Ion atmosphere around nucleic acid

The poyion-ion preferential interaction coefficient Gamma describes the exclusion of coions and accumulations of counterions in the vicinity of a polyion in an aqueous solution. We give tight upper and lower bounds for Gamma when the polyion can be modeled by a cylinder of infinite length but of arbitrary charge density. This case can be used as a model for long strands of DNA or RNA in an aqueous solution containing univalent cations. The salt dependence of Gamma is predicted from low to intermediate and high salt concentrations. We also indicate how the bounds for the infinite polyion can be exploited to place bounds for polyions of length greater than a constant on the order of the inverse Debye screening length.     

An experimental and theoretical study of the gas-phase decomposition of monoprotonated peptide nucleic acids

Peptide nucleic acids (PNAs) are DNA/RNA mimics which have recently generated considerable interest due to their potential use as antisense and antigene therapeutics and as diagnostic and molecular biology tools. These synthetic biomolecules were designed with improved properties over corresponding oligonucleotides such as greater binding affinity to complementary nucleic acids, enhanced cellular uptake, and greater stability in biological systems. Because of the stability and unique structure of PNAs, traditional sequence confirmation methods are not effective. Alternatively, electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry shows great potential as a tool for the characterization and structural elucidation of these oligonucleotide analogs. Extensive gas-phase fragmentation studies of a mixed nucleobase 4-mer (AACT) and a mixed nucleobase 4-mer with an acetylated N-terminus (N-acetylated AACT) have been performed. Gas-phase collision-induced dissociation of PNAs resulted in water loss, cleavage of the methylene carbonyl linker containing a nucleobase, cleavage of the peptide bond, and the loss of nucleobases. These studies show that the fragmentation behavior of PNAs resembles that of both peptides and oligonucleotides. Molecular mechanics (MM+), semiempirical (AM1), and ab initio (STO-3G) calculations were used to investigate the site of protonation and determine potential low energy conformations. Computational methods were also employed to study prospective intramolecular interactions and provide insight into potential fragmentation mechanisms.     

Quantitative determination of nucleic acids in salmonidae milt by various methods

Procedures for the determination of total nucleic acids from ultraviolet absorption and for the separate determination of DNA and RNA by means of color reactions using the same tissue extracts have been developed. The results of the total and separate determination of the nucleic acids and the analysis of milts preserved by various methods are given. The discrepancies between the total amount of nucleic acids determined by the color reactions and by ultraviolet absorption do not exceed ±1.9%.All-Union Scientific-Research Institute of Applied Biochemistry. Biolar Scientific Industrial Association, Olaine. Translated from Khimiya Prirodnykh Soedinenii, No. 1, pp. 122–126, January–February, 1989.     

Force field parameters for rotation around chi torsion axis in nucleic acids

To raise the accuracy of the force field for nucleic acids, several parameters were elaborated, focusing on the rotation around chi torsion axis. The reliability of molecular dynamics (MD) simulation was significantly increased by improving the torsion parameters at C8--N9--C1'--X (X = H1', C2', O4') in A, G and those at C6--N1--C1'--X in C, T, and U. In this work, we constructed small models representing the chemical structure of A, G, C, T, and U, and estimated energy profile for chi-axis rotation by executing numerous quantum mechanical (QM) calculations. The parameters were derived by discrete Fourier transformation of the calculated QM data. A comparison in energy profile between molecular mechanical (MM) calculation and QM one shows that our presently derived parameters well reproduce the energy surface of QM calculation for all the above torsion terms. Furthermore, our parameters show a good performance in MD simulations of some nucleic acids. Hence, the present refinement of parameters will enable us to perform more accurate simulations for various types of nucleic acids.     

Voltammetric study of the interaction of ciprofloxacin-copper with nucleic acids and the determination of nucleic acids

The behavior of the ciprofloxacin (CPFX) complex with copper, Cu(II)L₂, at a mercury electrode has been investigated in borax–boric acid buffer. The adsorption phenomena were observed by linear sweep voltammetry. The mechanism of the electrode reaction was found to be reduction of Cu(II)L₂ adsorbed on the surface of the electrode by an irreversible charge transfer to metal amalgam, Cu(0)(Hg). In the presence of DNA, the formation of the electrochemically non-active complexes Cu(II)L₂–DNA results in the decrease of the equilibrium concentration of Cu(II)L₂ and its peak current. Under the optimum conditions, the decrease of the peak current is proportional to DNA concentration. The linear ranges are 6.67×10⁻⁸ to 1.20×10⁻⁵ g ml⁻¹ for calf thymus DNA (ctDNA), 3.30×10⁻⁸ to 2.33×10⁻⁶ g ml⁻¹ for fish sperm DNA (fsDNA) and 1.0×10⁻⁸ to 1.2×10⁻⁶ g ml⁻¹ for yeast RNA. The detection limits are 5.00×10⁻⁹, 3.00×10⁻⁹ and 2.50×10⁻⁹ g ml⁻¹, respectively. This method exhibits good recovery and high sensitivity.     

