DNA Cleavage Agents Research Articles

2-Phenylquinoline–Carbohydrate Hybrids: Molecular Design, Chemical Synthesis, and Evaluation of a New Family of Light-Activatable DNA-Cleaving Agents

Artificial intercalator–carbohydrate hybrids such as that shown in the scheme cleave DNA at the site of guanine on irradiation with UV light with a long wavelength. The hybrids also exhibit strong cytotoxicity when irradiated. The hybrid system is very important for DNA cleavage, and the cytotoxic activity correlates with the DNA-cleaving capacity

Low-molecular-weight chromium-binding substance and biomimetic [Cr 3O(O 2CCH 2CH 3) 6(H 2O) 3] + do not cleave DNA under physiologically-relevant conditions

Chromium(III) tris(picolinate), Cr(pic) 3, is currently a very popular nutritional supplement; however, at physiologically-relevant concentrations, it has recently been demonstrated to cleave DNA [J.K. Speetjens, R.A. Collins, J.B. Vincent, S.A. Woski, Chem. Res. Toxicol. 12 (1999) 483]. A number of other chromium-containing compounds have been proposed as substitutes for Cr(pic) 3. Of particular interest are low-molecular-weight chromium-binding substance (LMWCr) and [Cr 3O(O 2CCH 2CH 3) 6(H 2O) 3] + 1. The former compound has recently been identified as the biologically active form of chromium in mammals, activating the kinase activity of insulin receptor in the presence of insulin. Complex 1 is a functional biomimetic for LMWCr. Both compounds have been proposed as possible nutritional supplements and therapeutics for adult-onset diabetes. This work demonstrates that these complexes, unlike Cr(pic) 3, are poor DNA-cleaving agents and may represent safer materials for human consumption.

Organization of Open Complexes at Escherichia coliPromoters: LOCATION OF PROMOTER DNA SITES CLOSE TO REGION 2.5 OF THE ς70 SUBUNIT OF RNA POLYMERASE

A cysteine-tethered DNA cleavage agent has been used to locate the position of region 2.5 of sigma70 in transcriptionally competent complexes between Escherichia coli RNA polymerase and promoters. In this study we have engineered sigma70 to introduce a unique cysteine residue at a number of positions in region 2.5. Mutant proteins were purified, and in each case, the single cysteine residue used as the target for covalent coupling of the DNA cleavage agent p-bromoacetamidobenzyl-EDTA.Fe (FeBABE). RNA polymerase core reconstituted with tagged sigma derivatives was shown to be transcriptionally active. Hydroxyl radical-based DNA cleavage mediated by tethered FeBABE was observed for each derivative of RNA polymerase in the open complex. Our results show that region 2.5 is in close proximity to promoter DNA just upstream of the -10 hexamer. This positioning is independent of promoter sequence. A model for the interaction of this region of sigma with promoter DNA is discussed.

The Interactions of Amino Acids and Peptides with DNA

DNA cleavage agents have received considerable attention for multiple purposes, such as the strategy for site-selective inhibition of gene expression. Small molecules with DNA cleavage activity are used as research tools for the investigation of nucleic acids structures. Examples of oxidative cleavage catalysts have been reported. Recently. much effort has been devoted to the development of DNA hydrolysis catalysts. More artificial catalysts for the hydrolysis of DNA are desirable for the extreme hydrolytic stability of the phosphodiester bonds of DNA.

Dithiolanone-oxide DNA-cleaving agents. Neighboring group assisted production of hydroxyl radicals: [formula omitted], City University of New York, Brooklyn College, Brooklyn, NY 11210

Dithiolanone-oxide DNA-cleaving agents. Neighboring group assisted production of hydroxyl radicals: [formula omitted], City University of New York, Brooklyn College, Brooklyn, NY 11210

Resveratrol as a new type of DNA-cleaving agent

The first demonstration of DNA cleavage by resveratrol ‘3,5,4′-trihydroxy- trans-stilbene’ is presented. Resveratrol mediated relaxation of pBR322 at micromolar concentrations in the presence of Cu 2+. Evidence is provided that resveratrol is capable of binding to DNA, and that the Cu 2+-dependent DNA damage is more likely caused by a copper-peroxide complex rather than by a freely diffusible oxygen species.

