Cholesterol and its fatty acid esters in native DNA preparations: lipid analysis,computer simulation of their interaction with DNA and cholesterol binding to immobilized oligodeoxyribonucleotides

Supramolecular DNA complexes were isolated from rat normal cells and murine tumors. The content of DNA-bound lipids (cholesterol and its esters) was determined. The content of cholesterol esters is higher than that of free cholesterol; the lipid content in tumor cells is higher than in normal cells. Using the molecular mechanics approach, it is demonstrated for the first time that cholesterol and its esters with stearic, oleic, linoleic, and linolenic acids bind to the DNA minor groove more strongly than with the major groove. The calculated DNA binding energies of cholesterol and its esters depend on both the number of double bonds in the fatty acid residue and on the DNA nucleotide composition. The formation of stable complexes between cholesterol molecules and d(AT)-rich oligonucleotides was demonstrated using biological microchip containing immobilized octadeoxyribonucleotides. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 2138–2144, September, 2005.     

Hydrogen-bonding interaction of urea with DNA bases: A density functional theory study

This work deals with the interaction between urea and DNA bases (adenine, thymine, guanine, and cytosine). The optimized geometries, binding energies, and harmonic vibrational frequencies are calculated using the DFT/B3LYP functional combined with the 6–31+G(d,p) basis set. Their interactions are studied aiming to understand more about the nature of the intercalation binding forces between urea and DNA. Fourteen stable complexes are found on the potential energy surface. The structures are cyclic; they are stabilized by NH...O/N and CH...O interactions. The binding energies range from −19.9 kJ·mol⁻¹ to −74.0 kJ·mol⁻¹. The obtained formation energies indicate that Urea:G and Urea:C are more favorable than Urea:T and Urea:A. In addition, the Atoms in Molecules theory is performed to study the hydrogen bonds in the complexes.     

The influence of serum fatty acid binding proteins on arachidonic acid uptake by macrophages

The role of serum fatty acid binding proteins (FABPs) in arachidonic acid (AA) uptake by murine peritoneal macrophages has been studied. The kinetics of [³H]arachidonic acid uptake by the cells was investigated over a wide range of AA concentration (10⁻¹⁰–10⁻⁵ M). It was shown that these putative fatty acid transporters dramatically change the uptake processes. In the presence of FABPs, the time-course curves of AA uptake exhibited two distinct periods: one with a rapid AA uptake during the first hour with an equilibrium in 1–2.5 h and another with an equilibrium reached in 20 h, whereas in the absence of FABPs the uptake curves were smooth without kinks and with the equilibrium reached in 10 h. In addition, it was shown that the amount of incorporated AA was linearly dependent on the concentration of AA over the range of 10⁻¹⁰–10⁻⁶ M in the presence of serum FABPs and 10⁻¹⁰–10⁻⁷ M in their absence. We assume that the changes in the character of AA uptake by macrophages in the presence of FABP soccur due to the interaction of FABPs with the cell plasma membrane.     

Study of non-covalent interactions of luotonin A derivatives and the DNA minor groove as a first step in the study of their analytical potential as DNA probes

The interaction between DNA and several newly synthesized derivatives of the natural anticancer compound luotonin A has been studied. The results from our work reveal an effective and selective alkaloid/double-stranded DNA (ds-DNA) interaction. In the presence of increasing amounts of ds-DNA, a noticeable fluorescence quenching of the luotonin A derivatives under study was observed. However, this effect did not take place when single-stranded DNA (ss-DNA) was employed. The association constant alkaloids/ds-DNA was calculated by quantitation of such a quenching effect. The influence of other quenchers, namely Co²⁺ and Br⁻ on the native fluorescence of luotonin A and derivatives was also studied, and a remarkable quenching effect was observed for both ions. We have also investigated how by binding DNA the alkaloids could get protected from the external Co²⁺ and Br⁻ quenchers. The Stern–Volmer constants (K _SV) for Co²⁺ and Br⁻ quenching effect on the studied alkaloids were considerably reduced (10–50%) after incubation of the compounds in the presence of DNA with regard to the K _SV values in absence of DNA. An increase in the fluorescence anisotropy values of luotonins was also produced only in the presence of ds-DNA but not in the case of ss-DNA. To better characterize the nature of that interaction, viscosimetry assays and ethidium bromide displacement studies were conducted. With regard to DNA reference solutions, the viscosity of solutions containing DNA and luotonin A derivatives was reduced or not significantly increased. It was also observed that the studied compounds were unable to displace the intercalating agent ethidium bromide. All of these results, together with the obtained association constants values (K _ass = 2.2 × 10² – 1.3 × 10³), support that neither covalent nor intercalating interactions luotonin A derivatives/ds-DNA are produced, leading to the conclusion that these alkaloids bind ds-DNA through the minor groove. The specific changes in the fluorescence behavior of luotonin A and derivatives distinguishing between ss-DNA and ds-DNA binding, lead us to propose these compounds as attractive turn-off probes to detect DNA hybridization.     

