R.KpnI, an HNH superfamily REase, exhibits differential discrimination at non-canonical sequences in the presence of Ca2+ and Mg2+

KpnI REase recognizes palindromic sequence, GGTAC↓C, and forms complex in the absence of divalent metal ions, but requires the ions for DNA cleavage. Unlike most other REases, R.KpnI shows promiscuous DNA cleavage in the presence of Mg²⁺. Surprisingly, Ca²⁺ suppresses the Mg²⁺-mediated promiscuous activity and induces high fidelity cleavage. To further analyze these unique features of the enzyme, we have carried out DNA binding and kinetic analysis. The metal ions which exhibit disparate pattern of DNA cleavage have no role in DNA recognition. The enzyme binds to both canonical and non-canonical DNA with comparable affinity irrespective of the metal ions used. Further, Ca²⁺-imparted exquisite specificity of the enzyme is at the level of DNA cleavage and not at the binding step. With the canonical oligonucleotides, the cleavage rate of the enzyme was comparable for both Mg²⁺- and Mn²⁺-mediated reactions and was about three times slower with Ca²⁺. The enzyme discriminates non-canonical sequences poorly from the canonical sequence in Mg²⁺-mediated reactions unlike any other Type II REases, accounting for the promiscuous behavior. R.KpnI, thus displays properties akin to that of typical Type II REases and also endonucleases with degenerate specificity in its DNA recognition and cleavage properties.     

Structure-activity relationship on DNA binding and anticancer activities of a family of mixed-ligand oxidovanadium(V) hydrazone complexes

The title family of mixed-ligand oxidovanadium(V) hydrazone complexes are [V^VO(HL¹)(hq)] (1) and [V^VO(HL²)(hq)] (2), where (HL¹)^2? and (HL²)^2? are the dinegative form of 2-hydroxybenzoylhydrazone of acetylacetone (H₃L¹) and benzoylacetone (H₃L²), respectively, and hq^? is the mononegative form of 8-hydroxyquinoline (Hhq). Complexes were used to determine their binding constant with CT DNA using various spectroscopic techniques namely, electronic absorption, fluorescence and circular dichroism spectroscopy. The binding constant values suggest the intercalative mode of binding with the CT DNA and follow the order: 2 > 1. The bulky size as well as electron withdrawing property of the phenyl group (which is present in the β-diketone part of the hydrazone moiety in complex 2 in place of a CH₃ group in complex 1) is responsible for the higher activity of 2 than 1. Complexes were screened for cytotoxic activity on cervical cancer cells and were found to be potentially active (IC₅₀ value for 1 and 2 is 33 and 29 μM, respectively), even better than the widely used cis-platin (IC₅₀ = 63.5 μM) and carboplatin (IC₅₀ = > 200 μM) which is evident from the respective IC₅₀ value. Nuclear staining experiment suggests that these complexes kill the SiHa cancer cells through apoptotic mode. The molecular docking study also suggested the intercalative mode of binding of these complexes with CT DNA and HPV 18 DNA.     

Fluoroquinolones stimulate the DNA cleavage activity of topoisomerase IV by promoting the binding of Mg2 + to the second metal binding site

