A 23Na and 31P NMR investigation of the binding of Ni2+ to Na-DNA

A ²³Na and ³¹P NMR study of the Na-DNA and Na-DNA-Ni systems in aqueous solution has been undertaken. Analysis of the relaxation rates provides evidence that Ni²⁺ displaces Na⁺ ions from the condensation layer of Na-DNA. Furthermore, it was found that Ni²⁺ binds specifically to the DNA phosphate to some extent and that multiple chemical equilibria are involved in the interactions.     

Determination of drug-macromolecule binding parameters by numerical analysis

A method is described for calculating the binding parameters of a drug to a macromolecule from data obtained by indirect techniques, such as spectroscopy, assuming the existence of only one class of binding sites. A critical evaluation of the performance of the method is presented, showing that the errors which previously reported methods may produce are avoided. Some examples that make use of experimental data determined for phenylbutazone and oxyphenbutazone by means of UV difference spectroscopy are given.     

Dynamics of large elongated RNA by NMR carbon relaxation

We present an NMR strategy for characterizing picosecond-to-nanosecond internal motions in uniformly 13C/15N-labeled RNAs that combines measurements of R1, R1rho, and heteronuclear 13C{1H} NOEs for protonated base (C2, C5, C6, and C8) and sugar (C1') carbons with a domain elongation strategy for decoupling internal from overall motions and residual dipolar coupling (RDC) measurements for determining the average RNA global conformation and orientation of the principal axis of the axially symmetric rotational diffusion. TROSY-detected pulse sequences are presented for the accurate measurement of nucleobase carbon R1 and R1rho rates in large RNAs. The relaxation data is analyzed using a model free formalism which takes into account the very high anisotropy of overall rotational diffusion (Dratio approximately 4.7), asymmetry of the nucleobase CSAs and noncollinearity of C-C, C-H dipolar and CSA interactions under the assumption that all interaction tensors for a given carbon experience identical isotropic internal motions. The approach is demonstrated and validated on an elongated HIV-1 TAR RNA (taum approximately 18 ns) both in free form and bound to the ligand argininamide (ARG). Results show that, while ARG binding reduces the amplitude of collective helix motions and local mobility at the binding pocket, it leads to a drastic increase in the local mobility of "spacer" bulge residues linking the two helices which undergo virtually unrestricted internal motions (S2 approximately 0.2) in the ARG bound state. Our results establish the ability to quantitatively study the dynamics of RNAs which are significantly larger and more anisotropic than customarily studied by NMR carbon relaxation.     

微透析取样-流动注射电化学检测测定表柔比星与牛血清白蛋白体外结合参数

建立了微透析取样-流动注射电化学检测法测定表柔比星与牛血清白蛋白体外结合参数的方法。流动相为pH 3.0的0.1 mol/L H3PO4-NaH2PO4缓冲液(含3.4×10﹣5mol/L Na2EDTA),流速为0.3 mL/min。电化学检测的工作电极为玻碳电极,工作电位为0.52V。表柔比星浓度在5.0×10-5～5.0×10-7 mol/L范围内与峰电流呈良好的线性关系,其相关系数为0.9997,检出限为2.0×10-7mol/L。结合微透析取样,实现了对表柔比星与牛血清白蛋白结合参数的测定。表柔比星与牛血清白蛋白的体外结合符合Scatchard曲线,结合常数和结合位点数分别为2.41×104L/mol和4.02。     

A solid-state 23Na NMR study of monovalent cation binding to double-stranded DNA at low relative humidity

We report a solid-state (23)Na NMR study of monovalent cation (Li(+), Na(+), K(+), Rb(+), Cs(+) and NH(4) (+)) binding to double-stranded calf thymus DNA (CT DNA) at low relative humidity, ca 0-10%. Results from (23)Na--(31)P rotational echo double resonance (REDOR) NMR experiments firmly establish that, at low relative humidity, monovalent cations are directly bound to the phosphate group of CT DNA and are partially dehydrated. On the basis of solid-state (23)Na NMR titration experiments, we obtain quantitative thermodynamic parameters concerning the cation-binding affinity for the phosphate group of CT DNA. The free energy difference (DeltaG degrees ) between M(+) and Na(+) ions is as follows: Li(+) (-1.0 kcal mol(-1)), K(+) (7.2 kcal mol(-1)), NH(4) (+) (1.0 kcal mol(-1)), Rb(+) (4.5 kcal mol(-1)) and Cs(+) (1.5 kcal mol(-1)). These results suggest that, at low relative humidity, the binding affinity of monovalent cations for the phosphate group of CT DNA follows the order: Li(+) > Na(+) > NH(4) (+) > Cs(+) > Rb(+) > K(+). This sequence is drastically different from that observed for CT DNA in solution. This discrepancy is attributed to the different modes of cation binding in dry and wet states of DNA. In the wet state of DNA, cations are fully hydrated. Our results suggest that the free energy balance between direct cation-phosphate contact and dehydration interactions is important. The reported experimental results on relative ion-binding affinity for the DNA backbone may be used for testing theoretical treatment of cation-phosphate interactions in DNA.     

