Competitive DNA Binding Studies Research Articles

DNA minor groove binding of a well known anti-mycobacterial drug dapsone: A spectroscopic, viscometric and molecular docking study

Dapsone is a sulfone drug mainly used as anti-microbial and anti-inflammatory agent for the treatment of various diseases including leprosy. Recently, its interaction with protein (bovine serum albumin) is evidenced. But, the binding propensity of this anti-mycobacterial drug towards DNA is still unknown. Also, the mode of dapsone-DNA interaction (if any) is still an unknown quantity. In this study, we have taken a thorough attempt to understand these two unknown aspects using various biophysical and in silico molecular docking techniques. Both UV–visible and fluorescence titrimetric studies indicated that dapsone binds to CT-DNA with a binding constant in order of 104 M−1. Circular dichroism, thermal denaturation and viscosity experiments revealed that dapsone binds to the grooves of CT-DNA. Competitive DNA binding studies clearly indicated the minor groove binding property of this anti-mycobacterial drug. Molecular docking provided detailed information about the formation of hydrogen bonding in the dapsone-DNA complex. This in silico study further revealed that dapsone binds to the AT-rich region of the minor groove of DNA having a relative binding energy of −6.22 kcal mol−1. Overall, all these findings evolved from this study can be used for better understanding the medicinal importance of dapsone.

DNA Targeting Long-Chain Alkoxy Appended Tin(IV) Porphyrin Scaffolds: Photophysical and Antimicrobial PDT Investigations.

Tin(IV) porphyrin scaffolds having long-chain (C8 and C16) alkoxyphenyl group at one meso position were synthesized with axial dichloro and dihydroxo ligands. Modifications with respect to the alkoxy chain length and the axial ligands were investigated using UV-vis and fluorescence spectroscopy as well as cyclic voltammetry. Significantly higher molar absorption coefficients were noted with dichloro axial ligands whereas higher fluorescence quantum yields were observed for C8 alkoxy chain substituents. Electrochemical redox data revealed that the porphyrin ring became difficult to reduce consequent to the presence of electron donating alkoxy chain. Evaluation of the aggregation behavior in different organic solvents and DMF-water mixture has been carried out. The singlet oxygen production and photostability data are supportive of their suitability for antibacterial photodynamic therapy. The antibacterial studies carried out in Gram negative (E. coli) and Gram positive (B. subtilis) bacteria using agar well diffusion and LB broth assay revealed selective toxicity in B. Subtilis cells. Fluorescence microscopy and competitive DNA binding studies with Hoechst 33342 revealed DNA binding at the minor groove which was further substantiated with molecular docking studies.

Synthesis, structural characterization, antibacterial activity, DNA binding and computational studies of bis(2-methyl-1H-imidazole κN3)silver(I)dichromate(VI)

A new silver complex [Ag(C4H6N2)2]2Cr2O7 (1) derived from Ag2[CrO4] and 2-methylimidazole has been synthesized and fully characterized by Single crystal X-ray diffraction, UV–Vis, FT-IR, elemental analysis, DFT and AIM calculations. The crystal structure of 1 shows that the discrete, ionic compound of [Ag(C4H6N2)2]2Cr2O7 consists of two [Ag(C4H6N2)2]+ cations bridged by a [Cr2O7]2− counter anion. In each of the [Ag(C4H6N2)2]+ complexes, the Ag center is coordinated by two N atoms from two distinct neutral monodentate 2-methylimidazole ligands in an almost linear geometry with AgN distances between 2.068(4) Å and 2.076(4) Å and NAgN bond angles of 179.4(2)° and 173.8(2)°. The NH⋯O and CH⋯ O hydrogen bonds, π⋯π stacking, CH⋯π and Ag⋯O interactions play an important role in the structural stabilization of the complex to generate a three-dimensional framework. The antibacterial activity and molecular docking studies of the free 2-methylimidazole ligand and the title complex show that these compounds have ability to inhibit the growth of the tested bacteria. A scanning probe microscopy (SPM) study of the treated bacteria was carried out to investigate the structural changes caused by the interactions between the complex and target bacteria. The interaction of the complex 1 with the E.coli DNA (E-DNA) has been studied by UV–Vis absorption, competitive DNA-binding studies with ethidium bromide by fluorescence and gel electrophoresis techniques. These experiments indicate that the complex interacts with DNA by intercalative binding.

