1,10-Phenanthroline-copper, a footprinting reagent for single-stranded regions of RNAs

Copper(II) and silver(I)-1,10-phenanthroline-5,6-dione complexes interact with double-stranded DNA: further evidence of their apparent multi-modal activity towards Pseudomonas aeruginosa

Tackling microbial resistance requires continuous efforts for the development of new molecules with novel mechanisms of action and potent antimicrobial activity. Our group has previously identified metal-based compounds, [Ag(1,10-phenanthroline-5,6-dione)₂]ClO₄ (Ag-phendione) and [Cu(1,10-phenanthroline-5,6-dione)₃](ClO₄)₂.4H₂O (Cu-phendione), with efficient antimicrobial action against multidrug-resistant species. Herein, we investigated the ability of Ag-phendione and Cu-phendione to bind with double-stranded DNA using a combination of in silico and in vitro approaches. Molecular docking revealed that both phendione derivatives can interact with the DNA by hydrogen bonding, hydrophobic and electrostatic interactions. Cu-phendione exhibited the highest binding affinity to either major (− 7.9 kcal/mol) or minor (− 7.2 kcal/mol) DNA grooves. In vitro competitive quenching assays involving duplex DNA with Hoechst 33258 or ethidium bromide demonstrated that Ag-phendione and Cu-phendione preferentially bind DNA in the minor grooves. The competitive ethidium bromide displacement technique revealed Cu-phendione has a higher binding affinity to DNA (K_app = 2.55 × 10⁶ M⁻¹) than Ag-phendione (K_app = 2.79 × 10⁵ M⁻¹) and phendione (K_app = 1.33 × 10⁵ M⁻¹). Cu-phendione induced topoisomerase I-mediated DNA relaxation of supercoiled plasmid DNA. Moreover, Cu-phendione was able to induce oxidative DNA injuries with the addition of free radical scavengers inhibiting DNA damage. Ag-phendione and Cu-phendione avidly displaced propidium iodide bound to DNA in permeabilized Pseudomonas aeruginosa cells in a dose-dependent manner as judged by flow cytometry. The treatment of P. aeruginosa with bactericidal concentrations of Cu-phendione (15 µM) induced DNA fragmentation as visualized by either agarose gel or TUNEL assays. Altogether, these results highlight a possible novel DNA-targeted mechanism by which phendione-containing complexes, in part, elicit toxicity toward the multidrug-resistant pathogen P. aeruginosa.

Transition-metal norharmane compounds as possible cytotoxic agents: New insights based on a coordination chemistry perspective

New first-row transition-metal compounds with the ligand norharmane (9H-Pyrido[3,4-b]indole; Hnor) are reported. The compounds have the general formula [M(LL)(Hnor)(NO₃)₂](MeOH)_0-1 (M=Co, Ni, Cu, Zn; LL=2,2'-bipyridyl (bpy), 1,10-phenanthroline (phen)) and have been characterized by physical and analytical methods. X-ray structural analysis revealed that the compound of formula [Cu(phen)(Hnor)(NO₃)₂], (1) has a distorted 6-coordinated octahedrally-based geometry, with a planar-based [CuN₃O] core, where Cu-L varies between 1.99 and 2.04Å and two weak axial CuO contacts (2.209 and 2.644Å) from two different nitrates. Based on spectroscopic similarities, the other compounds appear to have the same or very similar coordination geometries. The compounds showed clear cell growth inhibitory effects in two different cancer cell lines in vitro, with the copper and zinc complexes being the most toxic and in fact almost comparable to cisplatin. Flow-cytometry analysis confirmed induction of apoptosis in cancer cells treated with the compounds. Interestingly, co-incubation of the cells with metal complexes and CuCl₂ induced an increase in the cytotoxic effects, most likely due to the conversion of the metal compounds in the corresponding, and most active, copper analogues.

Ternary Zinc(II)-Dipeptide Complexes for the Hydrolytic Cleavage of DNA at Physiological pH

A series of Zn(II) complexes with cysteinylglycine (CysGly) and histidylserine (HisSer), and of CysGly and histidylphenylalanine (HisPhe) were investigated. Complex stabilities were determined potentiometrically, and binding geometries were probed by means of 1H-NMR spectroscopy, using Co(II) instead of Zn(II) as a spectroscopic marker. The ternary 1:1:1 complexes [Zn(II)(CysGly)(HisSer)] and [Zn(II)(CysGly)(HisPhe)] were shown by UV experiments, fluorescence titration, and gel electrophoresis to intercalate with DNA, and to hydrolytically cleave supercoiled DNA (form-I), partly also circular (form-II) DNA, under physiological conditions (37 degrees, H2O, pH 7.5).

