DNA-bound lipids: computer modeling of DNA interaction with stearic acid and unsaturated fatty acids

It was shown for the first time by computer experiments that fatty acids are strongly bound to DNA. This is consistent with the presence of free fatty acids in the specimens of DNA-bound lipids isolated from various cells. Binding of all fatty acids to the DNA minor groove is stronger than to the major groove, which is correlated with the presence of two pools of free fatty acids isolated from DNA specimens by biochemical methods. Since DNA polymerase is also bound to the DNA minor groove, fatty acids can play an important role in the regulation mechanism of DNA replication and signal transmission. The energy of interaction of fatty acids with DNA depends on both the number of double bonds and the geometric configuration of the fatty acid and the nucleotide composition of DNA. Dependence on the bond energy in the DNA—fatty acid complex on the nucleotide composition attests to the possibility of site-specific binding of lipids to DNA. On passing from a saturated fatty acid to unsaturated acids containing one, two, or three double trans-bonds, the bond energy of DNA with the fatty acid gradually decreases. The presence of one or three double cis-bonds results in weakening of the strength of the DNA—fatty acid complexes compared to those with the saturated acid. The strongest binding between DNA and fatty acid was found for the unsaturated acid with two double cis-bonds (linoleic). This can be explained by the fact that the bent (boomerang) shape of the molecule of this acid follows the curve of the DNA helix. The pattern of variation of the energy of DNA complexes with stearic, linoleic, oleic, and linolenic acids correlates with experimental data on the melting points of these complexes: the more stable the DNA—fatty acid complex, the lower the melting point of DNA.     

Fluorescence quenching of ethidium ion by porphyrin cations and quaternary ammonium surfactants in the presence of DNA

Fluorescence quenching of free and DNA-bound ethidium bromide (EB) by a number of quaternary ammonium and other compounds was studied. For free EB or bound EB at lower DNA concentration the fluorescence quenching follows the Stern–Volmer equation and at higher DNA concentration follows an exponential model. At least at low quencher concentrations the quenching efficiency varies with DNA or NaCl concentrations and is about 100 times greater for bound than free EB. The quenching pathways may involve energy transfer and conformational loosening or distortion of the DNA helix in addition to possible electron transfer.     

Lipids and alkaloids from <Emphasis Type="Italic">Heliotropium lasiocarpum</Emphasis>

Lipids of seeds with pericarp and an admixture of the air-dried aerial part (AP) of Heliotropium lasiocarpum Fisch. et Mey. (Boraginaceae) were studied. The contents and component and fatty-acid compositions of neutral lipids, glycolipids, phospholipids, and strongly bound lipids were established. It was found that part of the alkaloids was extracted together with the lipids from these plant organs. The chromatographic mobility of the heliotrope alkaloids was determined under the lipid separation conditions.     

Radiopharmaceuticals in nuclear medicine diagnostic procedures and the problem of radiation protection

Taken into account the extremely high radiotoxicity of DNA-bound Auger emitters the values of absorbed and equivalent dose for various radionuclides commonly used in nuclear medicine diagnostic procedures were reevaluated. The results show that the equivalent dose is highly depend on the fraction of activity bound to the DNA, illustrating the importance of subcellular distribution of Auger electron emitters in assessing the equivalent dose.     

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.     

Interaction of rac-[Ru(5,6-dmp)3]2+ with DNA: enantiospecific DNA binding and ligand-promoted exciton coupling

