,3-b]quinoline, phen = 1,10-phenanthroline and bnp = dibenzo[b,g][1,8]naphthyridine), were synthesized and structurally characterized. Spectroscopic data suggested an octahedral geometry for all the complexes. Binding studies of these complexes with double-stranded (ds)DNA were analyzed by absorption spectra, viscosity, and thermal denaturation studies. The results revealed that the metal complex intercalates into the DNA base stack as intercalator. The oxidative cleavage activities of the complexes were studied with supercoiled pUC19 DNA using gel electrophoresis and the results show that the complexes have potent nuclease activity.

Ruthenium(II) polypyridyl complexes and DNA--from structural probes to cellular imaging and therapeutics

In the last few decades, coordination complexes based on d(6) metal centres and polypyridyl ligand architectures been developed as structure- and site-specific reversible DNA binding agents. Due to their attractive photophysical properties, much of this research has focused on complexes based on ruthenium(II) centres and, more recently, attention has turned to the use of these complexes in biological contexts. As the rules that govern the cellular uptake and cellular localisation of such systems are determined they are finding numerous applications ranging from imaging to therapeutics. This review illustrates how the interdisciplinary nature of this research-which takes in synthetic chemistry, biophysical and in cellulo studies-makes this an exciting area in which an array of further applications are likely to emerge.

DFT/TDDFT STUDY ON DNA-BINDING AND SPECTRAL PROPERTIES OF "LIGHT SWITCH" COMPLEX [Ru(phen)2 (taptp)]2+ IN AQUEOUS SOLUTION

The theoretical studies on the electronic structure, DNA-binding, and absorption-spectral properties of "light switch" complex [ Ru ( phen )2( taptp )]2+ (phen = 1,10-phenanthroline; taptp = 4,5,9,18-tetraazaphenanthreno-[9,10-b]triphenylene) in aqueous solution have been carried out using density functional theory (DFT) and time-dependent DFT (TDDFT) methods. The results show the following: (i) The solvent effect makes all the frontier molecular orbital energies of complex to increase to a certain extent; however, the energies (ε LUMO + x) of some frontier unoccupied molecular orbitals (MOs) in aqueous solution are still negative and rather lower than those of the energies (ε HOMO - x) of some frontier-occupied MOs of DNA-base pairs, and thus the complex in aqueous solution is still an excellent electron-acceptor in its DNA-binding. (ii) The solvent effect further shows that simply increasing the conjugative planar area of intercalative ligand may be ineffective on the improvement of DNA-binding of the resulting complex because of going along with the increase in the LUMO (and LUMO + x) energy. It is the reason why the DNA-binding affinity of "light switch" complex [ Ru ( phen )2( taptp )]2+ is not better than that of the well-known complex [ Ru ( phen )2( dppz )]2+ yet. (iii) The three main experimental bands (~450 nm, ~360 nm, and ~290 nm) of the studied complex in aqueous solution were further well calculated, simulated, and explained by the TDDFT computations.

DNA intercalating studies of [Ru(bpy)2dmt]2+ with two vacant nitrogen atoms by introducing copper(II) ions

A novel, yet effective method for identifying DNA-binding modes of [Ru(bpy)(2)dmt](2+) (where bpy = 2,2'-bipyridine and dmt = 2,3-dimethyl-1,4,8,9-tetra-aza-triphenylene) on an indium tin oxide electrode has been successfully developed by introducing Cu(2+) ion and ethylenediaminetetraacetic acid. The results from emission spectra and fluorescence microscopic images suggested that [Ru(bpy)(2)dmt](2+) not only associates with Cu(2+) ion in both the absence and presence of DNA but also shows strong affinity with DNA in the presence of Cu(2+). Evidence for the strong binding of [Ru(bpy)(2)dmt](2+) to DNA was determined from the interface studies using electrochemical methods. The present study suggests that a combination of photoluminescence measurement with electrochemical methods identifies the DNA-binding behavior of luminescent molecules with redox activities. [Ru(bpy)(2)dmt](2+) binds to DNA via an intercalative mode.

