Hydrolysis of DNA by cerium(IV)/EDTA complex

Homogeneous solutions are formed from equimolar amounts of Ce(NH₄)₂(NO₃)₆ and EDTA. These solutions hydrolyze single-stranded DNA far more efficiently than double-stranded DNA. In contrast, Ce(IV) hydroxide gel, obtained in the absence of EDTA, hydrolyzes both single-stranded and double-stranded DNAs at almost the same rates. In order to achieve this substrate-specificity sufficiently, the mole ratio of EDTA to Ce(NH₄)₂(NO₃)₆ must be 1.0 or greater. By using this remarkable specificity of Ce(IV)/EDTA complex, gap-site in substrate DNA is selectively hydrolyzed. The scission-site is modulated by use of appropriate combination of oligonucleotide additives. The reactions have been kinetically analyzed.     

Artificial DNA cutters for DNA manipulation and genome engineering

This tutorial review provides recent developments in artificial cutters for site-selective scission of DNA with the focus on chemistry-based DNA cutters. They are useful tools for molecular biology and biotechnology, since their site-selectivity of scission is much higher than that of naturally occurring restriction enzymes and also their scission site is freely chosen. In order to prepare these cutters, a DNA-cutting molecule is combined with a sequence-recognizing molecule in a covalent or non-covalent way. At targeted sites in single-stranded and double-stranded DNAs, the scission occurs via either oxidative cleavage of nucleotides or hydrolysis of phosphodiester linkages. Among many successful examples, an artificial restriction DNA cutter, prepared from Ce(iv)/EDTA and pseudo-complementary peptide nucleic acid, hydrolyzed double-stranded DNA at the target site. The scission site and scission specificity are determined simply in terms of the Watson-Crick rule so that even the whole genome of human beings was selectively cut at one predetermined site. Consistently, homologous recombination in human cells was successfully promoted by this tool. For the purpose of comparison, protein-based DNA cutters (e.g., zinc finger nucleases) are also briefly described. The potential applications of these cutters and their future aspects are discussed.     

Metal ion-induced site-selective RNA hydrolysis by use of acridine-bearing oligonucleotide as cofactor

New types of noncovalent ribozyme-mimics for site-selective RNA scission are prepared by combining metal ions with oligonucleotides bearing an acridine. Lanthanide(III) ions and various divalent metal ions (Zn(II), Mn(II), Cu(II), Ni(II), Co(II), Mg(II), and Ca(II)) are employed without being bound to any sequence-recognizing moiety. The modified oligonucleotide forms a heteroduplex with the substrate RNA, and selectively activates the phosphodiester linkages in front of the acridine. As a result, these linkages are preferentially hydrolyzed over the others, even though the metal ions are not fixed anywhere. The scission is efficient under physiological conditions, irrespective of the sequence at the target site. Site-selective RNA scission is also successful with the combination of an oligonucleotide bearing an acridine at its terminus, another unmodified oligonucleotide, and the metal ion. In a proposed mechanism, the acridine pushes the unpaired ribonucleotide out of the heteroduplex and changes the conformation of RNA at the target site for the sequence-selective activation.     

A fluorescent molecular switch for room temperature operation based on oligonucleotide hybridization without labeling of probes or targets

A molecular switch was prepared by self-assembly. Neutravidin served as a template that allowed for a biotinylated probe oligonucleotide to be placed adjacent to a biotinylated long-chain linker that was terminated with thiazole orange (TO). Hybridization of probe oligonucleotide with target to form double-stranded DNA resulted in intercalation of the adjacent TO probe. This was a reversible process that could be tracked by fluorescence intensity changes. Formamide was used as a denaturant for double-stranded DNA, and could be used to depress thermal denaturation temperatures. In this work formamide had a dual function, providing for control of hybridization selectivity at room temperature, while concurrently ameliorating non-specific adsorption to improve signal-to-noise when using thiazole orange as a fluorescence signalling agent to determine oligonucleotide hybridization. Room temperature single nucleotide polymorphism (SNP) discrimination for oligonucleotide targets was achieved both in solution and for molecular switches that were immobilized onto optical fibers. In solution, a concentration of 18.5% formamide provided greater than 40-fold signal difference between single-stranded DNA and double-stranded DNA, in contrast to only a 2-fold difference in the absence of formamide. Selectivity for SNP determination in solution was demonstrated using targets of varying lengths including a 141-base PCR amplicon. The improved signal-to-noise achieved by use of formamide is likely due to preferential displacement of dye molecules that are otherwise electrostatically bound to the polyanionic nucleic acid backbone.     