Like polarity ion/ion reactions enable the investigation of specific metal interactions in nucleic acids and their noncovalent assemblies

A rare example of ion/ion reaction between species of like polarity was shown to take place during the transfer of metal cations from nucleic acid substrates to chelating agents in the gas phase. Gaseous anionic reactants were generated from separate solutions of analyte and chelator by using a dual nanospray setup. The respective multiply charged ions shared the same path and were allowed to react for a predetermined interval in an rf-only hexapole before high-resolution analysis by Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. Efficient transfer of sodium and magnesium ions was readily observed with significant reduction of the nonspecific adducts that are typically associated with decreased sensitivity and resolution in the analysis of nucleic acid samples. Metal cations were abstracted from the initial analyte without being replaced by protons, in a process that was clearly dependent on the concentration of chelator in the auxiliary emitter and on the time spent by the reactants in the hexapole element. A survey of the properties of selected anionic chelators showed that their known affinity for a target cation in solution was more critical than their maximum anionic charge in determining the outcome of the transfer process. The analysis of selected assemblies requiring divalent cations to preserve their structural integrity and functional properties demonstrated that ion/ion reactions were clearly capable of discriminating between nonspecific interactions and specific coordination based on transfer susceptibility. These examples demonstrated that the ability to selectively eliminate nonspecific adducts in the gas phase, after the desolvation process is complete, offers a unique opportunity for studying specific metal binding in biological systems without resorting to separation procedures that may adversely affect the position of binding equilibria in solution and disrupt the assemblies under investigation.     

Selective decomposition of nucleic acids by laser irradiation on probe-tethered gold nanoparticles in solution

We have developed a new method for selective decomposition of nucleic acids. The method utilizes a high temperature and pressure region (HTP region, hereafter) around a gold nanoparticle, which was generated when the gold nanoparticle was irradiated with a pulsed laser in aqueous solution. A probe DNA molecule whose sequence was complementary to a part of a target DNA molecule was bound to the gold nanoparticle surface. In a solution containing both the target and non-target DNA molecules, the gold nanoparticle selectively attached to the target DNA through hybridization of the probe DNA. When the gold nanoparticle was excited by a pulsed laser, the HTP region was generated in the close vicinity of the gold nanoparticle and then the target DNA molecules inside of this region were decomposed. The non-target DNA molecules having no part complementary to the probe DNA were scarcely decomposed by laser irradiation. When the gold nanoparticle was excited by an intense laser, the non-target DNA molecules were also decomposed, because some of them were located inside the inflated HTP region. We discussed the mechanism of the decomposition of the DNA molecules by the HTP region.     

Thermal decomposition of thorium(IV) complexes with benzenecarboxylic acids in air atmosphere

The conditions and products of thermal decomposition of thorium(IV) complexes with general formula Th(R-C₆H₄COO)₄ (whereR=2-CH₃, 3-CH₃, 4-CH₃), Th(OH)₂(4-CH₃C₆H₄COO)₂. H₂O and Th(OH)₂(R-C₆H₄COO)₂·nH₂O (whereR=2-COO, 3-COO,n=2;R=4-COO,n=1) were studied. Anhydrous thorium(IV) complexes decompose in two steps. On heating, tetra(2-methylbenzoato)-thorium(IV) decomposes to yield ThO₂ through the intermediate ThOCO₃ whereas tetra(3-methylbenzoato)thorium(IV) and tetra(4-methylbenzoato)thorium(IV) decompose to ThO₂ through oxocomplexes. Hydrated thorium(IV) complexes are dehydrated in one step and then anhydrous complexes decompose to ThO₂. Di [1,2-(benzene)dicarboxylato]dihydroxythorium(IV) decomposes directly to ThO₂, whereas the 1,3- and 1,4-isomers through the intermediate thorium(IV) oxocarbonates.     