Ribosomal localization of translation initiation factor IF2

Bacterial translation initiation factor IF2 is a GTP-binding protein that catalyzes binding of initiator fMet-tRNA in the ribosomal P site. The topographical localization of IF2 on the ribosomal subunits, a prerequisite for understanding the mechanism of initiation complex formation, has remained elusive. Here, we present a model for the positioning of IF2 in the 70S initiation complex as determined by cleavage of rRNA by the chemical nucleases Cu(II):1,10-orthophenanthroline and Fe(II):EDTA tethered to cysteine residues introduced into IF2. Two specific amino acids in the GII domain of IF2 are in proximity to helices H3, H4, H17, and H18 of 16S rRNA. Furthermore, the junction of the C-1 and C-2 domains is in proximity to H89 and the thiostrepton region of 23S rRNA. The docking is further constrained by the requisite proximity of the C-2 domain with P-site-bound tRNA and by the conserved GI domain of the IF2 with the large subunit's factor-binding center. Comparison of our present findings with previous data further suggests that the IF2 orientation on the 30S subunit changes during the transition from the 30S to 70S initiation complex.

DNA hydrolytic cleavage by the diiron(III) complex Fe(2)(DTPB)(mu-O)(mu-Ac)Cl(BF(4))(2): comparison with other binuclear transition metal complexes

The binuclear structure of Fe(2)(DTPB)(mu-O)(mu-Ac)Cl(BF(4))(2) (DTPB = 1,1,4,7,7-penta (2'-benzimidazol-2-ylmethyl)-triazaheptane, Ac = acetate) was characterized by UV-visible absorption and infrared spectra and NMR and ESR. The binding interaction of DNA with the diiron complex was examined spectroscopically. Supercoiled and linear DNA hydrolytic cleavage by the diiron complex is supported by the evidence from anaerobic reactions, free radical quenching, high performance liquid chromatography experiments, and enzymatic manipulation such as T4 ligase ligation, 5'-(32)P end-labeling, and footprinting analysis. The estimation of rate for the supercoiled DNA double strand cleavage shows one of the largest known rate enhancement factors, approximately 10(10) against DNA. Moreover, the DNA hydrolysis chemistry needs no coreactant such as hydrogen peroxide. The poor sequence-specific DNA cleavage indicated by the restriction analysis of the pBR322 DNA linearized by the diiron complex might be due to the diiron complex bound to DNA by a coordination of its two ferric ions to the DNA phosphate oxygens, as suggested by spectral characterizations. The hydrolysis chemistry for a variety of binuclear metal complexes including Fe(2)(DTPB)(mu-O)(mu-Ac)Cl(BF(4))(2) is compared. It is established that the dominant factors for the DNA hydrolysis activities of the binuclear metal complexes are the mu-oxo bridge, labile and anionic ligands, and open coordination site(s). Concerning the hydrolytic mechanisms, the diiron complex Fe(2)(DTPB)(mu-O)(mu-Ac)Cl(BF(4))(2) might share many points in common with the native purple acid phosphatases.

Artificial nucleases

The oxidation of DNA and RNA provides a facile approach for investigating the interaction of nucleic acids with proteins and oligonucleotides. In this article, we have outlined our understanding of the mechanism of DNA scission by 1,10-phenanthroline-copper(I) in the presence of hydrogen peroxide. We also discuss results obtained by using 1,10-phenanthroline-oligonucleotide conjugates in probing the size of the transcriptionally active open complex. Finally, we outline an effective method for converting DNA-binding proteins into site-specific modification agents by using 1,10-phenanthroline-copper(I).

A simple copper(II)-L-histidine system for efficient hydrolytic cleavage of DNA

Copper(II)-L-histidine complexes effectively promote the cleavage of plasmid DNA and dideoxynucleotide dApdA at physiological pH and temperature. Studies of the mechanism of plasmid DNA cleavage by added radical scavengers, using rigorously anaerobic experiments, analyses for malondialdehyde-like products, religation assays, and HPLC analyses, indicate that DNA cleavage mediated by Cu(L-His) occurs via a hydrolytic path. The hydrolytic cleavage rate constants at 37 degrees C are estimated to be 0.76 h-1 for the decrease of form I and 0.25 h-1 for the increase of form III. The phosphoimager picture reveals that Cu(L-His) cleaves DNA with a certain sequence specificity (preferentially at 5'-GT-3'). The dinucleotide hydrolysis shows, with [Cu(L-His)] = 0.8 mM, rate enhancement factors of > 10(8). Interestingly, histidine-metal ion interactions (with Cu(II), Ni(II), Zn(II), etc.) have been used for various applications, e.g., protein purification, cross-linking, and targeting proteins to lipid bilayers. Our findings may provide the basis for developing new applications and new ways to design more effective and useful catalysts for DNA cleavage. Cu(L-His) is one of only a few well-defined metal complexes demonstrated to hydrolytically cleave dideoxynucleotides and DNA.