Novel luminescent nanoparticles for DNA detection

Highly luminescent LaF(3):Ce(3+)/Tb(3+) nanocrystals were successfully prepared and surface functionalized via Layer-by-Layer technology. These as-prepared nanocrystals are highly resistant to photobleaching and pretty dispersible in aqueous solution. Due to the efficient luminescence quenching of the nanocrystals by nucleic acids, a facile fluorescence quenching method was developed for the detection of trace amount of nucleic acids. Under optimal conditions, the fluorescence intensity was proportional to the DNA concentration over the range of 0.60-25.0microgmL(-1) for calf thymus DNA (ct-DNA) and 0.60-30.0microgmL(-1) for herring sperm DNA (hs-DNA), respectively. The corresponding detection limit is 0.21microgmL(-1) for ct-DNA and 0.31microgmL(-1) for hs-DNA, respectively. The results indicated that the reported method is simple and rapid with wide linear range. Also, the recovery and relative standard deviation of this method are reasonable and satisfactory.

pH- and DNA-induced dual molecular light switches based on a novel ruthenium(II) complex

A novel Ru(II) complex, [Ru(bpy)(2)(btppz)]Cl(2), where bpy=2,2'-bipyridine and btppz=benzo[h]tripyrido[3,2-a:2',3'-c:2'',3''-j]phenazine, has been synthesized and characterized. The pH effects on UV-visible (UV-vis) absorption and emission spectra of the complex have been studied and ground- and excited-state ionization constants of the complex have been derived. The calf thymus DNA (ct-DNA) binding properties of the complex were investigated with UV-vis absorption and luminescence spectrophotometric titrations, steady-state emission quenching by [Fe(CN)(6)](4-), DNA competitive binding with ethidium bromide, DNA melting experiments, reverse salt titrations and viscosity measurements. The complex was demonstrated to act as dual molecular switches: pH-induced "on-off" emission switch with an on-off intensity ratio of approximately 54 which is favorably compared with those reported for structurally analogous Ru(II) complexes, and a DNA molecular light switch with a luminescence enhancement factor of 22 as it intercalatively bound to the DNA.

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.

DNA affinity binding studies using a fluorescent dye displacement technique: the dichotomy of the binding site

We have observed a number of discrepancies and contradictions in the use of a fluorescent intercalator displacement assay in surveying the binding affinities of dinuclear polypyridyl ruthenium(II) complexes with DNA. By a modification of the assay using the fluorescent minor-groove binder 4',6-diamidino-2-phenylindole, rather than intercalating dyes (ethidium bromide or thiazole orange), results were obtained for all complexes studied which were consistent with relative affinities and stereoselectivities observed with other techniques, including NMR, affinity chromatography and equilibrium dialysis. It is believed that the difference in binding mode between the minor groove-binding Ru(II) complexes and the intercalating fluorescent dyes they are displacing may contribute to these discrepancies.

AT-dependent luminescence of DNA-threading ruthenium complexes

Whereas the emission from the ruthenium complex deltadelta-[mu-bidppz(phen)4Ru2]4+ (P) is five times larger when intercalated into poly(dAdT)2 than when intercalated into ct-DNA, the homologue deltadelta-[mu-bidppz(bipy)4Ru2]4+ (B) has a smaller quantum yield and a red-shifted emission. The origin of this difference is here investigated by studying intercalation into oligonucleotides containing a central AT-tract. Increasing the length of the AT-tract increases the emission quantum yield for P but decreases it for B. However, not even four helix turns of AT base pairs is enough to mimic poly(dAdT)2. B and P thus use the increased flexibility with increasing length of the AT-tract in opposite ways, whereas B gets more prone to quenching by water, P gets more protected from quenching. The earlier reported gradual increase of the intercalation rate with AT-stretch length is thus paralleled by a gradual change in the equilibrium properties of the intercalated state.