Cation binding to parvalbumin studied by 113Cd and 23Na NMR. Peak assignment of rabbit (pI 5.5) parvalbumin

Cation binding to three apoparvalbumins was studied by means of 113Cd NMR. The 3 parvalbumins that were investigated were carp pI 4.25, rabbit pI 5.5 and pike pI 5.0. The results showed that Cd2+ ions bind to the EF and CD sites of carp apoparvalbumin pI 4.25 with about the same affinity. For rabbit (pI 5.5) apoparvalbumin, Cd2+ binds preferentially to the EF site, while for pike (pI 5.0) apoparvalbumin, it was the CD site that exhibited somewhat higher affinity for Cd2+. The effect of Mn2+ on the 113Cd signals of rabbit parvalbumin was used to assign the 113Cd NMR signals to the EF and CD sites. The Mn2+ paramagnetic effect on rabbit and pike parvalbumins differed from that obtained for carp parvalbumin. This is in agreement with the assumption that the beta-lineage parvalbumins possess a third external site of higher affinity than the alpha-lineage parvalbumins. Furthermore, 23Na NMR was used to study Na+-Mg2+ competition in the native carp (pI 4.25) parvalbumin. The results showed that Na+ and Mg2+ compete for the same site, the third external site.     

Nuclear magnetic relaxation and ionic solvation of23Na+ and81Br− in aqueous mixtures of simple amides

Ion-solvent interactions of Na⁺ and Br^– in binary aqueous mixtures of formamide,N-methylformamide (NMF), andN,N-dimethylformamide (DMF) are studied by use of²³Na and⁸¹Br magnetic relaxation times, extrapolated to zero salt concentration. The relaxation times, which are controlled by quadrupolar interaction, have been measured over the complete mixture range and are compared with a simplified theoretical formula. It turned out that the²³Na⁺ relaxation in H₂O-formamide and H₂O-NMF mixtures is in excellent agreement with theoretical predictions, implying nonpreferential solvation of Na⁺ in these systems. Small deviations of experimental from theoretical results in H₂O+DMF possibly indicate weak selective hydration of the cation. In the case of the anionic nuclei⁸¹Br^–, deviations from the theoretical curve occur which are to be expected, especially for systems where hydrophobic effects play a role. On the other hand, it is demonstrated that these deviations can easily be explained within the electrostatic theory by differences in structural details of the anionic solvation sphere in the mixtures compared to the pure solvents.     

Tracing the reactive melting of glass-forming silicate batches by in situ 23Na NMR

The kinetics of the reaction of batches of powdered quartz and sodium carbonate was studied by in situ (23)Na nuclear magnetic resonance (NMR) spectroscopy using a laser-heated probe. We show for the first time that the technique allows one to study solid-state reactions at high temperatures with good time resolution and without the risk of quenching artifacts. The reaction is controlled by solid-state Na(+) diffusion across the grain interface. Independent of the batch composition, the first reaction product is crystalline sodium metasilicate, Na(2)SiO(3), even if the temperature is high enough for much of the composition space between silica and metasilicate to be above the equilibrium liquidus. Fast Na(+) diffusion allows the reaction front to cross the grain interface and form the solid product before liquid intermediate equilibrium products can be formed. This purely solid-state reaction slows down as the thickness of the interface increases; the reaction is more deceleratory than published models suggest. If excess quartz is present, it reacts in a second step involving a liquid film wetting the excess grains. Once this reaction has started, it pulls the reaction into the thermodynamic regime, which leads to an increase even in the rate of the first step leading to intermediate solid metasilicate.     

23Na, 29Si, and 13C MAS NMR investigation of glass-forming reactions between Na2CO3 and SiO2