Manipulation of Single‐Stranded DNA by Using an Artificial Site‐Selective DNA Cutter Composed of Cerium(IV)/EDTA and Phosphonate–Oligonucleotide Conjugates

An artificial site‐selective DNA cutter to hydrolyze single‐stranded DNA at a desired site was prepared from Ce^IV/ethylenediamintetraacetic acid (EDTA) and two ethylenediamine‐N,N,N′,N′‐tetrakis(methylenephosphonic acid)–oligonucleotide conjugates. By using this cutter, the sense strand of a blue fluorescent protein (BFP) gene was selectively cut at a predetermined site in the chromophore‐coding region. The upstream fragment obtained by the site‐selective scission was ligated with the downstream fragment of the closely related green fluorescent protein (GFP) gene so that the 5′‐ and 3′‐end portions of the chromophore came from the BFP fragment and the GFP fragment, respectively. The recombinant gene was successfully expressed in E. coli and the chimeric chromophore emitted green fluorescence as expected.     

Catalytic hydrolysis of peptides by cerium(IV)

Oligopeptides are efficiently hydrolyzed by Ce(IV) to the corresponding amino acids under mild conditions. The pseudo first-order rate constants for the hydrolysis of H-Gly-Phe-OH and H-Gly-Gly-OH at pH 7.0 and 50 degrees C are 3.5 x 10(-1) and 2.8 x 10(-1) h(-1), with [Ce(NH4)2(NO3)6]0=10mM (the half-lives are 2.0 and 2.5 h). The catalytic activity of the Ce(IV) is far greater than those of other lanthanide ions and non-lanthanide ions. No oxidative cleavage was observed under the reaction conditions. Catalytic turnover of the Ce(IV) was also evidenced. The hydrolysis is fast especially when the substrates have no metal-coordinating side chains. Tripeptides and tetrapeptides are hydrolyzed at the similar rates as the dipeptides. In the hydrolysis of tripeptides, the amide linkage near the N-terminus is preferentially hydrolyzed. Neither the N-carbobenzyloxy derivative nor the amide of H-Gly-Phe-OH is hydrolyzed to a measurable extent, showing that both the terminal amino group and the carboxylate are coordinated to the Ce(IV) ion. This complexation is further confirmed by 1H NMR spectroscopy. The Ce(IV) ion is therefore one of the most active catalysts for peptide hydrolysis.     

Design of a triple-helix-specific cleaving reagent

BACKGROUND: Double-helical DNA can be recognized sequence specifically by oligonucleotides that bind in the major groove, forming a local triple helix. Triplex-forming oligonucleotides are new tools in molecular and cellular biology and their development as gene-targeting drugs is under intensive study. Intramolecular triple-helical structures (H-DNA) are expected to play an important role in the control of gene expression. There are currently no good probes available for investigating triple-helical structures. We previously reported that a pentacyclic benzoquinoquinoxaline derivative (BQQ) can strongly stabilize triple helices. RESULTS: We have designed and synthesized the first triple-helix-specific DNA cleaving reagent by covalently attaching BQQ to ethylenediaminetetraacetic acid (EDTA). The intercalative binding of BQQ should position EDTA in the minor groove of the triple helix. In the presence of Fe(2+) and a reducing agent, the BQQ-EDTA conjugate can selectively cleave an 80 base pair (bp) DNA fragment at the site where an oligonucleotide binds to form a local triple helix. The selectivity of the BQQ-EDTA conjugate for a triplex structure was sufficiently high to induce oligonucleotide-directed DNA cleavage at a single site on a 2718 bp plasmid DNA. CONCLUSIONS: This new class of structure-directed DNA cleaving reagents could be useful for cleaving DNA at specific sequences in the presence of a site-specific, triple-helix-forming oligonucleotide and also for investigating triple-helical structures, such as H-DNA, which could play an important role in the control of gene expression in vivo.     

Efficient and specific strand scission of DNA by a dinuclear copper complex: comparative reactivity of complexes with linked tris(2-pyridylmethyl)amine moieties

