Single‐Cell Investigations of Silver Nanoparticle–Bacteria Interactions

Interaction of bacteria with citrate‐reduced silver nanoparticles (AgNPs) of size 25 nm ± 8.5 nm is studied using Raman spectroscopy in conjunction with plasmon resonance imaging of single bacterial cells. Distribution of isolated nanoparticles (NPs) inside Escherichia coli (ATCC 25922; E. coli) is observed by hyperspectral imaging (HSI) as a function of incubation time. Time‐dependent degradation of bacterial DNA upon incubation of AgNPs with E. coli is proven by Raman spectroscopic studies. While attachment of NPs is evident in HSI, molecular changes are evident from the surface‐enhanced Raman spectra of adsorbed DNA and its fragments. Distinct enhancement of DNA features is observed upon interaction of AgNPs and the number of such distinct features increases with incubation time, reaches a maximum, and decreases afterwards. This systematic interaction of DNA with the NPs system and its gradual chemical evolution is proven by investigating isolated plasmid DNA. A comparative Raman study with silver ions has shown that DNA features are observable only when bacteria are incubated with AgNPs. Energetics of interaction examined with microcalorimetry suggests the exothermicity of ?1.547 × 10¹⁰ cal mol^?1 for the NP–bacteria system. Specific interaction of AgNPs with exocyclic nitrogen present in the bases, adenine, guanine, and cytosine, leads to the changes in DNA.     

Symmetry of electrostatic interaction between pyrophosphate DNA molecules

We study chiral electrostatic interaction between artificial ideal homopolymer DNA-like molecules in which a number of phosphate groups of the sugar-phosphate backbone are exchanged for the pyrophosphate ones. We employ a model in which the DNA is considered as a one-dimensional lattice of dipoles and charges corresponding to base pairs and (pyro)phosphate groups, respectively. The interaction between molecules of the DNA is described by a pair potential U of electrostatic forces between the two sets of dipoles and charges belonging to respective lattices describing the molecules. Minima of the potential U indicate orientational ordering of the molecules and thus liquid crystalline phases of the DNA. We use numerical methods for finding the set of minima in conjunction with symmetries verified by the potential U . The symmetries form a non-commutative group of 8th order, S . Using the group S we suggest a classification of liquid crystalline phases of the DNA, which allows several cholesteric phases, that is polymorphism. Pyrophosphate forms of the DNA could clarify the role played by charges in their liquid crystalline phases, and open experimental research, important for nano-technological and bio-medical applications.     

Stabilization of Pt nanoparticles by single stranded DNA and the binary assembly of Au and Pt nanoparticles without hybridization

The non-specific interaction between single stranded DNA (ssDNA) and 12 nm Pt nanoparticles is investigated in this work. The data show a strong and non-specific interaction between the two which can be exploited for the stabilization of Pt nanoparticles in aqueous solutions. Based on the experimental findings, a non-hybridization based protocol to assemble 17 nm Au and Pt nanoparticles (12 nm cubic and 3.6 nm spherical) by single-stranded DNA was developed. Transmission electron microscopy (TEM) and UV–visible spectroscopy confirmed that Au and Pt nanoparticles could be assembled by the non-specific interaction in an orderly manner. The experimental results also caution against the potential pitfalls in using DNA melting point analysis to infer metal nanoparticle assembly by DNA hybridization.     

Interaction of a New Fluorescent Probe with DNA and its Use in Determination of DNA

In this paper we reported a metal complex 1-Zn (2,5-di-[2-(3,5-bis(2-pyridylmethyl)amine-4-hydroxy-phenyl)-ethylene]-pyrazine-Zn) as a fluorescent probe sensing DNA. The result of the competitive experiment of the probe with ethidium bromide (EB) to bind DNA, absorption spectral change and polarization change in the presence and absence of DNA revealed that interaction between the probe and DNA was via intercalation. Ionic strength experiment showed the existence of electrostatic interaction as well. Scatchard plots also confirmed the combined binding modes. The fluorescence enhancement of the probe was ascribed to highly hydrophobic environment when it bound the macromolecules such as DNA, RNA or denatured DNA. The binding constant between the probe and DNA was estimated as 3.13 × 10⁷ mol⁻¹ L. The emission intensity increase was proportional to the concentration of DNA. Based on this, the probe was used to determine the concentration of calf thymus DNA (ct-DNA). The corresponding linear response ranged from 2.50 × 10⁻⁷ to 4.75 × 10⁻⁶ mol L⁻¹, and detection limit was 1.93 × 10⁻⁸ mol L⁻¹ for ct-DNA.     