Synthesis, crystal structure and Hirshfeld surface analysis of copper(II) complexes: DNA- and BSA-binding, molecular modeling, cell imaging and cytotoxicity

In order to explore the structure–activity relationship of complexes, two copper(II) complexes, [Cu(dimethoxybpy)2](PF6)2 (1) and [Cu(dimethylbpy)2Cl]PF6 (2) (dimethoxybpy is 4,4′-dimethoxy-2,2′-bipyridine and dimethylbpy is 4,4′-dimethyl-2,2′-bipyridine), have been synthesized and characterized by several physicochemical techniques. The single-crystal X-ray structures of 1 and 2 exhibit distorted square-planar and distorted square-pyramidal structure, respectively. The Hirshfeld surface analysis and the associated 2D fingerprint plots of 1 and 2 have been also studied to evaluate intermolecular interactions. The DNA binding properties of 1 and 2 have been investigated by absorption and emission spectra, viscosity, cyclic voltammetry, circular dichroism and competitive DNA–binding studies, which indicate that the complexes interact with DNA through partial intercalation. The results of absorption and emission spectra, synchronous fluorescence and circular dichroism show that the complexes bind with BSA. The results exhibit that the complex 1 has stronger binding ability to DNA and BSA than the complex 2. Molecular docking technique has been used to evaluate and understand the interaction mode of 1 and 2 with DNA and BSA. The in vitro cytotoxicity of the complexes against MCF-7, A-549 and HT-29 cell lines has been assayed by MTT method. The complexes exhibit significant cytotoxicity in cell lines with IC50 values ranging from 1.5 to 53μM. Based on the results of cytotoxicity, it would appear that the complex 2 has better cytotoxicity than the complex 1 under the same experimental conditions, suggesting that the hydrophobicity of methyl groups on the complex enhances the anticancer activity. The results of the microscopic analyses of cancer cells confirm the results of cytotoxicity.

Green synthesis of anticancerous honeycomb PtNPs clusters: Their alteration effect on BSA and HsDNA using fluorescence probe

The screening and characterization of cancer cells has been challenging due to sample insufficiency and extravagant. In this article, we highlighted easy green synthesis of Platinum nanoparticles (PtNPs) in the honeycomb like clusters, and their optical properties (by HRTEM, XRD, DLS, Zeta potential, EDAX, and UV–Visible techniques). PtNPs were responsive of binding mechanisms with the bovine serum albumin (BSA), herring sperm deoxyribonucleic acid (HsDNA) and cytotoxicity of human carcinomas cell. We are able to elucidate the responses of various concentrations of PtNPs for the control of MDA-MB-468 cell and binding conformation of BSA and HsDNA by using multi-spectroscopic techniques under the physiological conditions. The extent of quenching was in agreement of PtNPs-BSA binding reaction was mainly a static. The Ksv, K, the number of binding sites at different temperatures and the thermodynamic parameters between BSA and PtNPs were calculated. The positive ΔS0 and negative ΔH0, ΔG0 values indicated that the binding pattern was determined by spontaneous hydrogen bond electrostatic interaction of BSA with esterage like activity. The binding properties of the PtNPs with HsDNA have been investigated by thermal denaturation, competitive DNA-binding studies with ethidium bromide (EB), Hochest-33258 and relative viscosity. The negative ΔH0, ΔS0 and ΔG0 values indicated that the hydrophilic interaction were main force in spontaneity in binding mechanism of PtNPs to HsDNA. GI50 value of PtNPs demonstrated that these nanoparticles showed cytotoxicity against MDA-MB-468 human breast cancer cell line. Our results also clarified that PtNPs bind to BSA and can be effectively transported in the body and eliminated. PtNPs showed minor groove binding with HsDNA, which could be a useful guideline for further versatile approach to develop biomedical coatings with different functions of drug design.