Structural analysis of metal ion ligation to nucleotides and nucleic acids using pulsed EPR spectroscopy

Metal ions play key structural and functional roles in many nucleic acid systems, particularly as required cofactors for many catalytic RNA molecules (ribozymes). We apply the pulsed EPR technologies of electron spin-echo envelope modulation and electron spin-echo-electron nuclear double resonance to the structural analysis of the paramagnetic metal ion Mn(II) bound to nucleotides and nucleic acids. We demonstrate that pulsed EPR, supplemented with specific isotope labeling, can characterize ligation to nucleotide base nitrogens, outer-sphere interactions with phosphate groups, distances to sites of specific (2)H atom labels, and the hydration level of the metal ion. These techniques allow a comprehensive structural analysis of the mononucleotide model system MnGMP. Spectra of phenylalanine-specific transfer RNA from budding yeast and of the hammerhead ribozyme demonstrate the applicability of the methods to larger, structured RNA systems. This suite of experiments opens the way to detailed structural characterization of specifically bound metal ions in a variety of ribozymes and other nucleic acids of biological interest.     

Thermal decomposition of thorium(IV) salts of benzene carboxylic acids in air atmosphere

The thermal stabilities of thorium(IV) salts of ortho-, meta- and para-hydroxy- and aminobenzoic acids were studied. The salts were prepared as hydrated compounds with general formula Th(OH)₂(R-C₆H₄COO)₂·nH₂O, wereR = OH or NH₂, andn = 2, 3 or 4, while the salt of 3-aminobenzoic acid was anhydrous. On heating, the salts undergo dehydration in two or three steps and di(R-benzoato)dihydroxothorium(IV) or di(2-hyroxybenzoato)oxothorium(IV) is then transformed directly to ThO₂.The temperatures of beginning of decomposition and ThO₂ formation decrease with decreasing values of the Hammett constant and von Bakkum constant ⁿ.

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Zusammenfassung Es wurde die Thermostabilität der Thorium(IV)-salze von ortho-, meta- und para-Hydroxy- und Aminobenzoylsäure untersucht.Die Salze wurden als hydratierte Verbindungen der allgemeinen Formel Th(OH)₂(R-C₆H₄COO)₂·nH₂O mitR=OH oder NH₂ undn=2,3 oder 4 gefertigt, während das Salz der 3-Aminobenzoylsäure unhydratiert war. Beim Erhitzen zeigen die Salze eine Dehydratation in zwei oder drei Stufen und anschließend werden Di(R-benzoato)dihydroxothorium(IV) oder Di(2-hydroxybenzoato)oxothorium(IV) direkt in ThO₂ umgewandelt.Die Temperaturen für das Einsetzen der Zersetzung und der ThO₂-Bildung sinken mit abnehmenden Werten für die Hammet-Konstante und die Bakkum-Konstante

     

Cationic liposomes and nucleic acids

During the past decade, cationic lipids have emerged as the primary choice for gene delivery in vitro, i.e. transfection of cultured cells. A number of lipids with cationic head groups have been synthesized and evaluated. However, their success in vivo for gene therapy has been limited. To date, simple electrostatic complexes of cationic lipid mixtures with DNA have been hampered in numerous aspects: lack of colloidal stability, relatively low efficiency observed as expression levels or % of transfected cells, short duration of expression, and most importantly, non-specific interactions with many cells and tissues. Appreciation of the complexity of in vivo requirements, and especially opposing requirements for extra- and intracellular trafficking, is leading to engineered designs of gene delivery vectors containing cationic lipids. These designs attempt to assemble layered colloidal systems that accommodate the multiple functions required to traverse the various extra- and intracellular barriers. Successful development of such systems will depend on the ability to characterize and optimize each step rather than rely only on reporter gene expression, in addition to the obvious need to characterize the layered nature of the complexes. Importantly, many pharmacological aspects must be considered, especially control of the biodistribution and toxicity. Initial reports on such systems appear to provide at least a proof of the concept.     

Effects of sequence and structure in the separation of nucleic acids using ion pair reverse phase liquid chromatography

Ion pair reverse phase high performance liquid chromatography on non-porous alkylated poly(styrene-divinylbenzene) particles enables the high resolution separation of double stranded DNA fragments. To further understand the separation mechanisms involved in ion pair reverse phase liquid chromatography we have analysed the effects of curved or "bent" DNA fragments with respect to their separation using both gel electrophoresis and ion pair reverse phase liquid chromatography. Size dependent separations of curved DNA fragments that migrate anomalously during gel electrophoresis were observed using ion pair reverse phase liquid chromatography. To further study the sequence effect and resulting changes in hydrophobicity of the duplex DNA, PCR fragments were generated that contain uracil in place of thymine. The resulting fragments were shown to elute with shorter retention times, demonstrating that sequence-specific effects can alter the retention of duplex DNA. The study was extended to the investigation of non-canonical B-DNA structures (Holliday junctions) under various chromatographic conditions, demonstrating that the coaxial stacking of the helices in such structures, in the presence of magnesium causes a change in retention.     