The compound [Cu(II)(2)(D(1))(H(2)O)(2)](ClO(4))(4) (D(1) = dinucleating ligand with two tris(2-pyridylmethyl)amine units covalently linked in their 5-pyridyl positions by a -CH(2)CH(2)- bridge) selectively promotes cleavage of DNA on oligonucleotide strands that extend from the 3' side of frayed duplex structures at a site two residues displaced from the junction. The minimal requirements for reaction include a guanine in the n (i.e. first unpaired) position of the 3' overhang adjacent to the cleavage site and an adenine in the n position on the 5' overhang. Recognition and strand scission are independent of the nucleobase at the cleavage site. The necessary presence of both a reductant and dioxygen indicates that the intermediate responsible for cleavage is produced by the activation of dioxygen by a copper(I) form of the dinuclear complex. The lack of sensitivity to radical quenching agents and the high level of site selectivity in scission suggest a mechanism that does not involve a diffusible radical species. The multiple metal center exhibits a synergy to promote efficient cleavage as compared to the action of a mononuclear analogue [Cu(II)(TMPA)(H(2)O)](ClO(4))(2) (TMPA = tris(2-pyridylmethyl)amine) and [Cu(OP)(2)](2+) (OP = 1,10-phenanthroline) at equivalent copper ion concentrations. The dinuclear complex, [Cu(II)(2)(D(1))(H(2)O)(2)](ClO(4))(4), is even capable of mediating efficient specific strand scission at concentrations where [Cu(OP)(2)](2+) does not detectably modify DNA. The unique coordination and reactivity properties of [Cu(II)(2)(D(1))(H(2)O)(2)](ClO(4))(4) are critical for its efficiency and site selectivity since an analogue, [Cu(II)(2)(DO)(Cl(2))](ClO(4))(2), where DO is a dinucleating ligand very similar to D(1), but with a -CH(2)OCH(2)- bridge, exhibits only nonselective cleavage of DNA. The differences in the reactivity of these two complexes with DNA and their previously established interaction with dioxygen suggest that specific strand scission is a function of the orientation of a reactive intermediate.     

Aqueous polymerization of acrylamide initiated by cerium (IV)–ethylenediamine tetraacetic acid redox system

Ethylenediamine tetraacetic acid (EDTA) terminated polyacrylamide was obtained by using the EDTA–cerium(IV) ammonium nitrate [Ce(IV)] redox initiator in the aqueous polymerization of acrylamide. The polymerization behaviors as a function of the concentration of Ce(IV), EDTA, and acrylamide as well as temperature were studied. The consumption rate of cerium(IV) depends a first-order reaction on the ceric ion concentration ([Ce(IV)]). The complex formation constant (K) and disproportionation constant (k_d) of Ce(IV)–EDTA chelated complex are 1.67 × 10⁴ and 3.77 × 10^?3, respectively. The rate dependences of polymerization on monomer concentration and EDTA concentration both follow a second-order reaction in the run of initial monomer concentration ([M]_i) equal to 0.2 mol dm^?3. The number average molecular weight increases linearly with the ratio of [M]_i/[Ce(IV)]_i. The mechanism and kinetics for the polymerization was proposed. The kinetic parameters involved were determined. © 1992 John Wiley & Sons, Inc.     

The oxidative decarboxylation of polyaminocarboxylic acids

Summary The reaction between Ce(IV) and EDTA was followed titrimetrically and spectrophotometrically, and was found to occur in stages. Four equivalents of Ce(IV) are reduced per mole of EDTA almost instantaneously at room temperature. With increasing temperature and reaction time an ultimate of about 14 equivalents of Ce (IV) is consumed per mole of EDTA. Carbon dioxide, formaldehyde, and other yet unidentified compounds are the products of oxidation of EDTA. The kinetics of the reaction in aqueous sulfuric acid was studied over the temperature range 11.7°–40°C by a spectrophotometric technique. The effects of the acidity of the medium and of added salts are reported.

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Oxydative Decarboxylierung von PolyaminocarbonsäurenI. Untersuchung der Reaktion von ÄDTE mit Ce(IV) in saurer Lösung

Zusammenfassung Die Reaktion zwischen Ce(IV) und ÄDTE wurde volumetrisch und spektroskopisch (UV) verfolgt. Dabei wurde gefunden, daß die Reaktion in Stufen verläuft. Bei Zimmertemperatur wurden vier Äquivalente Ce(IV) je Mol ÄDTE beinahe sofort reduziert. Mit zunehmender Temperatur und Reaktionszeit wurden bis zu 14 Äquivalente Ce(IV) je Mol ÄDTE verbraucht. Die Oxydationsprodukte von ÄDTE sind Kohlendioxid, Formaldehyd und andere noch nicht identifizierte Verbindungen. Die Reaktionskinetik in wäßriger Schwefelsäure wurde spektroskopisch (UV) im Temperaturbereich von 11,7°–40°C untersucht. Die Einflüsse der Acidität der Lösung und der zugefügten Salze werden angegeben.