Counterion vibrations in the DNA low-frequency spectra

The vibrations of univalent metal cations with respect to phosphate groups of the DNA backbone are described using the four-mass model approach (S.N. Volkov, S.N. Kosevich, J. Biomol. Struct. Dyn. 8, 1069 (1991)) extended in this paper. The force constant of the counterion-phosphate interaction is determined by considering the DNA with counterions as a lattice of ion crystal. For such ion-phosphate lattice the Madelung constant and the dielectric constant are estimated. The obtained value of the Madelung constant is lower than for the NaCl crystal, and its value is about 1.3. The dielectric constant is within 2.3-2.7 depending on the counterion type and form of the double helix. The calculations of the low-frequency spectra show that for the DNA with metal cations Na⁺ , K⁺ , Rb⁺ and Cs⁺ the frequency of ion-phosphate vibrations decreases from 174 to 96cm^-1 as the counterion mass increases. The obtained frequencies agree well with the vibrational spectra of polynucleotides in a dry state which prove our suggestion about the existence of the ion-phosphate lattice around the DNA double helix. The amplitudes of conformational vibrations for DNA in B -form are calculated as well. The results demonstrate that light counterions ( Na⁺ do not disturb the internal dynamics of the DNA. However, heavy counterions ( Cs⁺ have effect on the internal vibrations of the DNA structural elements.     

The Mechanism of Benzothiazole Styrylcyanine Dyes Binding with dsDNA: Studies by Spectral-Luminescent Methods

In the presented work studies of the interaction mode of monomer and two homodimer benzothiazole styryl dyes containing spermine-like linkage/tail group with the double stranded (ds) DNA are reported. For these dyes, equilibrium constant of dye binding to DNA (K _b), as well as the number of dsDNA base pairs occupied by one bound dye molecule (n) were determined. The data obtained show that the presence of spermine-like group containing quaternary nitrogen (Bos-5) results in increase of K _b value as compared to this of unsubstituted analogue (Sbt). Besides, for the dimer dyes containing benzothiazole styryl chromophores, the K _b value is either five times higher (DBos-13) or almost the same (DBsu-10) as compared to this of corresponding monomer Sbt, depending on the position in the benzothiazole ring where the linker is attached. Moreover, the n values for both dimers are significantly different as well, pointing to the bis-intercalative binding mechanism for DBos-13 and for the groove-binding one for DBsu-10. The conclusion about the dimer dyes-dsDNA binding mechanisms is also supported by the study of the fluorescent response of these dyes on the presence of AT- and GC-containing polynucleotides.     

Comparative Theoretical Study of Hyperfine Interactions of Muonium in A- and B-Form DNA

Muon Spin Relaxation (μSR) experiments in A- and B-form DNA have shown evidence for an enhanced electron mobility in the more closely-packed A-form. Besides dynamic effects (electronic diffusion) that could cause the observed difference in muon spin relaxation, one should also carefully examine the difference in the strengths of the hyperfine interactions of the muon (μ ⁺) with the moving electron in the two forms of DNA, since this could contribute to the observed difference in the muon spin relaxation rates as well. We have therefore investigated the (static) trapping properties of muon and muonium (μ ⁺ e ⁻) in A-form and B-form DNA from first-principles with the aim to understand how the different structural geometries of A- and B-form DNA can influence the hyperfine interaction of trapped muonium.     

Modeling of recognition sites of nucleic acid bases aaand amide side chains of amino acids. Combination of experimental and theoretical approaches

A combined experimental-theoretical approach to modeling of building blocks of recognition complexes formed by nucleic acid bases and the amino-acids side-chain amino group is reviewed. The approach includes the temperature dependent field-ionization mass spectrometry and ab initio quantum chemical calculations. The mass spectrometric technique allows determination of interaction enthalpies of biomolecules in the gas phase, and the results it produces are directly comparable to the results obtained through theoretical modeling. In our works we have analyzed both thermodynamic and structural aspects of the recognition complexes of four canonical nucleic acid bases and acrylamide, which models the side chain of asparagine and glutamine. It has been shown that all bases can interact with amide group of the amino acids via their Watson-Crick sites when being incorporated into a single strand DNA or RNA. Stability of the complexes studied, expressed as - ΔH (kJ mole^-1) decreases as: m⁹Gua (- 59.5) > m ¹Cyt (- 57.0) > m ⁹Ade (- 52.0) ≫m ¹Ura (- 40.6). We have determined that in the double stranded DNA only purine bases can be recognized. Received 5 February 2002 and Received in final form 14 March 2002 Published online 13 September 2002     

Recent developments in monitoring calcium and protein interactions in cells using fluorescence lifetime microscopy

Time-resolved fluorescence lifetime microscopy (TRFLM) allows the combination of the sensitivity of fluorescence lifetime to environmental parameters to be monitored in a spatial manner in single living cells, as well as providing more accurate, sensitive, and specific diagnosis of certain clinical diseases and chemical analyses. Here we discuss two applications of TRFLM: (1) the use of nonratiometric probes such as Calcium Crimson, for measuring Ca²⁺; and (2) quantification of protein interaction in living cells using green and blue fluorescent protein (GFP and BFP, respectively) expressing constructs in combination with fluorescence resonance energy transfer microscopy (FRET). With respect to measuring Ca²⁺ in biological samples, we demonstrate thatintensity-based measurements of Ca²⁺ with single-wavelength Ca²⁺ probes such as Calcium Crimson may falsely report the actual Ca²⁺ concentration. This is due to effects of hydrophobicity of the local environment on the emission of Calcium Crimson as well as interaction of Calcium Crimson with proteins, both of which are overcome by the use of TRFLM. The recent availability of BFP (P4-3) and GFP (S65T) (which can serve as donor and acceptor, respectively) DNA sequences which can be attached to the carboxy-or amino-terminal DNA sequence of specific proteins allows the dual expression and interaction of proteins conjugated to BFP and GFP to be monitored in individual cells using FRET. Both of these applications of TRFLM are expected to enhance substantially the information available regarding both the normal and the abnormal physiology of cells and tissues.     