Oxidation of guanines in the iron-responsive element RNA: similar structures from chemical modification and recent NMR studies

BACKGROUND

The translation or stability of the mRNAs from ferritin, maconitase, erythroid aminoevulinate synthase and the transferrin receptor is controlled by the binding of two iron regulatory proteins to a family of hairpin-forming RNA sequences called iron-responsive elements (IREs). The determination of high-resolution nuclear magnetic resonance (NMR) structures of IRE variants suggests an unusual hexaloop structure, leading to an intra-loop G-C base pair and a highly exposed loop guanine, and a special internal loop/bulge in the ferritin IRE involving a shift in base pairing not predicted with standard algorithms.

RESULTS

Cleavage of synthetic 55- and 30-mer RNA oligonucleotides corresponding to the ferritin IRE with complexes based on oxoruthenium(IV) shows enhanced reactivity at a hexaloop guanine and at a guanine adjacent to the internal loop/bulge with strong protection at a guanine in the internal loop/bulge. These results are consistent with the recent NMR structures. The synthetic 55-mer RNA binds the iron-regulatory protein from rabbit reticulocyte lysates. The DNA analogs of the 55- and 30-mers do not show the same reactivity pattern.

CONCLUSIONS

The chemical reactivity of the guanines in the ferritin IRE towards oxoruthenium(IV) supports the published NMR structures and the known oxidation chemistry of the metal complexes. The results constitute progress towards developing stand-alone chemical nucleases that reveal significant structural properties and provide results that can ultimately be used to constrain molecular modeling.

Chemical Nuclease Activity of 1,10-Phenanthroline-Copper. Isotopic Probes of Mechanism

The chemical nuclease 1,10-phenanthroline-copper cleaves DNA by oxidative attack on the deoxyribose moiety yielding 3'- and 5'-phosphomonoesters, free purine and pyrimidine, and 5-methylenefuranone as stable products. Kinetic isotope effects associated with deuterium substitution have been measured in an attempt to analyze the chemical mechanism of the scission reaction. A kinetic isotope effect of 2.7 is observed with completely perdeuterated DNA, which is substituted in the oxidatively sensitive deoxyribose moiety as well as in the bases. Surprisingly, no isotope effect is found upon cleavage of DNA deuterated in the thymidines at either C-1', C-2',2", or C-4', all positions from which hydrogen is lost during the course of the reaction, by either the 2:1 or the 1:1 1,10-phenanthroline-cuprous complexes. These results suggest that perdeuteration of DNA alters the ligand binding and/or conformational flexibility of the nucleic acid.

Scission of DNA at a preselected sequence using a single-strand-specific chemical nuclease

BACKGROUND

We were interested in developing a protocol for cleaving large DNAs specifically. Previous attempts to develop such methods have failed to work because of high levels of nonspecific background scission.

RESULTS

R-loop formation was chosen for sequence-specific targeting, a method of hybridization whereby an RNA displaces a DNA strand of identical sequence in 70% formamide using Watson-Crick base-pairing, leading to a three-stranded structure. R-loops are stabilized in aqueous solution by modifying the bases with chemical reagents. The R-loop was cleaved using a novel nuclease prepared from the Thr48-->Cys mutant of the single-strand-specific M-13 gene V protein (GVP), which was alkylated with 5-(iodoacetamido-beta-alanyl)1,10-phenanthroline. The cleavage products of the pGEM plasmid were cloned in to the pCR 2.1-TOPO vector. Adenovirus 2 DNA (35.8 kb; tenfold larger than the pGEM plasmid) was also cleaved quantitatively at a preselected sequence.

CONCLUSIONS

A new method for cleaving duplex DNA at any preselected sequence was developed. The cleavage method relies on the chemical conversion of M-13 GVP into a nuclease, reflecting GVP's specificity for single-stranded DNA. The GVP chimera is the first example of a semisynthetic secondary structure specific nuclease. The chemical nuclease activity of 1,10-phenanthroline-copper is uniquely suited to this technique because it oxidizes the deoxyribose moiety without generating diffusible intermediates, providing clonable DNA fragments. The protocol could be useful in generating large DNA fragments for mapping the contiguity of probes or defining the exon-intron structure of transcription units.

Footprinting RNA-protein complexes following gel retardation assays: application to the R-17-procoat-RNA and tat--TAR interactions

RNA-protein complexes isolated following a gel retardation assay can be footprinted within the gel matrix using the chemical nuclease activities of 4,7-dimethyl-, 5,6-dimethyl-, and 3,4,7,8-tetramethyl-1,10-phenanthroline-copper. These complexes are more reactive than 1,10-phenanthroline-copper but share its reaction preference for bulges and loops. The interaction of the coat protein of R-17 with its viral RNA target and tat- and tat-derived peptides with HIV TAR RNA have been studied. In both cases, the RNA sequence opposite a 2-3 nucleotide bulge are protected. Tat-derived peptides inhibit cleavage at sites which intact tat does not protect. These results are consistent with transcription studies which have suggested that truncation of tat increases nonspecific binding.