     

Cleavage of Nucleotides by Lanthanide Metal Complexes

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Simultaneous genotyping of indels and SNPs by mass spectroscopy

Nucleotide insertion/deletion polymorphisms (indels) in ApoE gene were precisely genotyped using artificial ribonucleases and MALDI-TOF MS. The RNA fragments for MS analysis were prepared by treating RNA specimens with our artificial ribonucleases, which consist of LuCl(3) (molecular scissors) and oligonucleotides bearing two acridine groups (RNA-activator for site-selective scission). RNA scission by Lu(III) ion always occurred at the phosphodiester linkages in front of the two acridines, even when the RNA specimens involved consecutive cytidine sequences of different lengths. Thus, even complicated mixtures of these indel specimens were completely genotyped by using only one acridine-bearing oligonucleotide and by subjecting the reaction mixture to single MS measurement. Moreover, single nucleotide polymorphism (SNP) in the consecutive sequences could be genotyped simultaneously with the indels.     

Free solution mobility of DNA molecules containing variable numbers of cationic phosphoramidate internucleoside linkages

The free solution electrophoretic mobility of an 118-base pair DNA fragment containing zero, three, six or nine cationic phosphoramidate internucleoside linkages has been measured by capillary electrophoresis. The electrophoretic mobility decreases with the increasing number of cationic phosphoramidate linkages, as expected because of the reduced negative charge on the DNA molecules. The decrease in mobility is approximately linear for DNA molecules containing three and six cationic phosphoramidate linkages, but begins to level off when nine cationic phosphoramidate linkages have been added. The mobility also varies somewhat depending on whether the modified phosphoramidate linkages are located at the 5'- or 3'-end of the DNA molecule.     

PostExcision Events in Human Nucleotide Excision Repair

The nucleotide excision repair system removes a wide variety of DNA lesions from the human genome, including photoproducts induced by ultraviolet (UV) wavelengths of sunlight. A defining feature of nucleotide excision repair is its dual incision mechanism, in which two nucleolytic incision events on the damaged strand of DNA at sites bracketing the lesion generate a damage‐containing DNA oligonucleotide and a single‐stranded DNA gap approximately 30 nucleotides in length. Although the early events of nucleotide excision repair, which include lesion recognition and the dual incisions, have been explored in detail and are reasonably well understood, the fate of the single‐stranded DNA gaps and excised oligonucleotide products of repair have not been as extensively examined. In this review, recent findings that address these less‐explored aspects of nucleotide excision repair are discussed and support the concept that postincision gap and excised oligonucleotide processing are critical steps in the cellular response to DNA damage induced by UV light and other environmental carcinogens. Defects in these latter stages of repair lead to cell death and other DNA damage signaling responses and may therefore contribute to a number of human disease states associated with exposure to UV wavelengths of sunlight, including skin cancer, aging and autoimmunity.     

DNA analysis by application of Pt nanoparticle electrochemical amplification with single label response

This study demonstrates a highly sensitive sensing scheme for the detection of low concentrations of DNA, in principle down to the single biomolecule level. The previously developed technique of electrochemical current amplification for detection of single nanoparticle (NP) collisions at an ultramicroelectrode (UME) has been employed to determine DNA. The Pt NP/Au UME/hydrazine oxidation reaction was employed, and individual NP collision events were monitored. The Pt NP was modified with a 20-base oligonucleotide with a C6 spacer thiol (detection probe), and the Au UME was modified with a 16-base oligonucleotide with a C6 spacer thiol (capture probe). The presence of a target oligonucleotide (31 base) that hybridized with both capture and detection probes brought a Pt NP on the electrode surface, where the resulting electrochemical oxidation of hydrazine resulted in a current response.     

Base excision repair synthesis of DNA containing 8-oxoguanine in Escherichia coli

8-oxo-7,8-dihydroguanine (8-oxo-G) in DNA is a mutagenic adduct formed by reactive oxygen species. In Escherichia coli, 2,6-dihydroxy-5N-formamidopyrimidine (Fapy)-DNA glycosylase (Fpg) removes this mutagenic adduct from DNA. In this report, we demonstrate base excision repair (BER) synthesis of DNA containing 8-oxo-G with Fpg in vitro. Fpg cut the oligonucleotide at the site of 8-oxo-G, producing one nucleotide gap with 3' and 5' phosphate termini. Next, 3' phosphatase(s) in the supernatant obtained by precipitating a crude extract of E. coli with 40% ammonium sulfate, removed the 3' phosphate group at the gap, thus exposing the 3' hydroxyl group to prime DNA synthesis. DNA polymerase and DNA ligase then completed the repair. These results indicate the biological significance of the glycosylase and apurinic/ apyrimidinic (AP) lyase activities of Fpg, in concert with 3' phosphatase(s) to create an appropriately gapped substrate for efficient BER synthesis of DNA containing 8-oxo-G.     