ChemInform Abstract: Ochratoxin A Acts as a Photoactivatable DNA Cleaving Agent

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Organometallic photonucleases: a novel class of DNA-cleaving agents.

The first demonstration of DNA cleavage by an organic radical generated via homolysis of a metal-alkyl bond in a Cp-metal complex is presented. Irradiation of CpW(CO)3CH3 (1.5 molecules/base pair) produced methyl radical, giving single-strand cleavage of pBR322 DNA. This process was inhibited by the general radical trap cysteine and by TEMPO, which traps carbon radicals but not oxygen-centered radicals.

Cytochrome c biogenesis is involved in the transposon Tn5‐mediated bleomycin resistance and the associated fitness effect in Escherichia coli

The transposon Tn5 ble gene and the Escherichia coli alkylation-inducible aidC locus are co-operatively involved in the resistance to the anti-cancer drug and DNA-cleaving agent bleomycin and enhance fitness of bacteria in the absence of the drug. In this report, we demonstrate that the aidC locus is identical to nrfG, the last gene of the nrf operon involved in the periplasmic formate-dependent nitrite reduction. In the presence of Ble, NrfG expression is specifically induced and restores both bleomycin resistance and its associated beneficial growth effect in an aidC- strain. In vitro DNA protection assays reveal that purified Ble prevents bleomycin-mediated DNA breakage, as do bleomycin-binding proteins. Similarities between haems of the cytochrome c biogenesis nrf pathway and iron bleomycin suggest a DNA repair-independent molecular mechanism for both bleomycin resistance and increased viability. The Ble protein binds bleomycin and prevents DNA breakage. It also induces the nrf locus that may assimilate bleomycin into haem for extracellular transport or inactivate bleomycin. Inactivation of potent DNA oxidants confers a better fitness to the bacterium carrying the transposon, suggesting a symbiotic relationship between host and transposon.

DNA cleavage by 7-methylbenzopentathiepin: a simple analog of the antitumor antibiotic varacin.

The compound 7-methylbenzopentathiepin, a simple analog of the benzopentathiepin antitumor antibiotic varacin, was shown to be a potent thiol-dependent DNA-cleaving agent. Biological experiments previously suggested that DNA cleavage might play a role in the cytotoxicity of varacin; however, this is the first direct evidence that benzopentathiepins can cause DNA strand breaks under physiologically relevant conditions.

Bidirectional binding of the TATA box binding protein to the TATA box.

By selective attachment of a DNA cleavage agent to specific residues in the yeast TATA box binding protein (yTBP), we demonstrate that, in solution, yTBP binds to the TATA boxes of both the adenovirus major late promoter and the yeast CYC1 promoter with only a modest preference in orientation and binds well to several overlapping binding sites. The general factors TFIIA and TFIIB each increase the rotational and translational selectivity of yTBP but are not sufficient, at least individually, to confer a unique polarity to the preinitiation complex. We conclude that TBP alone cannot define the productive orientation of general factor assembly on a promoter.

A Trapped Intermediate in the Copper(II)-Mediated Template Synthesis of an Amino Acid-Containing Ligand.

A transition metal ion-templating reaction that has been widely exploited for the synthesis of nitrogen macrocycles, sepulchrates, and linear tetradentate ligands is the template-directed Mannich condensation of carbon acid and aldehyde equivalents with amines. In the course of investigating the copper(II) template-directed synthesis of linear tetradentate amino acid-containing ligands for the design and synthesis of double-strand DNA cleavage agents, we have trapped and characterized an intermediate in the templating reaction. Condensation of bis(phenylalaninato)copper(II) with formaldehyde and nitroethane led to a nitro-substituent-bearing precursor complex that upon reduction is crystallographically characterized as ((2S)-5-amino-2-benzyl-6-hydroxy-5-methyl-3-azahexanoate)copper(II) (space group P2(1)2(1)2(1), a = 9.0066(5) Å, b = 11.1040(6) Å, c = 16.009(2) Å, alpha = beta = gamma = 90.0 degrees, Z = 4, R(1) = 0.0265, wR(2) = 0.0612). NMR investigation of the precursor complex and the precursor and product ligands shows that the templated ligands each contain only a single phenylalanine unit, not the two phenylalanine units expected on the basis of similar synthetic procedures. The structure of the reduced product confirms this conclusion and provides structural characterization of a template intermediate trapped during ligand assembly.