Competitive DNA-Binding Studies between Metal Complexes and GelRed as a New and Safe Fluorescent DNA Dye

The focus of this work is introduction of GelRed (GR) as a stable, sensitive and environmentally safe fluorescent DNA dye instead of the highly toxic ethidium bromide (EB). Competitive DNA-binding studies between metal complexes, [Cu(phen-dion)(phen)Cl]Cl (1), [Cu(phen-dione)(bpy)Cl]Cl (2), [Cu(dppt)2(H2O)]PF6 (3), [Ni(dppt)2Cl2] (4), [Zn(dppt)2Cl2] (5), and K3[Fe(CN)6] (6) (where phen-dione is 1,10-phenanthroline-5,6-dione, phen is 1,10- phenanthroline, bpy is 2,2'-bipyridine, and dppt is 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine), and GelRed have been investigated under physiological conditions by fluorescence spectroscopy. This simple method can reveal the binding affinity and mode of metal complexes with DNA. The method is based on the decrease of fluorescence derived from the displacement of GelRed from DNA by metal complexes. The % fluorescence decrease is directly related to the extent of DNA binding. Results indicate the DNA binding affinities of complexes follow the order 3>4>1>2>5>6. The significant quenching of the emission band of the GR-DNA with the addition of complexes 1, 3, and 4 suggests that complexes compete for DNA-binding sites with GR and displace GR from the GR-DNA, which is usually characteristic of the intercalative interaction of compounds with DNA. A small quenching of the emission band of the GR-DNA with the addition of the complex 2 was observed that show the complex weaker competes for DNA-binding sites with GR than complexes 1, 3, and 4. Results show complexes 5 and 6 cannot compete for DNA-binding sites with GR and their interaction with DNA is external binding (groove or electrostatic bindig).

The Zn(II) nanocomplex: Sonochemical synthesis, characterization, DNA- and BSA-binding, cell imaging, and cytotoxicity against the human carcinoma cell lines.

The focus of this article is preparation of a new kind of nanomaterial, the Zn(II) nanocomplex, to decrease growth of human carcinoma cell lines. The Zn(II) nanocomplex coordinated by phendione, [Zn(phendione)3](PF6)2 (where phendione is 1,10-phenanthroline-5,6-dione), has been synthesized by sonochemical method and characterized by FT-IR, dynamic light scattering (DLS), and scanning electron microscopy (SEM). The interaction of the complex and nanocomplex with fish sperm DNA (FS-DNA) has been investigated under physiological conditions by a series of experimental methods (fluorescence titration, viscosity, cyclic voltammetry (CV), competitive DNA-binding studies with ethidium bromide, and SEM). Results have indicated that the complex binds to FS-DNA by two biding modes, viz., electrostatic and partial insertion phendione between the base stacks of double-stranded DNA. The quenching constants (Ksv), binding constants (Kbin), and number of binding sites (n) at different temperatures, as well as thermodynamic parameters (ΔH(o), ΔS(o) and ΔG(o)) have been calculated for the BSA-complex system. Protein binding studies show that the complex and nanocomplex could bind with BSA. Results of synchronous fluorescence of BSA show that addition of the complex affect the microenvironment of both tyrosine and tryptophan residues during the binding process. The in vitro cytotoxicity of the complex and nanocomplex against the human carcinoma cell lines (MCF-7 and A-549) was evaluated by MTT assay. Results indicate that the complex and nanocomplex have greater cytotoxicity activity against MCF-7 with IC50 values of 0.2 and 0.9mg/L, respectively. Results of the microscopic analyses of the cancer cells confirm results of cytotoxicity.