BackgroundFluoroquinolones target bacterial type IIA topoisomerases, DNA gyrase and topoisomerase IV (Topo IV). Fluoroquinolones trap a topoisomerase–DNA covalent complex as a topoisomerase–fluoroquinolone–DNA ternary complex and ternary complex formation is critical for their cytotoxicity. A divalent metal ion is required for type IIA topoisomerase-catalyzed strand breakage and religation reactions. Recent studies have suggested that type IIA topoisomerases use two metal ions, one structural and one catalytic, to carry out the strand breakage reaction.MethodsWe conducted a series of DNA cleavage assays to examine the effects of fluoroquinolones and quinazolinediones on Mg^2 +-, Mn^2 +-, or Ca^2 +-supported DNA cleavage activity of Escherichia coli Topo IV.ResultsIn the absence of any drug, 20–30 mM Mg^2 + was required for the maximum levels of the DNA cleavage activity of Topo IV, whereas approximately 1 mM of either Mn^2 + or Ca^2 + was sufficient to support the maximum levels of the DNA cleavage activity of Topo IV. Fluoroquinolones promoted the Topo IV-catalyzed strand breakage reaction at low Mg^2 + concentrations where Topo IV alone could not efficiently cleave DNA.Conclusions and general significanceAt low Mg^2 + concentrations, fluoroquinolones may stimulate the Topo IV-catalyzed strand breakage reaction by promoting Mg^2 + binding to metal binding site B through the structural distortion in DNA. As Mg^2 + concentration increases, fluoroquinolones may inhibit the religation reaction by either stabilizing Mg^2 + at site B or inhibition the binding of Mg^2 + to site A. This study provides a molecular basis of how fluoroquinolones stimulate the Topo IV-catalyzed strand breakage reaction by modulating Mg^2 + binding.     

Differences between Ca2+ and Mg2+ in DNA binding and release by the SfiI restriction endonuclease: implications for DNA looping

Many enzymes acting on DNA require Mg²⁺ ions not only for catalysis but also to bind DNA. Binding studies often employ Ca²⁺ as a substitute for Mg²⁺, to promote DNA binding whilst disallowing catalysis. The SfiI endonuclease requires divalent metal ions to bind DNA but, in contrast to many systems where Ca²⁺ mimics Mg²⁺, Ca²⁺ causes SfiI to bind DNA almost irreversibly. Equilibrium binding by wild-type SfiI cannot be conducted with Mg²⁺ present as the DNA is cleaved so, to study the effect of Mg²⁺ on DNA binding, two catalytically-inactive mutants were constructed. The mutants bound DNA in the presence of either Ca²⁺ or Mg²⁺ but, unlike wild-type SfiI with Ca²⁺, the binding was reversible. With both mutants, dissociation was slow with Ca²⁺ but was in one case much faster with Mg²⁺. Hence, Ca²⁺ can affect DNA binding differently from Mg²⁺. Moreover, SfiI is an archetypal system for DNA looping; on DNA with two recognition sites, it binds to both sites and loops out the intervening DNA. While the dynamics of looping cannot be measured with wild-type SfiI and Ca²⁺, it becomes accessible with the mutant and Mg²⁺.     

The influence of pH on the inhibition of DNA cleavages induced by pyrogallol

Abstract

Induction of DNA damage by pyrogallol has been shown at physiological pH, but mutagenesis data also suggest there is inhibition in acidic media. In the present work, the plasmid pBSK was incubated with pyrogallol, under aerobic conditions at 37°C, at pH 7.4, 4.5 or 3.5, for 1, 3 or 5 h, in the absence or presence of Cu²⁺. Cleavage of the supercoiled DNA form was analyzed through topology modifications by agarose gel electrophoresis and quantified by densitometry. Independently of the presence of Cu²⁺ , DNA cleavage at pH 7.4 was significantly (P < 0.001) induced and occurred extensively after 1-h incubation. At pH 4.5, the cleavage was significantly (P < 0.05) induced only after 5 h incubation in the absence of Cu²⁺ , but was extensive (P < 0.001) after 1-h incubation when the metal ion was present. At pH 3.5, DNA cleavage was inhibited (P > 0.05), after 5-h incubation, even in the presence of Cu²⁺. Our results provide evidence that DNA cleavage by pyrogallol is pH-dependent, catalyzed by Cu²⁺ , and extensively decreased in acidic pH. Due to the abundant presence of the pyrogallate ion in physiological media, we suggest that this conjugate base form is responsible for DNA cleavage.     