Development of arylhydrazines and diphenyl arylhydrazidophosphates as photo-induced DNA-cleaving agents

Single-strand cleavage of DNA in a sodium phosphate buffer at pH 7.4 has been accomplished by photolysis of various arylhydrazines or diphenyl arylhydrazidophosphates with 312 nm UV light; the new processes involve the generation of HO˙ and singlet oxygen, respectively.

Design of DNA-Cleaving Agents

Abstract The review focuses on the molecular design of artificial sequence-specific DNA-cleavers which have recently been developed in our laboratories. These include: DNA cleavers mimicking natural antitumor antibiotic like enediyne antibiotics, bleomycins, and kapurimycin A3. The design of photochemical DNA-cleaving molecules is also described. These are classified as: i) nonselective DNA cleavers, ii) thymine selective DNA cleavers, iii) photo-Fenton reagents, iv) photoinducible DNA alkylating agents, and v) DNA cleavers via photoinduced electrontransfer. The scope and limitation of these DNA-cleaving agents are described with a special emphasis on the concept and strategy for designing novel sequence-specific DNA cleavers, as well as on the mechanistic aspects of their DNA cleavage.

DNA damage and mutagenesis by radiomimetic DNA-cleaving agents: bleomycin, neocarzinostatin and other enediynes

Bleomycin and the enediyne antibiotics effect concerted, simultaneous site-specific free radical attack on sugar moieties in both strands of DNA, resulting in double-strand breaks of defined geometry and chemical structure, as well as abasic sites with closely opposed strand breaks. The hypersensitivity of several mammalian double-strand break repair-deficient mutants to these agents confirms the role of these double-strand breaks in mediating cytotoxicity. In bacteria, mutagenesis by both bleomycin and neocarzinostatin appears to result from replicative bypass of abasic sites, the repair of which is blocked by the presence of closely opposed strand breaks. However, in mammalian cells, such abasic sites decompose to form double-strand breaks, and mutagenesis consists primarily of small deletions, large deletions, and gene rearrangements, all of which probably result from errors in double-strand break repair by a nonhomologous end-joining mechanism. Studies with the radiomimetic antibiotics emphasize the importance of this end-joining repair pathway, and these agents provide useful probes of its mechanistic details, particularly the effects of chemically modified DNA termini on repair.

DNA-cleaving agents mimic leinamycin

Three simple analogs of the natural product leinamycin retain the DNA-cleaving activity of the more complex parent compound, according to chemists at the University of Missouri, Columbia. But questions remain about the detailed molecular mechanism by which leinamycin and its analogs damage DNA. Dithiolanone oxide analogs of leinamycin may prove useful as anticancer agents or reagents for nucleic acid manipulation, says Kent S. Gates, a professor in the departments of chemistry and biochemistry at UM Columbia. We have submitted several analogs for testing as potential anticancer agents, and a couple of companies have informally expressed interest in the compounds. Gates synthesized the leinamycin analogs with graduate students Saeid J. Behroozi, Woongki Kim, and Jeffrey Dannaldson. The team reported their work earlier this month in Biochemistry [35,1768 (1996)]. Leinamycin was first isolated from Streptomyces bacteria in the late 1980s by Hirofumi Nakano, head of the oncology drug discovery group, rese...

2,2'-Bis(aminomethyl)-4,4'-bithiazole as a New Cu(II)-Dependent DNA Cleaving Agent.

A simple and readily available DNA cleaving agent, 2,2'-bis(aminomethyl)-4,4'-bithiazole at 50 μM concentration showed a significant cleaving activity for plasmid DNA only in the presence of Cu(II) under physiological conditions without any reducing agents.

1,2-Dithiolan-3-one 1-oxides: a class of thiol-activated DNA-cleaving agents that are structurally related to the natural product leinamycin.