Production of biodiesel by immobilized Candida sp. lipase at high water content

A new process for enzymatic synthesis of biodiesel at high water content (10–20%) with 96% conversion by lipase from Candida sp. 99–125 was studied. The lipase, a no-position-specific lipase, was immobilized by a cheap cotton membrane and the membrane-immobilized lipase could be used at least six times with high conversion. The immobilized lipase could be used for different oil conversion and preferred unsaturated fatty acids such as oleic acid to staturated fatty acids such as palmitic acid. The changes in concentration of fatty acids, diglycerides, and methyl esters in the reaction were studied and a mechanism of synthesis of biodiesel was suggested: the triglycerides are first enzymatically hydrolyzed into fatty acids, and then these fatty acids are further converted into methyl esters.     

Biophysical, spectroscopic vis-à-vis biochemical investigation on DNA–metalloprotein interaction: a model study involving cobalt(II)-glutathione complex

Abstract  

The interaction of cobalt(II)-glutathione (CoGSH) with deoxyribonucleic acid (DNA) has been studied by UV–vis, fluorescence, circular dichroism (CD), thin-film infrared (IR), and viscometric techniques. From the UV-spectroscopic method, binding constant (K _b) was determined and was found to be 2.3 × 10⁶ M⁻¹. In fluorimetric analysis, the quenching of fluorescence intensity of DNA bound to ethidium bromide (EB) was investigated. The Stern–Volmer quenching constant (K _sv) was also estimated from this study and was found to be 2.8 × 10⁶ M⁻¹at 37 °C. The solution CD spectra of DNA and DNA–CoGSH indicate that in each case, DNA exists in the ‘B’ conformation and suggested an intercalative binding mode. Thin-film IR data also reveal that DNA attains the ‘B’ family of conformations after interaction with CoGSH complex. The increase in DNA viscosity in the presence of CoGSH complexes is attributed to the lengthening of DNA helix due to intercalation.     

Molecular modeling of the binding mode of chiral metal complexes δ- and ∧-[Co(phen)2dppz]3+with B-DNA

Molecular modeling methods have been applied to the structural characterization of the interaction between chiral metal complexes [Co(phen)₂dppz]³⁺ (where phen = 1, 10-phenanthroline, dppz = dipyrido[3,2-a: 2′, 3′ -c]phenazine) and the oligonucleotide (B-DNA fragment). The natures of two kinds of the binding modes, which are currently intense controversy, have been explored. Barton proposed that there is enantio-selective DNA binding by the octahedral complexes and intercalative access by these complexes from the major groove; but Norden suggested that both enantiomers bind extremely strongly to DNA from the minor groove without any noticeable enantio-selectivity. Our results support and extend structural models based upon Norden’s studies, and conflict with Barton’ model.     