Ion atmosphere of three-way junction nucleic acid

The ion atmosphere of three-armed symmetric Y-shaped and asymmetric y-shaped A-RNA junctions in aqueous solution containing multivalent ions is described within the framework of a polyelectrolyte model. The fraction of "screening counterions" per polyion charge that shield the residual unneutralized charges from interacting with one another and the condensed counterions per polyion charge as a function of sodium and magnesium ion concentrations are determined. The predictions for the slope of log(k(o)/k(f)) as a function of Na+ and Mg2+ concentration, where k(o) and k(f) are the opening and folding rates of the three-helix junction molecule, respectively, are compared with experimental data (Kim et al. Proc. Nat. Acad. Sci. U.S.A. 2002, 96, 9077-9082).     

Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules

An explicit ion, implicit water solvent model for molecular dynamics was developed and tested with DNA and RNA simulations. The implicit water model uses the finite difference Poisson (FDP) model with the smooth permittivity method implemented in the OpenEye ZAP libraries. Explicit counter-ions, co-ions, and nucleic acid were treated with a Langevin dynamics molecular dynamics algorithm. Ion electrostatics is treated within the FDP model when close to the solute, and by the Coulombic model when far from the solute. The two zone model reduces computation time, but retains an accurate treatment of the ion atmosphere electrostatics near the solute. Ion compositions can be set to reproduce specific ionic strengths. The entire ion/water treatment is interfaced with the molecular dynamics package CHARMM. Using the CHARMM-ZAPI software combination, the implicit solvent model was tested on A and B form duplex DNA, and tetraloop RNA, producing stable simulations with structures remaining close to experiment. The model also reproduced the A to B duplex DNA transition. The effect of ionic strength, and the structure of the counterion atmosphere around B form duplex DNA were also examined.     

Computer simulation of the ionic atmosphere around Z-DNA

We describe a coarse-grained model for Z-DNA that mimics the DNA shape with a relatively small number of repulsive interaction sites. In addition, negative charges are placed at the phosphate positions. The ionic atmosphere around this grooved Z-DNA model is then investigated with Monte Carlo simulation. Cylindrically averaged concentration profiles as well as the spatial distribution of ions have been calculated. The results are compared to those for other DNA models differing in the repulsive core. This allows the examination of the effect of the DNA shape in the ionic distribution. It is seen that the penetrability of the ions to the DNA groove plays an important role in the ionic distribution. The results are also compared with those reported for B-DNA. In both conformers the ions are structured in alternating layers of positive and negative charge. In Z-DNA the layers are more or less concentric to the molecular axis. Besides, no coions enter into the single groove of this conformer. On the contrary, the alternating layers of B-DNA are also structured along the axial coordinate with some coions penetrating into the major groove. In both cases we have found five preferred locations of the counterions and two for the coions. The concentration of counterions reaches its absolute maximum at the narrow Z-DNA groove and at the minor groove of B-DNA, the value of the maximum being higher in the Z conformer.     

Halogenation of the components of nucleic acids

Summary Preparative methods have been worked out for the bromination of unprotected deoxy-AMP, deoxy-GMP, and deoxy-CMP and methods have been devised for the isolation and purification of the bromine derivatives.Some physicochemical characteristics (UV spectra, R_f values on thin-layer and paper chromatography, coefficients of millimolar extinction) of the bromine derivatives of the DNA components obtained have been determined.Moscow. Translated from Khimiya Prirodnykh Soedinenii, No. 4, pp. 524–527, July–August, 1976.     

Halogenation of the components of nucleic acids

Chemistry of Natural Compounds - Preparative methods have been worked out for the bromination of unprotected deoxy-AMP, deoxy-GMP, and deoxy-CMP and methods have been devised for the isolation and...     

Interaction of nucleic acids with the glycocalyx

Mammalian cells resist the uptake of nucleic acids. The lipid bilayer of the plasma membrane presents one barrier. Here, we report on a second physicochemical barrier for uptake. To create a sensitive probe for nucleic acid-cell interactions, we synthesized fluorescent conjugates in which lipids are linked to DNA oligonucleotides. We found that these conjugates incorporate readily into the plasma membrane but are not retained there. Expulsion of lipid-oligonucleotide conjugates from the plasma membrane increases with oligonucleotide length. Conversely, the incorporation of conjugates increases markedly in cells that lack the major anionic components of the glycocalyx, sialic acid and glycosaminoglycans, and in cells that had incorporated highly cationic lipids into their plasma membrane. We conclude that anionic oligosaccharides provide a formidable barrier to the uptake of nucleic acids by mammalian cells. This conclusion has implications for genomic stability, as well as the delivery of genes and siRNAs into mammalian cells.