The X-ray crystal structure of the complex rac-[Ru(5,6-dmp)(3)]Cl(2) (5,6-dmp = 5,6-dimethyl-1,10-phenanthroline) reveals a distorted octahedral coordination geometry with the Ru-N bond distances shorter than in its phen analogue. Absorption spectral titrations with CT DNA reveal that rac-[Ru(5,6-dmp)(3)](2+) interacts (K(b), (8.0 +/- 0.2) x 10(4) M(-1)) much more strongly than its phen analogue. The emission intensity of the 5,6-dmp complex is dramatically enhanced on binding to DNA, which is higher than that of the phen analogue. Also, interestingly, time-resolved emission measurements on the DNA-bound complex shows biexponential decay of the excited states with the lifetimes of short- and long-lived components being higher than those for the phen analogue. The CD spectral studies of rac-[Ru(5,6-dmp)(3)](2+) bound to CT DNA provide a definite and elegant evidence for the enantiospecific interaction of the complex with B-form DNA. Competitive DNA binding studies using rac-[Ru(phen)(3)](2+) provide support for the strong binding of the complex with DNA. The Delta-enantiomer of rac-[Ru(5,6-dmp)(3)](2+) binds specifically to the right-handed B-form of poly d(GC)(12) at lower ionic strength (0.05 M NaCl), and the Lambda-enantiomer binds specifically to the left-handed Z-form of poly d(GC)(12) generated by treating the B-form with 5 M NaCl. The strong electronic coupling of the DNA-bound complex with the unbound complex facilitates the change in its enantiospecificity upon changing the conformation of DNA. The (1)H NMR spectra of rac-[Ru(5,6-dmp)(3)](2+) bound to poly d(GC)(12) reveal that the complex closely interacts most possibly in the major grooves of DNA. Electrochemical studies using ITO electrode show that the 5,6-dmp complex stabilizes CT DNA from electrocatalytic oxidation of its guanine base more than the phen analogue does.     

Anchor dependency for non-glycerol based cationic lipofectins: mixed bag of regular and anomalous transfection profiles

Although detailed structure-activity, physicochemical and biophysical investigations in probing the anchor influence in liposomal gene delivery have been reported for glycerol-based transfection lipids, the corresponding investigation for non-glycerol based simple monocationic transfection lipids have not yet been undertaken. Towards this end, herein, we delineate our structure-activity and physicochemical approach in deciphering the anchor dependency in liposomal gene delivery using fifteen new structural analogues (lipids 1-15) of recently reported non-glycerol based monocationic transfection lipids. The C(14) analogues in both series 1 (lipids 1-6) and series 2 (lipids 7-15) showed maximum efficiency in transfecting COS-1 and CHO cells. However, the C(12) analogue of the ether series (lipid 3) exhibited a seemingly anomalous behavior compared with its transfection efficient C(10) and C(14) analogues (lipids 2 and 4) in being completely inefficient to transfect both COS-1 and CHO cells. The present structure-activity investigation also convincingly demonstrates that enhancement of transfection efficiencies through incorporation of membrane reorganizing unsaturation elements in the hydrophobic anchor of cationic lipids is not universal but cell dependent. The strength of the interaction of lipids 1-15 with DNA was assessed by their ability to exclude ethidium bromide bound to the DNA. Cationic lipids with long hydrophobic tails were found, in general, to be efficient in excluding EtBr from DNA. Gel to liquid crystalline transition temperatures of the lipids was measured by fluorescence anisotropy measurement technique. In general (lipid 2 being an exception), transfection efficient lipids were found to have their mid transition temperatures at or below physiological temperatures (37 degrees C).     

Copper(II)–Girard's T complex as a promising anti‐tumor agent

A copper(II) complex was evaluated for its anti‐tumor activity. Firstly, electrophoretic studies were applied on the complex. These studies revealed the binding of the complex to calf thymus DNA, leading to a delay in electrophoretic mobility of the DNA molecule. Secondly, spectroscopic data pointed out that the λ_max of DNA was shifted to a longer wavelength, which was accompanid by a hyperchromic shift. Moreover, the λ_max of copper(II) complex was shifted to a shorter wavelength. The favorable reaction conditions between the DNA molecule and the copper(II) complex were studied. Thirdly, The effects of the ligand and the Cu(II) ion were tested separately on the DNA molecule by electrophoresis technique. Furthermore, the fluorescence quenching of DNA bound ethidium ion by Cu(II)‐Girard's T complex was noticed. The IR spectral data of DNA before and after the reaction with the copper(II) complex indicated that the interaction takes place through the carbonyl group of DNA nucleobases. Finally, a significant increase in the mean survival of EAC (Ehrlich ascites carcinoma) tumor‐bearing mice was observed when treated with the copper(II) complex. The tumor volume was also significantly reduced (p < 0.0001). Electrophoretic studies showed that the DNA pattern extracted from EAC cells of tumor‐bearing mice was affected after treatment with the copper(II) complex. Flow cytometric studies showed that this complex may be taken into consideration in seeking novel anti‐tumor agents. Copyright © 2010 John Wiley & Sons, Ltd.     