Biophysical,spectroscopic vis-à-vis biochemical investigation on DNA–metalloprotein interaction: a model study involving cobalt(II)-glutathione complex

Abstract  The interaction of cobalt(II)-glutathione (CoGSH) with deoxyribonucleic acid (DNA) has been studied by UV–vis, fluorescence, circular dichroism (CD), thin-film infrared (IR), and viscometric techniques. From the UV-spectroscopic method, binding constant (K _b) was determined and was found to be 2.3 × 10⁶ M⁻¹. In fluorimetric analysis, the quenching of fluorescence intensity of DNA bound to ethidium bromide (EB) was investigated. The Stern–Volmer quenching constant (K _sv) was also estimated from this study and was found to be 2.8 × 10⁶ M⁻¹at 37 °C. The solution CD spectra of DNA and DNA–CoGSH indicate that in each case, DNA exists in the ‘B’ conformation and suggested an intercalative binding mode. Thin-film IR data also reveal that DNA attains the ‘B’ family of conformations after interaction with CoGSH complex. The increase in DNA viscosity in the presence of CoGSH complexes is attributed to the lengthening of DNA helix due to intercalation. Graphical Abstract  The spectrophotometric, CD, thin film IR, viscometric and fluorimetric studies on the interaction of CoGSH with DNA indicated an intercalative binding mode with the retention of ‘B’ conformation of DNA.      

The nature of ion exchange selectivity of phenol-formaldehyde sorbents with respect to cesium and rubidium ions

The structure of aqua complexes of alkali metal ions Me⁺(H₂O) _n , n = 1−6, where Me is Li, Na, K, Rb, and Cs, and complexes of 2,6-dimethylphenolate anion (CH₃)₂PhO⁻ selected as a model of the elementary unit of phenol-formaldehyde ion exchanger with hydrated alkali metal cations Me⁺(H₂O) _n , n = 0−5, was studied by the density functional method. The energies of successive hydration of the cations and the energies of binding of alkali metal hydrated cations with (CH₃)₂PhO⁻ depending on the number of water molecules n were calculated. It was shown that the dimethylphenolate ion did not have specific selectivity with respect to cesium and rubidium ions. The energies of hydration and the energies of binding of alkali metal cations with (CH₃)₂PhO⁻ decreased in the series Li⁺ > Na⁺ > K⁺ > Rb⁺ > Cs⁺ as n increased. The conclusion was drawn that the reason for selectivity of phenol-formaldehyde and other phenol compounds with respect to cesium and rubidium ions was the predomination of the ion dehydration stage in the transfer from an aqueous solution to the phenol phase compared with the stage of binding with ion exchange groups.     

Sequence dependence of DNA radioprotection by the thiols WR-1065 and WR-151326

Sequence-dependent variations of DNA structure modulate radiation-induced strand breakage. Thiols reduce breakage by scavenging damaging radiolytic OH ^. and repairing sugar radicals. As shown by sequencing gel electrophoresis, WR-1065 radioprotection is modulated by sequence, whereas that of WR-151326, a larger thiol, is more evenly distributed. Molecular modelling was performed on complexes of a 53 bp oligonucleotide (belonging to a natural restriction fragment) with one molecule of WR-1065 or WR-151326. Energy minimised structures exhibit a broadening of the minor groove of an AAATT motif upon WR-1065 binding, and a narrowing of the groove upon WR-151326 binding. Consequently, the accessibility to OH^˙ of H4′ (whose abstraction leads to strand breakage) increases near WR-1065, whereas it decreases near WR-151326. This modifies locally the otherwise homogeneous radioprotection. The effect of WR-151326 strengthens the protection at all tested binding sites, whereas that of WR-1065 diminishes it in some regions, in good agreement with the observed radioprotection distribution. Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 11 November 1998     