Thermodynamic stability and energetics of DNA duplexes containing major intrastrand cross-links of second-generation antitumor dinuclear PtII complexes

The effects of major DNA intrastrand cross-links of antitumor dinuclear Pt^II complexes [{trans-PtCl(NH₃)₂}₂-μ-{trans-(H₂N(CH₂)₆NH₂(CH₂)₂NH₂(CH₂)₆NH₂)}]⁴⁺ (1) and [{PtCl(DACH)}₂-μ-{H₂N(CH₂)₆NH₂(CH₂)₂NH₂(CH₂)₆NH₂)}]⁴⁺ (2) (DACH is 1,2-diaminocyclohexane) on DNA stability were studied with emphasis on thermodynamic origins of that stability. Oligodeoxyribonucleotide duplexes containing the single 1,2, 1,3, or 1,5 intrastrand cross-links at guanine residues in the central TGGT, TGTGT, or TGTTTGT sequences, respectively, were prepared and analyzed by differential scanning calorimetry. The unfolding of the platinated duplexes was accompanied by unfavorable free energy terms. The efficiency of the cross-links to thermodynamically destabilize the duplex depended on the number of base pairs separating the platinated bases. The trend was 1,5→1,2→1,3 cross-link of 1 and 1,5→1,3→1,2 cross-link of 2. Interestingly, the results showed that the capability of the cross-links to reduce the thermodynamic stability of DNA (ΔG ₂₉₈⁰) correlated with the extent of conformational distortions induced in DNA by various types of intrastrand cross-links of 1 or 2 determined by chemical probes of DNA conformation. We also examined the efficiency of the mammalian nucleotide excision repair systems to remove from DNA the intrastrand cross-links of 1 or 2. The efficiency of the excinucleases to remove the cross-links from DNA depended on the length of the cross-link; the trend was identical to that observed for the efficiency of the intrastrand cross-links to thermodynamically destabilize the duplex. Thus, the results are consistent with the thesis that an important factor that determines the susceptibility of the intrastrand cross-links of dinuclear platinum complexes 1 and 2 to be removed from DNA by nucleotide excision repair is the efficiency of these lesions to thermodynamically destabilize DNA.     

Synthesis of hydroxyferrocifen and its abilities to protect DNA and to scavenge radicals

Abstract  

The aim of this work was to clarify the effect of the position of the hydroxyl group on the antioxidant capacity of hydroxyferrocifen by means of a chemical kinetic method. Propionylferrocene and benzoylferrocene condensed with 4-hydroxydiphenylketone, 3,4-dihydroxydiphenylketone, and 4,4′-dihydroxydiphenylketone to form FP3, FP4, FB3, and FB4 with a single hydroxyl group and FP34, FP44, FB34, and FB44 with two hydroxyl groups. These hydroxyferrocifens were applied in Cu²⁺/glutathione (GSH)-induced, hydroxyl radical (·OH)-induced, and 2,2′-azobis(2-amidinopropane hydrochloride) (AAPH)-induced oxidation of DNA, and in trapping 2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonate) cationic radical (ABTS^+·). It was found that these hydroxyferrocifens acted as prooxidants in Cu²⁺/GSH-induced oxidation of DNA and exhibited very weak effects on ·OH-induced oxidation of DNA. FP3, FP4, FB3, and FB4 can only retard the rate of AAPH-induced oxidation of DNA, whereas FP44, FB44, FB34, and FP34 can trap 11.9, 7.1, 6.2, and 4.9 radicals, respectively, in AAPH-induced oxidation of DNA. The ability to trap ABTS^+· followed the order FB4 > FP44 > FB34 > FB44 > FP34. It was concluded that two hydroxyl groups at the para position of two benzene rings rather than at the ortho position in the same benzene ring were beneficial for hydroxyferrocifen to increase the antioxidant capacity.     