Effects of TEMED and EDTA on the structural and mechanical properties of NIPAAm/Na+MMT composite hydrogels

N‐isopropyl acrylamide (NIPAAm) hydrogels are known as thermosensitive crosslinked polymer networks. In this work, the network parameters of their composites, i.e., NIPAAm/sodium montmorillonite (NIPAAm/Na⁺MMT) hydrogels synthesized by free radical solution polymerization in the presence of two different types of accelerator (tetramethyl ethylenediamine (TEMED) and ethylenediamine tetraacetic acid (EDTA)) and initiator (potassium persulphate (K₂S₂O₈) and cerium ammonium nitrate ((NH₄)₂Ce(NO₃)₆), Ce(IV)) using five different clay content (in the range of 1.0–5.0 wt % of total monomer concentration) at 25 °C were presented and discussed. FTIR spectra, XRD patterns, SEM photographs, and network parameters of the samples indicated that the presence of COOH groups on EDTA molecules was resulted in the formation of exfoliated structures and the activity of EDTA/KPS redox pair was higher than those of TEMED/KPS and EDTA/Ce (IV) pairs. The compression moduli (G) of the hydrogels initiated with EDTA/Ce(IV) redox pair showed smooth and continual changings with increase in Na⁺MMT content (for swelling equilibrium at 25 °C) on the contrary of EDTA/KPS and TEMED/KPS pairs. It might be related to low initiator efficiency of cerium ammonium nitrate than KPS molecules, having higher effective crosslinking density with increasing clay content. On the other hand, the G moduli of NIPAAm/Na⁺MMT hydrogels (above their phase transition temperature) initiated with TEMED/KPS redox pair were higher than the others because of the more hydrophobic nature of TEMED molecules. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1256–1264, 2010     

Deep adsorptive desulfurization over Cu,Ce bimetal ion-exchanged Y-typed molecule sieve

In this paper, Ce(IV)–Y, Cu(II)–Y and Cu(II)–Ce(IV)–Y adsorbents were prepared by the liquid-phase ion-exchange Y zeolites with combined Cu and Ce ions at low temperature and room pressure. The adsorbents were characterized by means of X-ray diffraction, N₂-adsorption specific surface area measurements (BET), X-ray photoelectron spectroscopy, Pyridine adsorption infrared spectroscopy and Fourier transform infrared. The adsorptive desulfurization properties of these three adsorbents were studied in a fixed-bed unit through a model gasoline which made up of 1-octane solution of the refractory sulfur compounds (Such as thiophene and benzothiophene) and a certain amount of toluene or cyclohexene. The results indicate that Cu(II)–Ce(IV)–Y bind the organic sulfur compounds through two types of adsorption modes: π-complexation and direct sulfur–adsorbent interaction. The adsorption selectivity of sulfur compounds onto Cu(II)–Ce(IV)–Y decreased in the order: benzothiophene > 2,5-dimethylthiophene > 3-methylthiophene > thiophene. The effect of competition components on the metal ion-exchanged Y zeolites for sulfur removal in the order: cyclohexene > toluene. The Cu(II)–Ce(IV)–Y possesses the high sulfur adsorption capacity similar to Cu(II)–Y and high selectivity for sulfur compounds similar to Ce(IV)–Y, which can be attributed to the synergistic interaction between Cu²⁺ and Ce⁴⁺.     

Analysis of polymerase chain reaction-product by capillary electrophoresis with laser-induced fluorescence detection and its application to the diagnosis of medium-chain acyl-coenzyme A dehydrogenase deficiency

Capillary gel electrophoresis with laser-induced fluorescence (CGE-LIF) has been developed to detect polymerase chain reaction (PCR) amplified samples. LIF detection was performed using Thiazole Orange as the fluorescent intercalating dye. This method was ca. 100X as sensitive as that with UV detection. The highly sensitive CGE-LIF was applied to the detection of the most prevalent mutation (lysine³²⁹- to-glutamic acid substitution) in medium-chain acyl-coenzyme A dehydrogenase (MCAD) deficiency. The disorder, which shows an autosomal recessive inheritance, is known to be highly prevalent among Caucasian population and often mimics as Reye-like syndrome or sudden infant death.

A DNA fragment containing the mutation site was PCR-amplified with two sets of allele specific oligonucleotide primers, followed by CGE-LIF. The mutant allele produced a 175-base pairs DNA fragment, which the normal allele generated a 202-base pairs DNA fragment. CGE-LIF clearly distinguished these PCR products, facilitating rapid diagnosis of MCAD deficiency.