The two modes of binding of Ru(phen)2dppz2+ to DNA: Thermodynamic evidence and kinetic studies

The binding of Ru(phen)(2)dppz(2+) (dppz=dipyrido[3,2-a:2',3'-c]phenazine) to DNA was investigated at pH 7.0 and 25 degrees C using stopped-flow and spectrophotometric methods. Equilibrium measurements show that two modes of binding, whose characteristics depend on the polymer to dye ratio (C(P)/C(D)), are operative. The binding mode occurring for values of C(P)/C(D) higher than 3 exhibits positive cooperativity, which is confirmed by kinetic experiments. The reaction parameters are K=2 x 10(3)M(-1), omega=550, n=1, k(r)=(1.9+/-0.5) x 10(7)M(-1)s(-1) and k(d)=(9.5+/-2.5)x10(3)s(-1) at I=0.012 M. The results are discussed in terms of prevailing surface interaction with DNA grooves accompanied by partial intercalation of the dppz residue. The other binding mode becomes operative for C(P)/C(D)<3 and the equilibria analysis shows this is an ordinary intercalation mode (K=1.3 x 10(6) M(-1), n=1.5 at I=0.012 M and K=2 x 10(5) M(-1), n=1.2 at I=0.21 M). Similar behaviour is displayed by double-stranded poly(A).

Base-specific and enantioselective studies for the DNA binding of iron(II) mixed-ligand complexes containing 1,10-phenanthroline and dipyrido[3,2-a:2',3'-c]phenazine

Base specificity and enantioselectivity for the DNA binding of [Fe(phen)2(dppz)]2+ (phen=1,10-phenanthroline and dppz=dipyrido[3,2-a:2',3'-c]phenazine) have been studied by determining the equilibrium binding constant (Kb) of the iron(II) complex to calf thymus DNA (ct-DNA), poly[(dA-dT)2], poly[(dG-dC)2] and poly[(dI-dC)2] using spectrophotometric titration and by monitoring the CD spectral profile of the iron(II) complex in the presence and absence of different types of DNA using circular dichroism (CD) spectroscopy, respectively. It has been shown that [Fe(phen)2(dppz)]2+ prefers to intercalate into the A-T and I-C sequences of poly[(dA-dT)2] and poly[(dI-dC)2] rather than into the G-C sequences of poly[(dG-dC)2] or into the base pairs of ct-DNA. In contrast to previous reports, it is a surprising observation that the enantioselectivity of the DNA binding for [Fe(phen)2(dppz)]2+ is base-dependent in nature. The Delta-enantiomer of [Fe(phen)2(dppz)]2+ is preferentially intercalated into the base pairs of poly[(dG-dC)2] or ct-DNA as indicated by its CD spectral profiles. On the other hand, the Lambda-enantiomer of [Fe(phen)2(dppz)]2+ is favorably intercalated into poly[(dA-dT)2] or poly[(dI-dC)2] as suggested by the opposite CD spectral profile. This preferential binding of Lambda-[Fe(phen)2(dppz)]2+)for the A-T sequence may be attributed to the fact that the binding site for the A-T sequence is relatively facile and thus the steric effect caused by the ancillary (non-intercalated) phen ligands is alleviated. The degree of enantioselectivity represented by inversion constants (Kinv) decreases as the salt concentration in the solution increases, indicating that electrostatic interaction is also operating in the ct-DNA-binding events of the iron (II) complex.

Nucleic acid intercalators and avidin probes derived from luminescent cyclometalated iridium(III)-dipyridoquinoxaline and -dipyridophenazine complexes