Synthesis, characterization, DNA interactions, DNA cleavage, radical scavenging activity, antibacterial, anti-proliferative and docking studies of new transition metal complexes

The compound N-(2-hydroxybenzylidene)-1-ethyl-1, 4-dihydro-7-methyl-4-oxo-1, 8 naphthyridine-3-carbohydrazide (LH) and its Cu (II), Co (II) and Zn (II) complexes were synthesized and characterized. The absorption spectral titrations and competitive DNA binding studies depicted those complexes of title compound bind to CT-DNA through intercalation. Interestingly [Cu (II)-(L2)] showed relatively high binding constant value (6.61 x 10(5) M(-1)) compared to [Co (II)-(L2)] (4.378× 10(5) M(-1)) and [Zn (II)-(L2)] (3.1x10(5) M(-1)). Ligand and its complexes were also examined for DNA nuclease activity against pBR-322 plasmid DNA, which showed that [Cu (II)-(L2)] had the best hydrolytic cleavage property displaying prominent double-strand DNA cleavage. In addition, antioxidant activities of the ligand and its metal complexes investigated through scavenging effects for DPPH radical in- vitro, indicated their potentiality as good antioxidants. The in vitro anti-bacterial study inferred the better anti-bacterial activity of [Cu (II)-(L2)] and this was also correlated theoretically by employing docking studies wherein [Cu (II)-(L2)] displayed good Gold score and Chem score. Finally the in vitro anti- proliferative activity of studied compounds was tested against HeLa and MCF-7 cell lines. Interestingly [Cu (II)-(L2)] displayed lower IC50 value and lower percentage of viability in both HeLa and MCF-7 cell lines.

A mononuclear Ni(II) complex with 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine: DNA- and BSA-binding and anticancer activity against human breast carcinoma cells

DNA- and BSA-binding properties of a mononuclear Ni(II) complex, [Ni(dppt)2Cl2] (dppt=5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine), have been investigated under physiological conditions. The interaction of the complex with the fish sperm DNA (FS-DNA) has been studied by UV–Vis absorption, thermal denaturation, viscosity measurement, competitive DNA-binding studies with ethidium bromide (EB) by fluorescence, and gel electrophoresis technique. The experimental results indicate that the complex interacts with DNA by intercalative binding mode. The competitive study with ethidium bromide (EB) shows that the complex competes for the DNA-binding sites with EB and displaces the DNA-bound EB molecule. The interactions of the dppt ligand and the complex with BSA have been studied by UV–Vis absorption and fluorescence spectroscopic techniques. The values of Kb for the BSA–dppt and the BSA–complex systems at room temperature were calculated to be 0.14×104M−1 and 0.32×105M−1, respectively, indicating that the complex has stronger tendency to bind with BSA than the dppt ligand. The quenching constants (Ksv), binding constants (Kbin), and number of binding sites (n) at different temperatures, as well as the binding distance (r) and thermodynamic parameters (ΔH°, ΔS° and ΔG°) have been calculated for the BSA–dppt and the BSA–complex systems. The cytotoxicities of the dppt ligand and the complex have been also tested against the human breast adenocarcinoma (MCF-7) cell line using the MTT assay. The results indicate that the dppt ligand and the complex display cytotoxicity against human breast cancer cell lines (MCF-7) with the IC50 values of 17.35μM and 13.00μM, respectively. It is remarkable that the complex can introduce as a potential anticancer drug.

DNA- and BSA-binding studies and anticancer activity against human breast cancer cells (MCF-7) of the zinc(II) complex coordinated by 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine

Binding studies of a mononuclear zinc(II) complex, [Zn(dppt)2Cl2] (dppt is 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine), with DNA and bovine serum albumin (BSA) have been investigated under physiological conditions. The binding properties of the complex with fish sperm DNA (FS-DNA) have been investigated by UV–Vis absorption, thermal denaturation, competitive DNA-binding studies with ethidium bromide (EB) by fluorescence, and gel electrophoresis techniques. The competitive study with (EB) shows that the complex can displace EB from the DNA-EB system and compete for the DNA-binding sites with EB, which is usually characteristic of the intercalative interaction of compounds with DNA. The value of the fluorescence quenching constant (Ksv) was obtained as 3.1×104M−1, indicating that this complex shows a high quenching efficiency and a significant degree of binding to DNA.Moreover, the intercalative binding mode has also been verified by the results of UV–Vis absorption, thermal denaturation and gel electrophoresis. The value of Kb at room temperature was calculated to be 1.97×105M−1, indicating that the complex possesses strong tendency to bind with DNA. This value is very greater than to the values obtained for other zinc(II) complexes. The interaction of the complex with BSA has been studied by UV–Vis absorption, fluorescence and circular dichroism (CD) spectroscopic techniques. The results indicate that the complex has a quite strong ability to quench the fluorescence of BSA and the binding reaction is mainly a static quenching process. The quenching constants (KSV), the binding constants (Kb), the number of binding sites at different temperatures, the binding distance between BSA and the complex (r), and the thermodynamic parameters (ΔHo, ΔSo and ΔGo) between BSA and the complex were calculated. The complex exhibits good binding propensity to BSA showing relatively high binding constant values. The positive ΔHo and ΔSo values indicate that the hydrophobic interaction is main force in the binding of the complex to BSA. Moreover, to evaluate the anticancer properties, the cytotoxicity of the complex has been tested against the human breast adenocarcinoma (MCF-7) cell lines using the MTT assay. The results indicate that the parent complex displays cytotoxicity against human breast cancer cell lines (MCF-7) with an IC50 value of 10.44μM. It is remarkable that the complex can introduce as a potential anticancer drug.

Mixed ligand μ-phenoxo-bridged dinuclear copper(ii) complexes with diimine co-ligands: efficient chemical nuclease and protease activities and cytotoxicity

The water soluble mixed ligand copper(II) complexes of the type [Cu(sal)(diimine)(ClO4)]21-5, where sal is salicylaldehyde and diimine is 2,2'-bipyridine (bpy, 1), 1,10-phenanthroline (phen, 2), 5,6-dimethyl-1,10-phenanthroline (5,6-dmp, 3), 3,4,7,8-tetramethyl-1,10-phenanthroline (3,4,7,8-tmp, 4) or dipyrido[3,2-d:2',3'-f]quinoxaline (dpq, 5), and [Cu(sal)(phen)(NO3)]2 (2a) have been successfully isolated and characterized by elemental analysis and other spectral techniques. The DNA binding and cleavage properties of 1-5 have been explored by using various physical and biochemical methods. The coordination geometry around copper(II) in the X-ray structures of 1, 2, 2a and 4 is described as an elongated octahedron. The UV-Vis and EPR spectral and ESI-MS studies reveal that in solution the dinuclear complexes dissociate into essentially mononuclear [Cu(sal)(diimine)]+ species with square-based geometry. The absorption spectral titrations and competitive DNA binding studies reveal that the intrinsic DNA binding affinity of the complexes depends upon the diimine co-ligand and is of the order of dpq (5) > 3,4,7,8-tmp (4) > 5,6-dmp (3) > phen (2) > bpy (1). The complexes 2 and 5 are involved in a partial intercalative interaction with DNA base pairs, while 3 and 4 are involved in a hydrophobic interaction with DNA and 1 is involved in an electrostatic interaction with DNA, which is supported by viscosity studies. Interestingly, only 3 and 4 are selective in exhibiting a positive induced CD band (ICD) upon binding to DNA suggesting that they induce a B to A conformational change in DNA. All the complexes exhibit an oxidative DNA cleavage ability, which varies as 5 > 4 > 3 > 2 > 1. While 4 and 5 are unique in displaying prominent double-strand DNA cleavage even in the absence of an activator, 2 and 3 display only single-strand DNA cleavage. Interestingly, all the complexes exhibit oxidative double-strand DNA cleavage in the presence of ascorbic acid, with 4 and 5 showing a DNA cleavage activity more prominent than 1 and 2. The ability of the complexes to bind and cleave the protein BSA varies in the order, 4 > 3 > 5 > 2 > 1. Interestingly, 3 and 4 cleave the protein in the presence of H2O2 as an activator in a non-specific manner suggesting that they can act as chemical proteases. It is remarkable that all the complexes exhibit cytotoxicity against human breast cancer cell lines (MCF-7) with a potency more than the widely used drug cisplatin indicating that they have the potential to act as effective anticancer drugs in a time dependent manner. The morphological assessment data obtained by using Hoechst 33258 staining reveal that 3 and 4 induce apoptosis much more effectively than the other complexes. Also, the alkaline single-cell gel electrophoresis study (comet assay) suggests that the same complexes induce DNA fragmentation more efficiently than others.