A two-state model for the multilamellar structure of a DNA/cationic lipid complex in the bulk

Polyanionic DNA can bind electrostatically with cationic lipids to form a complex used for gene delivery and nanostructure construction. Here, we reveal two multilamellar phases, L(I) and L(II), characterized by distinct states of lipid packing and DNA conformation in a DNA/cationic lipid complex in the bulk state. The L(II) phase, formed when the lipids are in excess of DNA in terms of overall ionic charge, is composed of B-DNA confined between the bilayers with the lipid tails aligning normal to the lamellar interface. When DNA becomes in excess of the lipids, the L(I) phase in which the DNA is bound with the tilted lipid chains adopting the A conformation is favored because this configuration offers more economical electrostatic binding between these two components.     

A Metabolomic Analysis of Cirrhotic Ascites

Ascites is a common complication of decompensated liver cirrhosis, and yet relatively little is known about its biochemical composition. We conducted two metabolomic investigations, comparing the profile of ascites from 33 cirrhotic patients and postoperative peritoneal drainage fluid from 33 surgical patients (Experiment 1). The profile of paired ascites and plasma was also compared in 17 cirrhotic patients (Experiment 2). Gas chromatography–mass spectrometry-based metabolomics identified 29 metabolites that significantly characterized ascites fluid, whether postoperative drainage fluid or plasma were used as controls. Ten elevated amino acids (glutamine, proline, histidine, tyrosine, glycine, valine, threonine, methionine, lysine, phenylalanine) and seven diminished lipids (laurate, myristate, palmitate, oleate, vaccenate, stearate, cholesterol) largely comprised the cirrhotic ascites metabolomic phenotype that differed significantly (adjusted p < 0.002 to 0.03) from peritoneal drainage fluid or plasma. The pattern of upregulated amino acids in cirrhotic ascites did not indicate albumin proteolysis by peritoneal bacteria. Bidirectional clustering showed that the more severe the cirrhosis, the lower the lipid concentration in ascitic fluid. The metabolomic compartment of ascites in patients with decompensated cirrhosis is characterized by increased amino acids and decreased lipids. These novel findings have potential relevance for diagnostic purposes.     

REE bound DNA in natural plant

The binding of rare earth elements (REEs) with nucleic acids in the leaves of fern Dicranopteris dichotoma (DD) has been studied by molecular activation analysis (MAA). The REEs bound DNA (REE-DNA) was obtained from the leaves of DD. The CTAB-based procedure was modified for extraction of total DNA. The purity of DNA was examined by UV spectroscopy. The DNA obtained was separated and determined by agarose gel electrophoresis further. Meanwhile, the contents of eight rare earth elements (La, Ce, Nd, Sm, Eu,Tb, Yb and Lu) in REE-DNA were detected by instrumental neutron activation analysis (INAA). The results showed that REE-DNA with higher purity could be extracted from plant using this method. It was also found that REEs were bound firmly with DNA in the leaves of DD. The molecular weight (MW) of REE-DNA band was about 22 kb in agarose gel electrophoresis.     

HPLC-ICP-MS determination of selenium distribution and speciation in different types of nut

In addition to determination of total selenium in nuts, the element distribution among different fractions (lipid extract, low molecular weight, and protein fractions), and speciation analysis were studied. Improved precision for total selenium determination was observed after elimination of lipids. Because selenium was not detected in any of the lipid extracts obtained from the different types of nuts (ICP-MS), in each determination and/or speciation procedure used in this work lipids were extracted (chloroform-methanol, 2:1) and discarded before analysis. In agreement with previously reported data, high selenium levels were found in Brazil nuts (those purchased without shells contained approximately a quarter the content than those purchased with shells) and significantly lower levels in walnuts, cashews, and pecans nuts. Low-molecular-weight compounds were extracted with perchloric acid (0.4 mol L(-1)) to furnish a fraction containing 3 to 15% of the total selenium in different types of nuts. The proteins were isolated from nut samples by dissolution in 0.1 mol L(-1) sodium hydroxide and subsequent precipitation with acetone. They were then dissolved in phosphate buffer pH 7.5. Analysis of protein fractions focused on selenium in two possible states - weakly and firmly bound to proteins. Results obtained for Brazil nuts by size-exclusion chromatography with on-line ICP-MS detection, in the absence and in the presence of beta-mercaptoethanol, showed that approximately 12% of total selenium was weakly bound to proteins. To obtain information about firmly bound selenium, the protein extracts were hydrolyzed enzymatically with proteinase K. Speciation was performed by means of ion-pairing HPLC-ICP-MS. The primary species found in all types of nuts was Se-methionine (19-25% of total selenium for different types of nuts).     