7-Deaza-2′-deoxyinosine: A Stable Nucleoside with the Ambiguous Base Pairing Properties of 2′-Deoxyinosine

Abstract

The base pairing ambiguity of 7-deaza-2′-deoxyinosine (c⁷I_d, 2) was studied and was found to be the same as that of 2′-deoxyinosine. The duplex stability decreases in the order [d(c⁷I-C) > d(c⁷I-A) > d(c⁷I-T) > d(c⁷I-G)]. Modified nucleosides were used to probe the various base pair motifs which were the same for dl and c⁷I_d. The 7-deazapurine nucleoside (2) is extremely stable against acid or base. As oligonucleotides can be prepared using phosphoramidite chemistry and DNA is accessible by enzymic polymerisation of the triphosphate of 2, the latter can be used as an universal nucleoside for the sequencing of DNA by chemical degradation and is otherwise a facile substitute of 2′-deoxyinosine when stability in acidic or alkaline solution is required.     

2-(3,5-Dibromo-4-hydroxyphenyl)imidazo[4,5-<Emphasis Type="Italic">f</Emphasis>][1,10]phenanthrolinoruthenium(II) complexes: synthesis,characterization, cytotoxicity,apoptosis, DNA-binding and antioxidant activity

A new ligand DBHIP and its two ruthenium(II) complexes [Ru(dmb)₂(DBHIP)](ClO₄)₂ (1) and [Ru(dmp)₂(DBHIP)](ClO₄)₂ (2) have been synthesized and characterized. The cytotoxicity of DBHIP and complexes 1 and 2 has been assessed by MTT assay. The apoptosis studies were carried out with acridine orange/ethidium bromide (AO/EB) staining methods. The binding behaviors of these complexes to calf thymus DNA (CT-DNA) were studied by absorption titration, viscosity measurements, thermal denaturation and photoactivated cleavage. The DNA-binding constants of complexes 1 and 2 were determined to be 8.64 ± 0.16 × 10⁴ (s = 1.34) and 2.79 ± 0.21 × 10⁴ (s = 2.17) M⁻¹. The results suggest that these complexes interact with DNA through intercalative mode. The studies on the mechanism of photocleavage demonstrate that superoxide anion radical (O₂ ^•–) and singlet oxygen (¹O₂) may play an important role in the DNA cleavage. The experiments on antioxidant activity show that these compounds also exhibit good antioxidant activity against hydroxyl radical (OH^•).     

Prevention by Ce3+ of DNA destruction caused by Hg2+ in fish intestine

The interactions between Hg²⁺, Ce³⁺, and the mixuure of Ce³⁺ and Hg²⁺, and DNA from fish intestine in vitro were investigated by using absorption spectrum and fluorescence emission spectrum. The ultraviolet absorption spectra indicated that the addition of Hg²⁺, Ce³⁺, and the mixture of Ce³⁺ and Hg²⁺ to DNA generated an obviously hypochromic effect. Meanwhile, the peak of DNA at 205.2 nm blue-shifted and at 258.2 nm red-shifted. The size of the hypochromic effect and the peak shift of DNA by metal ion treatments was Hg²⁺>Hg²⁺+Ce³⁺>Ce³⁺. The fluorescence emission spectra showed that with the addition of Hg²⁺, Ce³⁺, and the mixture of Ce³⁺ and Hg²⁺ the emission peak at about 416.2 nm of DNA did not obviously change, but the intensity reduced gradually and the sequence was Hg²⁺>Hg²⁺+Ce²⁺>Ce³⁺. Hg²⁺, Ce³⁺, and the mixture of Ce³⁺ and Hg²⁺ had 1.12, 0.19, and 0.41 binding sites to DNA, respectively; the fluorescence quenching of DNA caused by the metal ions all attributed to static quenching. The binding constants (K _A ) of binding siees were 8.98×10⁴ L/mol and 1.02×10⁴ L/mol, 5.12×10⁴ L/mol and 1.10×10³ L/mol, 6.66×10⁴ L/mol and 2.36×10³ L/mol, respectively. The results showed that Ce³⁺ could relieve the destruction of Hg²⁺ on the DNA structure.     