New ruthenium(ii) arene complexes of anthracenyl-appended diazacycloalkanes: effect of ligand intercalation and hydrophobicity on DNA and protein binding and cleavage and cytotoxicity

A series of half-sandwich Ru(II) arene complexes of the type [Ru(η(6)-arene)(L)Cl](PF6) 1-4, where arene is benzene (1, 2) or p-cymene (3, 4) and L is N-methylhomopiperazine (L1) or 1-(anthracen-10-ylmethyl)-4-methylhomopiperazine (L2), has been isolated and characterized by using spectral methods. The X-ray crystal structures of 2, 3 and 4 reveal that the compounds possess a pseudo-octahedral "piano-stool" structure equipped with the arene ligand as the seat and the bidentate ligand and the chloride ion as the legs of the stool. The DNA binding affinity determined using absorption spectral titrations with CT DNA and competitive DNA binding studies varies as 4 > 2 > 3 > 1, depending upon both the arene and diazacycloalkane ligands. Complexes 2 and 4 with higher DNA binding affinities show strong hypochromism (56%) and a large red-shift (2, 10; 4, 11 nm), which reveals that the anthracenyl moiety of the ligand is stacked into the DNA base pairs and that the arene ligand hydrophobicity also dictates the DNA binding affinity. In contrast, the monocationic complexes 1 and 3 are involved in electrostatic binding in the minor groove of DNA. The enhancement in viscosities of CT DNA upon binding to 2 and 4 are higher than those for 1 and 3 supporting the DNA binding modes of interaction inferred. All the complexes cleave DNA effectively even in the absence of an external agent and the cleavage ability is enhanced in the presence of an activator like H2O2. Tryptophan quenching measurements suggest that the protein binding affinity of the complexes varies as 4 > 2 > 3 > 1, which is the same as that for DNA binding and that the fluorescence quenching of BSA occurs through a static mechanism. The positive ΔH(0) and ΔS(0) values for BSA binding of complexes indicate that the interaction between the complexes and BSA is mainly hydrophobic in nature and the energy transfer efficiency has been analysed according to the Förster non-radiative energy transfer theory. The variation in the ability of complexes to cleave BSA in the presence of H2O2, namely, 4 > 2 > 3 > 1, as revealed from SDS-PAGE is consistent with their strong hydrophobic interaction with the protein. The IC50 values of 1-4 (IC50: 1, 28.1; 2, 23.1; 3, 26.2; 4, 16.8 μM at 24 h; IC50: 1, 19.0; 2, 15.9; 3, 18.1; 4, 9.7 μM at 48 h) obtained for MCF 7 breast cancer cells indicate that they have the potency to kill cancer cells in a time dependent manner, which is similar to cisplatin. The anticancer activity of complexes has been studied by employing various biochemical methods involving different staining agents, AO/EB and Hoechst 33258, which reveal that complexes 1-4 establish a specific mode of cell death in MCF 7 breast cancer cells. The comet assay has been employed to determine the extent of DNA fragmentation in cancer cells.

Mixed ligand ruthenium(II) complexes of 5,6-dimethyl-1,10-phenanthroline: The role of ligand hydrophobicity on DNA binding of the complexes