Six luminescent cyclometalated iridium(III)-dipyridoquinoxaline and -dipyridophenazine complexes [Ir(ppy)2(N-N)](PF6) (Hppy = 2-phenylpyridine; N-N = dipyrido[3,2-f:2',3'-h]quinoxaline, dpq (1); 2-n-butylamidodipyrido[3,2-f:2',3'-h]quinoxaline, dpqa (2); 2-((2-biotinamido)ethyl)amidodipyrido[3,2-f:2',3'-h]quinoxaline, dpqB (3); dipyrido[3,2-a:2',3'-c]phenazine, dppz (4); benzo[i]dipyrido[3,2-a:2',3'-c]phenazine, dppn (5); 11-((2-biotinamido)ethyl)amidodipyrido[3,2-a:2',3'-c]phenazine, dppzB (6)) have been designed as luminescent intercalators for DNA and probes for avidin. The structure of complex 4 has been studied by X-ray crystallography. The photophysical and electrochemical properties of the complexes have also been investigated. The binding of these complexes to double-stranded calf thymus DNA and synthetic double-stranded oligonucleotides poly(dA) x poly(dT) and poly(dG) x poly(dC) has been investigated by spectroscopic titrations. The interactions between the two biotin-containing complexes and avidin have been studied by 4'-hydroxyazobenzene-2-carboxylic acid (HABA) assays and emission titrations.

Chemical control of the DNA light switch: cycling the switch ON and OFF

The emission of the DNA light-switch complex [Ru(bpy)2(tpphz)]2+ (bpy = 2,2'-bipyridine, tpphz = tetrapyrido[3,2-a:2',3'-c:3' ',2' '-h:2' '',3' ''-j]phenazine) can be reversibly turned ON and OFF over several cycles. The tpphz and taptp (taptp = 4,5,9,18-tetraazaphenanthreno[9,10-b] triphenylene) ligands in [Ru(bpy)2(tpphz)]2+ and [Ru(bpy)2(taptp)]2+, respectively, intercalate between the DNA bases, and a 50-fold increase in emission intensity of [Ru(bpy)2(tpphz)]2+ is observed upon DNA intercalation. The [Ru(bpy)2(tpphz)]2+ DNA light switch can be turned OFF statically in the presence of Co2+, Ni2+, and Zn2+, and the emission can be fully restored by the addition of EDTA. Cycling of the DNA light switch OFF and ON can be accomplished through the successive introduction of Co2+ and EDTA, respectively, to solutions of DNA-bound [Ru(bpy)2(tpphz)]2+. Owing to the absence of additional coordination sites, the emission of DNA-intercalated [Ru(bpy)2(taptp)]2+ is not quenched by transition metal ions in solution. To our knowledge, this work presents the first example of a reversible DNA light switch.

Ruthenium(II) Complex of Hbopip: Synthesis, Characterization, pH-Induced Luminescence “Off−On−Off” Switch, and Avid Binding to DNA

A novel ruthenium(II) complex of [Ru(bpy)2(Hbopip)](ClO4)2 (in which bpy=2,2'-bipyridine, Hbopip=2-(4-benzoxazolyl)phenylimidazo[4,5-f][1,10]phenanthroline) was synthesized and characterized. The spectrophotometric pH titrations of the complex showed that it acted as a pH-induced luminescence "off-on-off" switch: a luminescence off-on switch with a luminescence enhancement factor of IpH=3.0/IpH=1.0=20 occurring over a narrow pH range of 1.00-3.00 plus a luminescence on-off switch with a luminescence enhancement factor of 3 over a pH range of 3.20-9.40. The excited-state ionization constant of the complex derived, pKa1*=3.06, is 1.36 pKa units greater than the ground-state pKa1=1.70, and pKa2*=5.01 and pKa3*=8.22 are comparable to the ground-state pKa2=5.23 and pKa3=8.22, respectively. The complex avidly bound to calf thymus DNA with a large binding constant of (1.2+/-0.3)x10(7) M-1 in buffered 50 mM NaCl, as evidenced by UV-vis and luminescence titrations, steady-state emission quenching by [Fe(CN)6]4-, DNA competitive binding with ethidium bromide, viscosity measurements, and DNA melting experiments.