Reinvestigation of 4-Thiothymidine-5′-triphosphate Synthesis

Abstract

The 4-Thiothymidine-5′-triphosphate 1 (S⁴TTP) was known to be a substrate for polymerase, however a commercial sample of this compound failed to be incorporated into DNA. Mass spectrometry combined to alkaline phosphatase digestion and ³¹P-NMR showed that this sample was in fact 5′-chloro-5′-deoxy-4-thiothymidine-3′-triphosphate 2 . The desired S⁴TTP was synthesized by two alternate routes, was fully characterized and was shown to be incorporated in a DNA polymerase assay.     

Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA

BackgroundThe i-motif is a tetrameric DNA structure based on the formation of hemiprotonated cytosine-cytosine (C⁺.C) base pairs. i-motifs are widely used in nanotechnology. In biological systems, i-motifs are involved in gene regulation and in control of genome integrity. In vivo, the i-motif forming sequences are subjects of epigenetic modifications, particularly 5-cytosine methylation. In plants, natively occurring methylation patterns lead to a complex network of C⁺.C, ^5mC⁺.C and ^5mC⁺.^5mC base-pairs in the i-motif stem. The impact of complex methylation patterns (CMPs) on i-motif formation propensity is currently unknown.MethodsWe employed CD and UV-absorption spectroscopies, native PAGE, thermal denaturation and quantum-chemical calculations to analyse the effects of native, native-like, and non-native CMPs in the i-motif stem on the i-motif stability and pK_a.ResultsCMPs have strong influence on i-motif stability and pK_a and influence these parameters in sequence-specific manner. In contrast to a general belief, i) CMPs do not invariably stabilize the i-motif, and ii) when the CMPs do stabilize the i-motif, the extent of the stabilization depends (in a complex manner) on the number and pattern of symmetric ^5mC⁺.^5mC or asymmetric ^5mC⁺.C base pairs in the i-motif stem.ConclusionsCMPs can be effectively used to fine-tune i-motif properties. Our data support the notion of epigenetic modifications as a plausible control mechanism of i-motif formation in vivo.General SignificanceOur results have implications in epigenetic regulation of telomeric DNA in plants and highlight the potential and limitations of engineered patterning of cytosine methylations on the i-motif scaffold in nanotechnological applications.     

Synthesis and Hybridization Properties of Oligonucleotides Containing (2 S ,3 R )-9-(2,3,4-Trihydroxybutyl)Adenine

The synthesis and properties of oligonucleotides (ONs) containing 9-(2,3,4-trihydroxybutyl)adenine, A ^C2 and A ^C3, are described. The ON containing A ^C2 involves the 3′ → 4′ and 3′ → 5′ phosphodiester linkages in the strand, whereas that containing A ^C3 possesses the 3′ → 4′ and 2′ → 5′ phosphodiester linkages. It was found that incorporation of the analogs, A ^C2 or A ^C3, into ONs significantly reduces the thermal and thermodynamic stabilities of the ON/DNA duplexes, but does not largely decrease the thermal and thermodynamic stabilities of the ON/RNA duplexes as compared with the case of the ON/DNA duplexes. It was revealed that the base recognition ability of A ^C2 is greater than that of A ^C3 in the ON/RNA duplexes.     