A QM/MM study of the binding of RAPTA ligands to cathepsin B

We have carried out quantum mechanical (QM) and QM/MM (combined QM and molecular mechanics) calculations, as well as molecular dynamics (MD) simulations to study the binding of a series of six RAPTA (Ru(II)-arene-1,3,5-triaza-7-phosphatricyclo-[3.3.1.1] decane) complexes with different arene substituents to cathepsin B. The recently developed QM/MM-PBSA approach (QM/MM combined with Poisson–Boltzmann solvent-accessible surface area solvation) has been used to estimate binding affinities. The QM calculations reproduce the antitumour activities of the complexes with a correlation coefficient (r ²) of 0.35–0.86 after a conformational search. The QM/MM-PBSA method gave a better correlation (r ² = 0.59) when the protein was fixed to the crystal structure, but more reasonable ligand structures and absolute binding energies were obtained if the protein was allowed to relax, indicating that the ligands are strained when the protein is kept fixed. In addition, the best correlation (r ² = 0.80) was obtained when only the QM energies were used, which suggests that the MM and continuum solvation energies are not accurate enough to predict the binding of a charged metal complex to a charged protein. Taking into account the protein flexibility by means of MD simulations slightly improves the correlation (r ² = 0.91), but the absolute energies are still too large and the results are sensitive to the details in the calculations, illustrating that it is hard to obtain stable predictions when full flexible protein is included in the calculations.     

Toward total structural analysis of cardiolipins: multiple-stage linear ion-trap mass spectrometry on the [M − 2H + 3Li]<Superscript>+</Superscript> ions

ESI multiple-stage linear ion-trap (LIT) mass spectrometric approaches for a near-complete structural characterization of cardiolipins (CLs), including identification of the fatty acyl substituents, assignment of the fatty acid substituents on the glycerol backbone, and location of the double-bond(s) or cyclopropyl group along the fatty acid chain are described. Upon collisionally activated dissociation (CAD) on the [M − 2H + 3Li]⁺ ions of CL in an ion-trap (MS²), two sets of fragment ions (designated as (a + 136) and (b + 136) ions) analogous to those previously reported for the [M − 2H + 3Na]⁺ ions were observed, leading to assignment of the phosphatidyl moieties attached to 1′- or 3′-position of the central glycerol. Further dissociation of the (a + 136) (or (b + 136)) ions (MS³) gives rise to the (a + 136 − R_{1(or 2)}CO₂Li) (or b + 136 − R_{1(or 2)}CO₂Li) ion pairs that identify the fatty acid moieties and their position on the glycerol backbone. This is followed by MS⁴ on the (a + 136 − R_{1(or 2)}CO₂Li) (or b + 136 − R_{1(or 2)}CO₂Li) ion to eliminate a tricylic glycerophosphate ester residue (136 Da) to yield the (a − R_{1(or 2)}CO₂Li) ion, which is then subjected to MS⁵. The MS5 spectrum contains the structural information that locates the double-bond(s) or cyclopropyl group of the fatty acid substituents. Finally, the subsequent MS⁶ on the dilithiated fatty acid ions generated from MS⁵ also yields feature ions that confirm the assignment.     

Hydrogen bonding interactions between α-, β-glucose,and methacrylic acid

Intermolecular interactions between α-, β-glucose, and methacrylic acid (MAA) have been investigated. Twenty-two possible conformations have been optimized at the DFT(B3LYP) level of theory with the 6-31G(d) basis set. The geometrical parameters for the most stable configurations of hydrogen bonding sites in the optimized systems have been determined. The binding energies ΔE _bind have been calculated at the MP2/6-311++G(d,p) level of approximation taking into account the basis set superposition error (BSSE) and the zero-point vibrational energies corrections. Results indicate that the most stabilized complexes form hydrogen bonds either through carboxylic and hemiacetal oxygen atoms acting as proton acceptors. Both, α- and β-anomers are studied in the pyranose six-membered ring. In all complexes, the nuclear quadrupole coupling constants (χ) for ¹⁷O nuclei were obtained about 10.0 MHz, while for the ²H atoms they vary from ≈200.0 to ≈350.0 kHz.     

Metal‐Ion‐Mediated Tuning of Duplex DNA Binding by Bis(2‐(2‐pyridyl)‐1H‐benzimidazole)