IRREVERSIBLE PHOTOBINDING TO SKIN CONSTITUENTS AFTER SYSTEMIC ADMINISTRATION OF CHLORPROMAZINE TO WISTAR RATS

From in vitro experiments it is known that chlorpromazine binds to protein and DNA/ RNA upon UV-irradiation. In the present study the possible photobinding of chlorpromazine (or its metabolites) in vivo was examined. Tritium labeled drug was administered intraperitoneally to female albino Wistar rats after which they were irradiated with light with maximum intensity at 310, 370 or 420 nm. After homogenization, unbound radioactivity in tissue of several organs was removed by dialysis. In the ears, eyes and skin of the back irreversibly bound radioactivity could be detected after irradiation with 310- and 370- but not with 420 nm light. Binding in the skin of the back after UVA irradiation was examined in more detail by separating epidermal lipids, DNA/RNA and proteins by a selective extraction/precipitation method. Radioactivity appeared to be bound to lipids and proteins but not to DNA/RNA.     

Use of SEC–ICP–MS with a collision cell for determining the interaction of chromium with DNA extracted from metal-contaminated soils

The potential of chromium to bind to DNA isolated directly from soil microbial communities was investigated in this study. An analytical scheme was developed to distinguish between chromium bound to DNA and its fragments or chromium contained elsewhere in an environmental DNA extract. DNA was extracted from chromium-contaminated soils and purified using DNA clean-up resins. Size-exclusion chromatography was employed due to its advantages in the separation and molecular weight approximation of large biomolecules. It was coupled with two on-line detection systems (spectrophotometric and inductively coupled plasma mass spectrometric) to study the binding of chromium to DNA or other components in a DNA extract. A collision cell was pressurized with helium to remove diatomic and polyatomic interferents resulting from the chosen mobile phase. Chromium peaks were observed in both the large and small molecular weight regions of the chromatogram; to further confirm that the environmentally extracted DNA contained Cr, the subsequently purified DNA was examined for total Cr using flow injection ICP–MS to accommodate small sample volumes. DNA samples isolated from the two soils examined contained 0.5–0.7 ppb Cr, indicating that DNA isolated directly from a chromium-contaminated soil has chromium bound to the nucleic acids.     

Lipids from Capsicum annuum Seeds

The composition of free and bound lipids from Capsicum annuum (Solanaceae) seeds was studied. Glycolipids, phospholipids, mono- and diacylglycerides, and free fatty acids were observed in the bound lipids.     

Interfacial ternary complex DNA/Ca/lipids at anionic vesicle surfaces

The electroporative transfer of gene DNA and other bioactive substances into tissue cells by electric pulses gains increasing importance in the new disciplines of electrochemotherapy and electrogenetherapy. The efficiency of the electrotransfer depends crucially on the adsorption of the gene DNA and oligonucleotides to the plasma cell membranes. Here it is shown that the adsorption of larger oligonucleotides such as fragments (ca. 300 bp) of sonicated calf-thymus DNA, to anionic lipids of unilamellar vesicles (diameter Phi=300+/-90 nm) is greatly enhanced by divalent cations such as Ca(2+)-ions. Applying centrifugation, bound and free DNA are monitored optically at the wavelength lambda=260 nm. Using arsenazo III as a Ca(2+)-indicator and atomic absorption spectroscopy (AAS), Ca(2+)-titrations of DNA and vesicles yield the individual equilibrium constants of Ca(2+)- and DNA-binding not only for the binary complexes: Ca/lipids, Ca/DNA and DNA/lipids, respectively, but also for the various processes to form the ternary complex DNA/Ca/lipids. The data provide the basis for goal-directed optimization protocols for the adsorption and thus efficient electrotransfer of oligonucleotides and polynucleotides into cells.     