A series of mixed ligand Ru(II) complexes of 5,6-dimethyl-1,10-phenanthroline (5,6-dmp) as primary ligand and 1,10-phenanthroline (phen), 2,2′-bipyridine (bpy), pyridine (py) and NH 3 as co-ligands have been prepared and characterized by X-ray crystallography, elemental analysis and 1H NMR and electronic absorption spectroscopy. The X-ray crystal structure of the complex [Ru(phen) 2(bpy)]Cl 2 reveals a distorted octahedral coordination geometry for the RuN 6 coordination sphere. The DNA binding constants obtained from the absorption spectral titrations decrease in the order, tris(5,6-dmp)Ru(II) > bis(5,6-dmp)Ru(II) > mono(5,6-dmp)Ru(II), which is consistent with the trend in apparent emission enhancement of the complexes on binding to DNA. These observations reveal that the DNA binding affinity of the complexes depend upon the number of 5,6-dmp ligands and hence the hydrophobic interaction of 5,6-dimethyl groups on the DNA surface, which is critical in determining the DNA binding affinity and the solvent accessibility of the exciplex. Among the bis(5,6-dmp)Ru(II) complexes, those with monodentate py ( 4) or NH 3 ( 5) co-ligands show DNA binding affinities slightly higher than the bpy and phen analogues. This reveals that they interact with DNA through the co-ligands while both the 5,6-dmp ligands interact with the exterior of the DNA surface. All these observations are supported by thermal denaturation and viscosity measurements. Two DNA binding modes – surface/electrostatic and strong hydrophobic/partial intercalative DNA interaction – are suggested for the mixed ligand complexes on the basis of time-resolved emission measurements. Interestingly, the 5,6-dmp ligands promote aggregation of the complexes on the DNA helix as a helical nanotemplate, as evidenced by induced CD signals in the UV region. The ionic strength variation experiments and competitive DNA binding studies on bis(5,6-dmp)Ru(II) complexes reveal that EthBr and the partially intercalated and kinetically inert [Ru(phen) 2(dppz)] 2+ (dppz = dipyrido[3,2- a:2′,3′- c]phenazine) complexes revert the CD signals induced by exciton coupling of the DNA-bound complexes with the free complexes in solution.

Interaction of rac-[Ru(5,6-dmp)3]2+ with DNA: Enantiospecific DNA Binding and Ligand-Promoted Exciton Coupling

The X-ray crystal structure of the complex rac-[Ru(5,6-dmp)(3)]Cl(2) (5,6-dmp = 5,6-dimethyl-1,10-phenanthroline) reveals a distorted octahedral coordination geometry with the Ru-N bond distances shorter than in its phen analogue. Absorption spectral titrations with CT DNA reveal that rac-[Ru(5,6-dmp)(3)](2+) interacts (K(b), (8.0 +/- 0.2) x 10(4) M(-1)) much more strongly than its phen analogue. The emission intensity of the 5,6-dmp complex is dramatically enhanced on binding to DNA, which is higher than that of the phen analogue. Also, interestingly, time-resolved emission measurements on the DNA-bound complex shows biexponential decay of the excited states with the lifetimes of short- and long-lived components being higher than those for the phen analogue. The CD spectral studies of rac-[Ru(5,6-dmp)(3)](2+) bound to CT DNA provide a definite and elegant evidence for the enantiospecific interaction of the complex with B-form DNA. Competitive DNA binding studies using rac-[Ru(phen)(3)](2+) provide support for the strong binding of the complex with DNA. The Delta-enantiomer of rac-[Ru(5,6-dmp)(3)](2+) binds specifically to the right-handed B-form of poly d(GC)(12) at lower ionic strength (0.05 M NaCl), and the Lambda-enantiomer binds specifically to the left-handed Z-form of poly d(GC)(12) generated by treating the B-form with 5 M NaCl. The strong electronic coupling of the DNA-bound complex with the unbound complex facilitates the change in its enantiospecificity upon changing the conformation of DNA. The (1)H NMR spectra of rac-[Ru(5,6-dmp)(3)](2+) bound to poly d(GC)(12) reveal that the complex closely interacts most possibly in the major grooves of DNA. Electrochemical studies using ITO electrode show that the 5,6-dmp complex stabilizes CT DNA from electrocatalytic oxidation of its guanine base more than the phen analogue does.