Apoptotic signaling induced by H2O2-mediated oxidative stress in differentiated C2C12 myotubes

AimsApoptotic signaling proteins were evaluated in postmitotic skeletal myotubes to test the hypothesis that oxidative stress induced by H₂O₂ activates both caspase-dependent and caspase-independent apoptotic proteins in differentiated C2C12 myotubes. We hypothesized that oxidative stress would decrease anti-apoptotic protein levels in C2C12 myotubes.Main methodsApoptotic regulatory factors and apoptosis-associated proteins including Bcl-2, Bax, Apaf-1, XIAP, ARC, cleaved PARP, p53, p21^Cip1/Waf1, c-Myc, HSP70, CuZnSOD, and MnSOD protein content were measured by immunoblots.Key findingsH₂O₂ induced apoptosis in myotubes as shown by DNA laddering and an elevation of apoptotic DNA fragmentation. Cell death ELISA showed increase in the extent of apoptotic DNA fragmentation following treatment with H₂O₂. Treatment with 4 mM of H₂O₂ for 24 or 96 h caused increase in Bax (56%, 227%), cytochrome c (282%, 701%), Smac/DIABLO (155%, 260%), caspase-3 protease activity (51%, 141%), and nuclear and cytosolic p53 (719%, 1581%) levels in the myotubes. As an estimate of the mitochondrial AIF release to the cytosol, AIF protein content measured in the mitochondria-free cytosolic fraction was elevated by 65% after 96 h treatment with 4 mM of H₂O₂. AIF measured in the nuclear protein fraction increased by 74% and 352% following treatment with 4 mM of H₂O₂ for 24 and 96 h, respectively. Bcl-2 declined in myotubes by 61% and 69% after 24 or 96 h of treatment in 4 mM H₂O₂, respectively.SignificanceThese findings indicate that both caspase-dependent and caspase-independent mechanisms are involved in coordinating the activation of apoptosis induced by H₂O₂ in differentiated myotubes.     

Aflatoxin B1 and DNA Adducts. Proposed Model for Surface Noncovalent and Covalent Complexes with N(7) of Guanine. II.

Abstract

An alternate model for surface noncovalent and surface covalent binding of aflatoxin B₁ to N(7) of guanine in DNA is proposed. This model considers the out-of-plane motions of C(8) of aflatoxin B₁ in those interactions.

The covalent intercalated fit of aflatoxin B₁ into DNA arises from steric adjustments made by DNA at the covalent intercalation site as well as local strain in the bond angles about N(7) of guanine and C(8) of aflatoxin B₁. The bond angle about N(7) deviates modestly from the sp² value toward the sp³ value.

This study suggests that the surface covalent aflatoxin B₁ -DNA complex serves only a minor role in aflatoxin's precarcinogenic interaction with DNA and is a likely correctable error.     

Enhancement of a pentacyclic tyrosine kinase inhibitor production in Cladosporium cf. cladosporioides by Cladosporol

The binaphthyl derivative cladosporol 3 was supplied from 60 to 200 mg l⁻¹ to shaken cultures of Cladosporium cf. cladosporioides. Compared to blank, fungal biomass was not affected by adding cladosporol till 100 mg l⁻¹: it rather increased at higher ratios between 150 and 200 mg l⁻¹. The production of the major pentacyclic metabolite 1, a cytokine production and tyrosine kinase inhibitor, was enhanced tenfold when cladosporol was supplied at the highest ratio (200 mg l⁻¹) to shaken growing cultures of the fungus. The bioconversion of cladosporol to cladosporol D through reductive cleavage of the epoxide group was also observed. Interest in this kind of metabolites lies in their potential activity vs DNA topoisomerase I.     

Sensitivity of Bacteriophage RB69 DNA Polymerase to n2-(p-n-Butylphenyl)-2′-Deoxyguanosinenucleotides

Abstract

The response of bacteriophage RB69 DNA polymerase to N²-(p-n-butylphenyl)-2′-deoxyguanosine 5′-triphosphate (BuPdGTP), related nucleotides and non-nucleoside inhibitors was measured and compared to values obtained for the closely related DNA polymerase from bacteriophage T4. Both enzymes showed similar responses to inhibitors in terms of K_i values and the ability to utilize BuPdGTP as a substrate. These results provide the relevance of using the recent crystal structure of RB69 DNA polymerase for analysis of BuPdGTP/B family DNA polymerase interactions.