Voltammetric measurements of the interaction of metal complexes with nucleic acids

Cyclic voltammetry and differential-pulse voltammetry at mm-sized electrodes were used to measure the decrease in the rate of diffusion of metal complexes upon binding to DNA and to extract the binding constants and effective binding site sizes. A linear correlation was observed between the site size determined electrochemically and the diameter of the complexes [site size: Cu(phen)2(2+) > Fe(phen)3(2+) > Co(bipy)3(3+) approximately Fe(bipy)3(2+) > Ru(NH3)6(3+)]. The binding constants were found to be influenced by the charge of the metal complex, the nature of ligand and the geometry about the metal centre. Competition experiments, in which differential pulse voltammetry was used to observe the release of bound metal complex on addition of a second DNA-binding molecule to the solution, were sensitive to the nature and location of the binding sites for the two species. Steady-state voltammetric experiments at microelectrodes are shown to have a number of advantages over cyclic voltammetry and differential pulse voltammetry at mm-sized electrodes for determination of binding constants. In particular, the steady-state diffusion limited current is directly proportional to the diffusion coefficient, rather than its square root, which improves the discrimination between DNA-bound and freely diffusing metal complex. Further, the kinetics of the binding process do not affect the steady state measurement, whereas for transient techniques, e.g., cyclic voltammetry, only a range of values can be extracted corresponding to the limits of fast and slow binding kinetics compared to the experimental timescale.     

Interactions of cyanine dyes with nucleic acids. XXIV. Aggregation of monomethine cyanine dyes in presence of DNA and its manifestation in absorption and fluorescence spectra.

Absorption, fluorescence emission and excitation spectra of benzothiazole cyanine dyes--thiazole orange (TO) and 7-methyl-6-(3-methyl-2,3-dihydro-1,3-benzothiazol-2-ylidenmethyl) [1,3] dioxolo [4',5':4,5] benzo [d] [1,3] thiazolium methylmethosulfate (Cyan 13)--were investigated over a wide concentration range. The dyes form aggregates with a 'sandwich'-like structure in water solution. At low dye to DNA concentrations ratios, Cyan 13 and TO monomers appear to interact with the DNA. On increasing the dye to DNA concentrations ratio, free dye molecules aggregate with the DNA-bound ones. The spectra of the free dye aggregates and the aggregates formed on the DNA, are characterized by an anomalously large (more than 100 nm) Stokes shift. This suggests, that the pi-electron systems of the aggregates undergo substantial changes in excited state, compared to those of the monomers. The formation of aggregates consisting of the free and DNA-bound dye molecules can be explained using the half-intercalation model of the interaction of the cyanine dye monomers with the DNA.     

Polyplexes and lipoplexes for mammalian gene delivery: from traditional to microarray screening

Gene therapy requires the development of non-toxic and highly efficient delivery systems for DNA and RNAi. Polycations, especially dendrimers, have shown enormous potential as gene transfer vehicles, displaying minimal toxicity with a broad range of cell lines. In this paper, a total of 13 dendrimers, up to G3.0, were constructed from AB(3) type isocyanate monomers using solid phase methodology and evaluated for transfection activity. Among the library of compounds prepared, a G3.0 dendrimer displayed comparable activity to Superfect. Gel retardation assays demonstrated that all of the compounds completely bound plasmid DNA, indicating the efficient formation of complexes between DNA and the dendrimers. A "transfection microarray" approach was developed for screening these compounds as well as a panel of lipoplexes (complexes of DNA with cationic lipids) and polyplexes (complexes of DNA with synthetic polycationic polymers), in 3D solution like micro-assay). Five cationic lipids with a cholesterol tail showed stronger or comparable transfection activity relative to Effectene. The new, micro-array screening method was rapid and miniaturized, offering the potential of high throughput screening of large libraries of transfection candidates, with thousands of library members per array, and the ability to rapidly screen a broad range of cell types.