Studies of double‐stranded‐DNA binding have been performed with three isomeric bis(2‐(n‐pyridyl)‐1H‐benzimidazole)s (n=2, 3, 4). Like the well‐known Hoechst 33258, which is a bisbenzimidazole compound, these three isomers bind to the minor groove of duplex DNA. DNA binding by the three isomers was investigated in the presence of the divalent metal ions Mg²⁺, Co²⁺, Ni²⁺, Cu²⁺, and Zn²⁺. Ligand–DNA interactions were probed with fluorescence and circular dichroism spectroscopy. These studies revealed that the binding of the 2‐pyridyl derivative to DNA is dramatically reduced in the presence of Co²⁺, Ni²⁺, and Cu²⁺ ions and is abolished completely at a ligand/metal‐cation ratio of 1:1. Control experiments done with the isomeric 3‐ and 4‐pyridyl derivatives showed that their binding to DNA is unaffected by the aforementioned transition‐metal ions. The ability of 2‐(2‐pyridyl)benzimidazole to chelate metal ions and the conformational changes of the ligand associated with ion chelation probably led to such unusual binding results for the ortho isomer. The addition of ethylenediaminetetraacetic acid (EDTA) reversed the effects completely.     

Oxovanadium complex as potential nucleic acid binder

DNA binding study of a vanadium(V) complex, Oxo-chloro-bis-N-phenylbenzohydroxamto-vanadium(V), derived from N-phenylbenzohydroxamic acid(PBHA) form a violet color complex with vanadium (V) in presence of hydrochloric acid is performed using absorption, fluorescence and viscometric techniques. The binding parameters of the PBHA-V(V) complex using calf thymus DNA (ct-DNA) and torula yeast RNA (t-RNA) have been determined. The complex shows the ability of cooperatively minor groove binding with ct-DNA as indicated by remarkable hyperchromicity and a blue shift of the absorption spectra. Quenching of metal complex calculation was carried out with Stern-Volmer equation and K_sv was found to be 2.32 ± 0.18 × 10⁴ M^?1, while in the case of t-RNA, enhancement is observed and that means the compound was not able to displace the Ethidium Bromide(EB)-t-RNA complex. Molecular docking was also applied to predict the mode of interaction of the hydroxamic acid with ct-DNA and t-RNA. DNA binding results of the complex are compared with those of the parent ligand.     

菲咯啉与1-萘甲酸配体共同构筑的多核Ca(Ⅱ)、双核Mn(Ⅱ)配合物的合成、结构及性质

设计、合成了2种配合物：[Ca(Phen)(Nap)₂]_n(1)和[Mn₂(Phen)₂(Nap)₄(H₂O)](2)(Phen=菲咯啉,HNap=1-萘甲酸)。通过红外光谱、元素分析、X射线单晶衍射和热重对其进行了结构表征。测定了配合物的激发光谱、发射光谱,以及配合物对人肺癌细胞(NCI-H460)、人乳腺癌细胞(MCF-7)、人肝癌细胞(HepG2)的体外抑制活性;利用紫外吸收光谱、荧光分光光度法研究了配合物与小牛胸腺DNA的相互作用。结果表明：配合物1、2的激发光谱和发射光谱具有很好的镜像关系,且配合物2的斯托克斯位移大于配合物1;配合物对3种癌细胞都有较好的抑制作用,但是2更优于1;配合物1和2与小牛胸腺DNA以静电作用发生沟面结合,结合常数分别为5.83×10³和6.46×10³L·mol^-1。     

Studies on phosphatidylglycerol with triple quadrupole tandem mass spectrometry with electrospray ionization: Fragmentation processes and structural characterization