[Ru(phen)2DPPZ]2+ is in contact with DNA bases when it forms a luminescent complex with single-stranded oligonucleotides

The luminescence intensity of the Delta- and Lambda-enantiomer of [Ru(phen)2DPPZ]2+ ([Ru(phenanthroline)2 dipyrido[3,2-a:2',3'-c]phenazine]2+) complex enhanced upon binding to double stranded DNA, which has been known as "light switch effect". The enhancement of the luminescence required the intercalation of the large ligand between DNA base pairs. In this study, we report the enhancement in the luminescence intensity when the metal complexes bind to single stranded oligonucleotides, indicating that the "light switch effect" does not require intercalation of the large DPPZ ligand. Oligonucleotides may provide a hydrophobic cavity for the [Ru(phen)2DPPZ]2+ complex to prevent the quenching by the water molecule. In the cavity, the metal complex is in contact with DNA bases as is evidenced by the observation that the excited energy of the DNA bases transfer to the bound metal complex. However, the contact of the metal complex with DNA bases is different from the stacking of DPPZ in the intercalation pocket. In addition to the normal two luminescence lifetimes, a short lifetime in the range of 1-2 ns was found for both the delta- and lambda-enantiomer of [Ru(phen)2DPPZ]2+ when complexed with single stranded oligonucleotides, which may be assigned to the metal complex that is outside of the cavity, interacting with phosphate groups of DNA.

Racemic D,L-[Co(phen)2dpq](3+)-DNA interactions: investigation into the basis for minor-groove binding and recognition

A study on the minor-groove recognition of B-DNA d(GTCGAC)2 by racemic D,L-[Co(phen)2dpq](3+), where phen and dpq stand for 1,10-phenanthroline and dipyrido [3,2-d:2,3-f]quinoxaline, respectively, was carried out with a one-, two-dimensional (1D, 2D) nuclear magnetic resonance (NMR) methodologies and molecular simulations. NMR investigations revealed that the metal complex intercalates into the DNA base stack from minor groove orientation with dpq as intercalator and dpq ligand participated in the nucleobase stack. Molecular docking simulations of these systems were consistent with the experimental results and revealed that the recognition shows obvious enantioselectivity: the L-isomer is favored at the pyrimidine-purine/purine-pyrimidine region, especially CG/GC sequence, while the D-isomer is favored at the pyrimidine-pyrimidine/purine-purine region, especially TC/AG sequence. Surprisingly, we found that the L-isomer would be enriched when racemic complex was employed. So contrary to general viewpoint, the L-isomer of complex recognized this right hand double helical DNA preferentially. Detailed analysis suggests that it is the electrostatic interactions that determine the steric interactions and then determine the whole recognition event.

DNA mediated resonance energy transfer from 4',6-diamidino-2-phenylindole to [Ru(1,10-phenanthroline)2L]2+

The binding site of Delta- and Lambda-[Ru(phenanthroline)2L]2+ (L being phenanthroline (phen), dipyrido[3,2-a:2'3'-c]phenazine (DPPZ), and benzodipyrido[3,2-a:2'3'-c]phenazine (benzoDPPZ)), bound to poly[d(A-T)2] in the presence and absence of 4',6-diamidino-2-phenylindole (DAPI) was investigated by circular dichroism and fluorescence techniques. DAPI binds at the minor groove of poly[d(A-T)2] and blocks the groove. The circular dichroism spectrum of all Ru(II) complexes are essentially unaffected whether the minor groove of poly[d(A-T)2] is blocked by DAPI or not, indicating that the Ru(II) complexes are intercalated from the major groove. When DAPI and Ru(II) complexes simultaneously bound to poly[d(A-T)2], the fluorescence intensity of DAPI decreases upon increasing Ru(II) complex concentrations. The energy of DAPI at excited state transfers to Ru(II) complexes across the DNA via the Förster type resonance energy transfer. The efficiency of the energy transfer is similar for both [Ru(phen)2DPPZ]2+ and [Ru(phen)2benzoDPPZ]2+ complexes, whereas that of [Ru(phen)3]2+ is significantly lower. The distance between DAPI and [Ru(phen)3]2+ is estimated as 0.38 and 0.64 Förster distance, respectively, for the Delta- and Lambda-isomer.