The glass-forming reactions between sodium carbonate (Na2CO3) and silica (SiO2) have been investigated by 23Na, 29Si, and 13C magic-angle spinning (MAS) NMR spectroscopy. The multinuclear MAS NMR approach identifies and quantifies reaction products and intermediates, both glassy and crystalline. A series of powdered batches of initial composition Na2CO3.xSiO2 (x = 1, 2) corresponding to a sodium metasilicate (Na2SiO3) and sodium disilicate (Na2Si2O5) stoichiometry were investigated after periods of isothermal and nonisothermal heat treatments at different temperatures. Analysis of the 23Na quadrupolar coupling parameters has identified the early reaction product in all cases as crystalline Na2SiO3. In the nonisothermal experiment, this reaction is preceded by an early silica-rich melt phase formed around 850 degrees C. The early reactions are controlled by solid-state Na+ diffusion across the reaction zone in the grain interface layer. Crystalline Na2SiO3 precipitates in the interface layer, increasing its thickness between the Na2CO3 and the SiO2 grains and slowing down the rate of Na+ migration. This creates a secondary phase, which is temperature dependent. At low temperatures, where Na+ migration is impaired, the production of Na2SiO3 ceases and silica-richer phases are precipitated. In the case of the sodium disilicate batch, where excess SiO2 is present, a secondary reaction of Na2SiO3 with SiO2 forming a glassy phase is observed. A transient carbon-bearing phase has been identified by 13C NMR as a NaCO3- complex loosely bound to bridging oxygens in the silicate network at the SiO2 grain surface.     

A new Na+ and K+ carrier from chemically modified monensin studied in human erythrocytes by 23Na nuclear magnetic resonance,K+ atomic absorption and H+ potentiometry

The transporting ability of a new monensin derivative 26-(1,2-diphenyl-1-ethoxy) monensin, highly active against Gram-positive bacteria, was explored with the human erythrocyte model using three technical approaches: ²³Na nuclear magnetic resonance (internal Na⁺), K⁺ atomic absorption (external K⁺) and H⁺ potentiometry (external H⁺) and compared with monensin 1 and 26-(4-chlorophenylurethane) monensin 3 of known transport selectivities for sodium and potassium respectively. Compound 2 proved to be a good carrier for both Na⁺ and K⁺ under our experimental conditions, thus constituting a new type of monensin derivative. The introduction of Li⁺, Rb⁺ or Cs⁺ in the external buffer as a replacement for Na⁺ led us to propose the transport sequence K⁺, Na⁺ ⪢ Rb⁺ > Li⁺ > Cs⁺ for 2.     

Separation of local asymmetry and selective solvation effects using the quadrupole relaxation of the23Na+ and87Rb+ ions in acetonitrile-water mixtures

Nuclear magnetic relaxation rates of²³Na⁺,⁸⁷Rb⁺, and¹⁴N in acetonitrile-water mixtures have been measured over the complete mixture range. The interaction of the quadrupole moment of ionic nuclei with electric field gradients is an excellent short ranged probe for the direct neighborhood of ions in solution. Thus the²³Na⁺ and⁸⁷Rb⁺ relaxation contains information about dynamics composition and symmetry of the inner solvation sphere in the mixed solvent. It was found that the relaxation rate of both ionic nuclei has an unexpected marked maximum in the acetonitrile (AN) rich region. The¹⁴N and²H relaxation rates of the solvent molecules revealed that the maximum could not be explained by dynamic effects. Further experimental results showed that it is caused by local symmetry changes. By measuring 1/T₁ of the cationic nuclei in AN-H₂O and AN-D₂O it was possible for the first time to separate quantitatively asymmetry effects from selective solvation effects. It turned out that both cations are strongly preferentially hydrated. Comparison of the results of two approaches for the evaluation of the D₂O-H₂O isotope effect led to interesting hints concerning the location of the electric point dipole in acetonitrile molecules having contact with cations.     

NMR artifacts caused by decoupling of multiple‐spin coherences: improved SLAP experiment

Contrary to common expectations, multiple‐spin coherences containing products of proton and heteronucleus operators (e.g. H_uC_x, u = x, y, z) can produce not only sidebands but also noticeable centerband NMR signals of the heteronucleus during acquisition under ¹H broadband decoupling. Such centerband signals of low abundant heteronuclei can be sources of relatively strong unexpected artifacts in NMR experiments that aim to detect very weak signals from much less‐abundant isotopomers, e.g. ¹³C–¹³C ones. These findings lead to a new design of Sign Labeled Polarization Transfer (SLAP) pulse sequence (MSS‐SLAP) with improved suppression of centerband peaks that are because of singly, e.g. ¹³C, labeled molecules (parent peaks). The MSS‐SLAP experiment and its MSS‐BIRD‐SLAP variant are compared with a few older SLAP versions. Copyright © 2015 John Wiley & Sons, Ltd.     