Mechanism of Gonadotropin Gene Expression: IDENTIFICATION OF A NOVEL NEGATIVE REGULATORY ELEMENT AT THE TRANSCRIPTION START SITE OF THE GLYCOPROTEIN HORMONE α-SUBUNIT GENE

Regulation of the glycoprotein hormone alpha-subunit (GPHalpha) gene has been studied extensively in pituitary and placental cell lines, but little is known of the transcriptional regulators important for its ectopic expression. To investigate the molecular basis for ectopic expression, it was critical to define cis-regulatory elements and their cognate trans-acting factors that modulate promoter activity in epithelial cell types that do not normally express GPH. DNA-mediated transient expression of promoter-reporter constructs was used to identify a novel negative regulatory element located at the GPHalpha gene transcription start site. Truncation or site-directed mutagenesis of this element produced up to a 10-fold increase in promoter activity. Electrophoretic mobility shift analysis detected a protein that binds specifically to a DNA motif encompassing the cap site. Based on competitive DNA binding studies with mutated oligonucleotides, it was determined that bases from -5 to -2 and +4 to +11 are critical for protein binding. The DNA sequence flanking the transcription start site from -9 to +11 is an imperfect palindrome; consequently, this motif is referred to as the cap site diad element (CSDE) and the cognate factor as the cap site-binding protein (CSBP). CSBP activity was present at different levels in nuclear extracts prepared from a variety of cell types. Significantly, the ratio of activities exhibited by the GPHalpha promoter with a mutated CSDE compared with the promoter with a wild-type CSDE was dependent on the transfected cell line and its content of CSBP. These results indicate that a negative regulatory element centered at the GPHalpha gene cap site and its cognate DNA-binding protein make a significant contribution to the production of alpha-subunit in a variety of tumor tissues. A detailed understanding of this cis/trans pair may further suggest a mechanism to explain, at least in part, how this gene becomes activated in nonendocrine tumors.

Similar DNA binding properties of free p70 (Ku) subunit and p70/p80 heterodimer

The Ku antigen consists of 70 and 80 kDa protein subunits (p70 and p80, respectively) that form the DNA binding component of a DNA-dependent protein kinase (DNA-PK). It is controversial whether the interaction of Ku with DNA is mediated by p70 alone or requires formation of p70/p80 dimers. In the present studies, the DNA binding properties of p70/p80 heterodimers and full-length human p70 expressed in the absence of p80 were investigated. The binding of free p70 and p70/p80 heterodimers to DNA showed similar sensitivity to high ionic strength buffers. Competitive DNA binding studies revealed that free p70, like the p70/p80 heterodimer, bound preferentially to linear double stranded DNA fragments, whereas tRNA and closed circular DNA molecules competed poorly with the radiolabeled linear DNA for binding to Ku. These studies suggest that free p70 and p70/p80 heterodimers have similar DNA binding properties, and that the interaction of Ku with DNA may depend primarily on the p70 subunit, possibly with implications for the assembly and function of DNA-PK.

Interaction of a Nuclear Factor-1-like Protein with the Regulatory Region of the Human Polyomavirus JC Virus

We have initiated a study to identify host proteins which interact with the regulatory region of the human polyomavirus JC (JCV), which is associated with the demyelinating disease, progressive multifocal leukoencephalopathy. We examined the interaction of nuclear proteins prepared from different cell lines with the JCV regulatory region by DNA binding gel retardation assays. Binding was detected with nuclear extracts prepared from human fetal glial cells, glioma cells, and HeLa cells. Little or no binding was detected with nuclear extracts prepared from human embryonic kidney cells. Competitive binding assays suggest that the nuclear factor(s) which interacted with the JCV regulatory region was different from those which interacted with the regulatory region of the closely related polyomavirus SV40. We found three areas in the JCV regulatory region protected from DNase I digestion: site A, located just upstream from the TATA sequence in the first 98-base pair (bp) repeat; site B, located upstream from the TATA sequence in the second 98-bp repeat; and site C, located just following the second 98-bp repeat. There were some differences in the ability of the nuclear factor(s) from the two brain cell lines and HeLa cells to completely protect the nucleotides within the footprint region. The results from the DNase I protective studies and competitive DNA binding studies with specific oligonucleotides, suggest that nuclear factor-1 or a nuclear factor-1-like factor is interacting with all three sites in the JCV regulatory region. In addition, the results suggest that the nuclear factor which interacts with the JCV regulatory region from human brain cell lines is different from the factor found in HeLa cells.