Negative-ion low-energy collisionally activated dissociation (CAD) tandem mass spectrometry of electrospray-produced ions permits structural characterization of phosphatidylglycerol (PG). The major ions that identify the structures arise from neutral loss of free fatty acid substituents ([M − H − R _x CO₂H]⁻) and neutral loss of the fatty acids as ketenes ([M − H − R′ _x CH = C = O]⁻), followed by consecutive loss of the glycerol head group. The abundances of the ions arising from neutral loss of the sn-2 substutient as a free fatty acid ([M − H − R₂CO₂H]⁻) or as a ketene ([M − H − R′₂CH = C = O]⁻) are greater than those of the product ions from the analogous losses at sn-1. Nucleophilic attack of the anionic phosphate site on the C-1 or the C-2 of the glycerol to which the carboxylates attached expels the sn-1 (R₁CO₂⁻) or the sn-2 (R₂CO₂⁻) carboxylate anion, resulting in a greater abundance of R₂COO⁻ than R₁COO⁻. These features permit assignments of fatty acid substituents and their position in the glycerol backbone. The results are also consistent with our earlier findings that pathways leading to those losses at sn-2 are sterically more favorable than those at sn-1. Fragment ions at m/z 227, 209 and 171 reflect the glycerol polar head group and identify the various PG molecules. Both charge-remote fragmentation (CRF) and charge-drive fragmentation (CDF) processes are the major pathways for the formation of [M − H − R _x COOH]⁻ ions. The CRF process involves participation of the hydrogen atoms on the glycerol backbone, whereas the CDF process involves participation of the exchangeable hydrogen atoms of the glycerol head group. The proposed fragmentation pathways are supported by CAD tandem mass spectrometry of the analogous precursor ions arising from the H-D exchange experiment, and further confirmed by source CAD in combination with tandem mass spectrometry.     

Effect of ethanol on the thermal stability of human serum albumin

The effect of ethanol on human serum albumin stability in aqueous solution was studied by use of differential scanning calorimetry. A deconvolution of DSC traces in 2-state model with ΔC _p=0 and ΔC _p≠0 was performed and analysed to obtain information on the interaction of ethanol with different parts of albumin molecule both fatty acid containing and fatty acid free. The differences in ethanol binding affinity for both kinds of albumin were found. At very low concentrations ethanol was observed to be a stabilizer of the folded state of albumin contrary to the higher concentration where its binding to the unfolded protein predominates.     

DNA binding and nuclease activity of cationic iron(IV) and manganese(III) corrole complexes

Cationic meso(4‐N‐methylpyridyl)‐based metallocorroles, μ‐oxo iron corrole dimer ( 1b ) and manganese corrole monomer ( 2b ), were synthesized and characterized. The interactions of these two metal corrole complexes with CT‐DNA were studied by UV–visible, fluorescence and circular dichroism spectroscopic methods, as well as by viscosity measurements. The results revealed that 1b interacts with CT‐DNA in a difunctional binding mode, i.e. non‐classical intercalation and outside groove binding with H‐aggregation, while 2b can interact with CT‐DNA via an outside groove binding mode only. The binding constants K_b of 1b and 2b were 4.71 × 10⁵ m ^?1 and 2.17 × 10⁵ m ^?1, respectively, indicating that 1b can bind more tightly to CT‐DNA than 2b . Furthermore, both complexes may cleave the supercoiled plasmid DNA efficiently in the presence of hydrogen peroxide or tert‐butyl hydroperoxide (TBHP), albeit 1b exhibited a little higher efficiency. The inhibitor tests suggested that singlet oxygen and high‐valent (oxo)iron(VI) corrole or (oxo)manganese(V) corrole might be the active intermediates responsible for the oxidative DNA scission. Copyright © 2014 John Wiley & Sons, Ltd.     

Discrimination among geometrical isomers of α-linolenic acid methyl ester using low energy electron ionization mass spectrometry

There is a consensus that electron impact ionization mass spectrometry is not capable of discriminating among geometrical isomers of unsaturated fatty acid methyl esters (and in general olefinic compounds). In this paper, we report the identification of all eight geometrical isomers of α-linolenic acid, one of the few essential ω-3 fatty acids that has attracted great attention, using low-energy electron ionization mass spectrometry. Three electron energies 70, 50, and 30 eV were studied and the mass spectrum of each isomer was obtained from the analysis of different concentrations of a standard mixture of α-linolenic acid methyl ester geometrical isomers to ensure the robustness of the method. Principal component analysis was employed to model the complex variation of m/z intensities across the isomers. Only using the data of 30 eV energy was complete differentiation among geometrical isomers observed. The unique cleavage pattern of the α-linolenic acid methyl ester isomers leading to a benzenium ion structure is discussed and general fragmentation rules are derived using the mass spectra of over 300 compounds with different kinds and levels of unsaturation. Application of the proposed method is not limited to α-linolenic acid. It can potentially be used to identify the geometrical isomers of any compounds with an olefinic chain.