The synthesis, Na+ binding properties of new coumarin-crown ethers

o-Dihydroxy-3-(methylphenyl)-chromenones (coumarins; 3a–3c) were synthesized from trimethoxybenzaldehydes through a reaction with the corresponding methylphenyl-acrylonitrile in pyridine·HCl and then H₃O⁺. Dihydroxycoumarins reacted with the ditosylate or dichloride derivatives of tri- or tetraethyleneglycols in the presence of CH₃CN/Na₂CO₃ and macrocyclic ethers with a coumarin moiety were obtained. The chromatographically purified new coumarin-crown ethers (5a–5f) were identified by IR, ¹H NMR, and Mass spectrometry. The binding constants of Na⁺ with the coumarin-crown ethers were determined in an 80 % dioxane/water binary solvent system at 25 °C from conductance measurements.     

Salicylaldimine-bridged dinuclear cyclopalladated complexes: Synthesis,characterization and BSA binding studies

Salicylaldimine-bridged dinuclear cyclopalladated complexes were synthesized by the reactions of cyclopalladated chloro dimers [Pd{(4-R)C₆H₃CH=N-C₆H₃–2,6-i-Pr₂}(μ-Cl)]₂ (R = H; OMe) with salen-based bridging ligands. The complexes were characterized by FTIR, NMR spectroscopy, elemental analysis and X-ray crystallography. The binding interaction of cyclopalladated complexes to bovine serum albumin (BSA) was investigated by UV–vis, fluorescence and synchronous fluorescence spectroscopy. The experimental results showed that these Pd (II) complexes could bind to BSA with high affinity and quench its intrinsic fluorescence by a static or combined process. Also the interaction of Pd complexes with BSA affected the conformation of the tryptophan and tyrosine residues.     

Characterization of a new hexasodium diphosphopentamolybdate hydrate, Na6[P2Mo5O23]x7H2O, by 23Na MQMAS NMR spectroscopy and X-ray powder diffraction

A novel hexasodium disphosphopentamolybdate hydrate, Na6[P2Mo5O23]x7H2O, has been identified using X-ray powder diffraction, 1H, 23Na, and 31P magic-angle spinning (MAS) NMR, and 23Na multiple-quantum (MQ) MAS NMR. Powder XRD reveals that the hydrate belongs to the triclinic spacegroup P1 with cell dimensions a = 10.090(3) A, b = 15.448(5) A, c = 8.460(4) A, alpha = 101.45(6) degrees, beta = 104.09(2) degrees, gamma = 90.71(5) degrees, and Z = 2. The number of water molecules of crystallization has been determined on the basis of a quantitative evaluation of the 1H MAS NMR spectrum, the crystallographic unit cell volume, and a hydrogen content analysis. The 23Na MQMAS NMR spectra of Na6[P2Mo5O23]x7H2O, obtained at three different magnetic fields, clearly resolve resonances from six different sodium sites and allow a determination of the second-order quadrupolar effect parameters and isotropic chemical shifts for the individual resonances. These data are used to determine the quadrupole coupling parameters (CQ and eta Q) from simulations of the complex line shapes of the central transitions, observed in 23Na MAS NMR spectra at the three magnetic fields. This analysis illustrates the advantages of combining MQMAS and MAS NMR at moderate and high magnetic fields for a precise determination of quadrupole coupling parameters and isotropic chemical shifts for multiple sodium sites in inorganic systems. 31P MAS NMR demonstrates the presence of two distinct P sites in the asymmetric unit of Na6[P2Mo5O23].7H2O while the 31P chemical shielding anisotropy parameters, determined for this hydrate and for Na6[P2Mo5O23]x13H2O, show that these two hydrates can easily be distinguished using 31P MAS NMR.     

Determination of protein-ligand binding affinity by NMR: observations from serum albumin model systems

The usefulness of bovine serum albumin (BSA) as a model protein for testing NMR methods for the study of protein-ligand interactions is discussed. Isothermal titration calorimetry established the binding affinity and stoichiometry of the specific binding site for L-tryptophan, D-tryptophan, naproxen, ibuprofen, salicylic acid and warfarin. The binding affinities of the same ligands determined by NMR methods are universally weaker (larger KD). This is because the NMR methods are susceptible to interference from additional non-specific binding. The L-tryptophan-BSA and naproxen-BSA systems were the best behaved model systems.     

Determination of the binding parameters for antithrombin-heparin fragment systems by affinity and frontal analysis continuous capillary electrophoresis

The suitability of affinity capillary electrophoresis (ACE) and frontal analysis continuous capillary electrophoresis (FACCE) for binding constant determination was investigated for complexes between heparin fragments and antithrombin III, one of the main target proteins in the coagulation cascade. In a 100 mM ionic strength phosphate buffer (pH 7.4), ACE was suitable to determine weak to medium interactions developed by short oligomeric heparin fragments, but it failed for decasaccharide, which presents a more complex irreversible interaction. However FACCE allowed evaluating the binding constant for these longer oligomeric fragments. Both experimental approaches were complementary for a wide variety of heparinic fragments.