Leinamycin is a recently discovered, thiol-dependent DNA-cleaving natural product. The mechanism of DNA cleavage by leinamycin is unknown. Inspired by this intriguing natural product, we have investigated the DNA-cleaving properties of three 1,2-dithiolan-3-one 1-oxides (1-3) that are structurally related to the suspected DNA-cleaving "core" of leinamycin. It was found that, similar to leinamycin, these three 1,2-dithiolan-3-one 1-oxides are thiol-dependent DNA-cleaving agents. At the concentrations of 1-3 used in these experiments (approximately 100 microM), efficient DNA cleavage is absolutely dependent on added thiol, with optimum cleavage occurring at 5-10 equiv (500 microM-1 mM) of added thiol. 2-Mercaptoethanol, glutathione, dithiothreitol, and thiophenol function with approximately equal efficiency as triggering agents for the cleavage reaction. DNA cleavage by 1-3 is not highly pH-dependent. Cleavage of DNA by these sulfur heterocycles is diminished by the removal of molecular oxygen from the reaction medium, by the radical scavengers methanol, ethanol, and mannitol, and by the enzyme catalase. Superoxide dismutase does not suppress DNA cleavage by these compounds. When diethylenetriaminepentaacetic acid is employed in these reactions as a chelator of adventitious trace metal ions, DNA cleavage is efficiently inhibited. The S-deoxy analog of 1 does not cleave DNA under conditions where 1 effects efficient thiol-mediated cleavage of DNA. These experiments indicate that, in concert with thiols, 1,2-dithiolan-3-one 1-oxides convert molecular oxygen to DNA-cleaving oxygen radicals. The marked effect of catalase further suggests that molecular oxygen is converted to hydrogen peroxide which ultimately cleaves DNA via a trace metal-dependent Fenton reaction. This work demonstrates that 1,2-dithiolan-3-one 1-oxides represent a general class of thiol-potentiated DNA-cleaving molecules.

Photoelectron Spectroscopy of the Trimethylene- methane Negative Ion. The Singlet−Triplet Splitting of Trimethylenemethane

Few reactive organic intermediates have elicited as much attention by experimentalists and theorists as trimethylenemethane (TMM, 1).1,2 The theoretical significance of this archetypal non-Kekule molecule was recognized by Moffitt and Coulson nearly 50 years ago,3 and it has since inspired numerous computational studies spanning the entire gamut of theoretical methods. TMM serves as a paradigm for basic theoretical concepts such as free valence, disjoint orbital analysis, and negative spin density in π systems, and it has been a consistently challenging subject for electronic structure calculations.4 Although trimethylenemethanes were commonly invoked as intermediates in the formation and rearrangement of methylenecyclopropanes,5 little was known experimentally about these molecules until 1966, when Dowd6 reported the EPR spectrum for 1 isolated in a glassy matrix at 88 K. Subsequent work by Dowd and co-workers verified the triplet ground state with 3-fold (D3h) symmetry that had been predicted for TMM.7,8 Many elegant spectroscopic and chemical experiments with TMM by the Pittsburgh group1a and with monocyclic derivatives by Berson and co-workers at Yale University1b have elevated our understanding of trimethylenemethanes to a high level. Practical applications of TMM derivatives now include organic ferromagnets,9 synthetic reagents,10 and even DNA-cleaving agents.11 Recently, Maier and co-workers reported lowtemperature matrix IR spectra for triplet 1 and its d2, d4, and d6 isotopomers.12,13 In contrast to the wealth of information available for the ground state of 1, very little is known experimentally about the excited singlet states. Of fundamental importance is the energy difference between the lowest energy singlet and triplet states, i.e., the “singlet-triplet splitting”. Ab initio molecular orbital and valence-bond calculations predict values of 14-20 kcal/ mol for the energy splitting between the XA′2 state and the aB1 state, 1a, which has one methylene group twisted out of the plane of the molecule.14,15 The lowest energy singlet state

Triazole Photonucleases: A New Family of Light Activatable DNA Cleaving Agents

Triazole Photonucleases: A New Family of Light Activatable DNA Cleaving Agents