Study on the toxic interactions of Ni with DNA using neutral red dye as a fluorescence probe

The interaction between Ni²⁺ and calf thymus DNA (ctDNA) was investigated in simulated physiological buffer (pH 7.4) using the Neutral Red (NR) dye as a spectral probe by UV-vis absorption and fluorescence spectroscopy, as well as CD spectra. The experimental results showed that the conformational changes in DNA helix induced by Ni²⁺ are the reason for the fluorescence quenching of the DNA-NR system. From the experimental results, conclusion can be drawn that Ni²⁺ can cause structural changes of ctDNA and bind with DNA by electrostatic interaction. At the same time, the paper proved that conformation changes of DNA can also lead to the fluorescence decrease of DNA-probe systems.     

Propagation and interaction of ion-acoustic solitary waves in a quantum electron-positron-ion plasma

This paper discusses the existence of ion-acoustic solitary waves and their interaction in a dense quantum electron-positron-ion plasma by using the quantum hydrodynamic equations.The extended Poincar’e-Lighthill-Kuo perturbation method is used to derive the Korteweg-de Vries equations for quantum ion-acoustic solitary waves in this plasma.The effects of the ratio of positrons to ions unperturbation number density p and the quantum diffraction parameter H e (H p) on the newly formed wave during interaction,and the phase shift of the colliding solitary waves are studied.It is found that the interaction between two solitary waves fits linear superposition principle and these plasma parameters have significantly influence on the newly formed wave and phase shift of the colliding solitary waves.The investigations should be useful for understanding the propagation and interaction of ion-acoustic solitary waves in dense astrophysical plasmas (such as white dwarfs) as well as in intense laser-solid matter interaction experiments.     

Dense coding with a two-qubit Heisenberg XYZ chain under the influence of phase decoherence

We investigate the joint effects of phase decoherence,Dzyaloshinskii-Moriya(DM) interaction and inhomogeneity of the external magnetic field(b) on dense coding in a two-qubit anisotropic Heisenberg XY Z spin chain.Analytical expressions are obtained for the dense coding capacity.It is found that valid dense coding is always possible with this model when the system is initially prepared in the maximum entangled state.Moreover,optimal dense coding can be implemented for this initial state as long as the mean spin-spin coupling constant J + of the XY plane is larger than b and the DM interaction despite the intrinsic decoherence.Non-maximal entangled initial states are found to be undesirable for dense coding with this model.     

Magnetic properties of DNA-templated Co/Cu naonoparticle chains

<正>According to ultraviolet(UV)-vis absorption spectra recorded in the DNA metallization process,DNA-templated Co/Cu binary nanoparticle chains are fabricated by incubating genome DNA of paralichthys olivaceus muscle in CoCl_2 and CuCl_2 mixture solution for 20 hours and reducing the complex for 2 hours.Transmission electron microscopy observation indicates that Co and Cu nanoparticles with 20 nm in diameter were randomly dispersed on the DNA template. The superconducting quantum interference device(SQUID) measurements display that the magnetic interaction between cobalt particles is greatly decreased by the copper particle.With increasing copper content,the coercivity of the systems enhance from 9 Oe to 100 Oe(1 Oe=79.5775 A/m).     

Critical Stability in Nuclei – An Old Problem Revisited

In this paper we will focus on the nucleon-nucleon interaction in relative S-states. The ¹S₀ interaction is known to be close to that for critical two-body binding. We will discuss two approaches to the NN interaction, which are equivalent on-shell but not off-shell. There is a well-defined transformation between these approaches [1]. One (my preferred approach) is to minimize the tensor forces far off-shell, which leads to more rapid convergence, but at the price of significant non-locality. This approach is used in a model of relativistic tensor quenching of OPEP [2]. With non-local NN interactions it is possible to fit not only NN observables, but also the NNN ground-state energies [3]. The other approach is to maximize the role of the and keep the interaction as local as possible [4]. This approach is also internally consistent, but requires additional NNN interactions to fit nuclear data. Also, we discuss briefly a so-called low momentum interaction [5, 6], which fits S-wave phase shifts quite well. This interaction is strongly non-local, and it can be approximated by a schematic separable interaction. Finally, we mention the Nambu–Jona-Lasinio model [7] and a good approximation, the Hulthen potential, which provides some insight into the near critical two-body binding.     

Phase diagrams in mixed spin-3/2 and spin-2 Ising system with two alternative layers within the effective-field theory

The phase diagrams in the mixed spin-3/2 and spin-2 Ising system with two alternative layers on a honeycomb lattice are investigated and discussed by the use of the effective-field theory with correlations. The interaction of the nearest-neighbour spins of each layer is taken to be positive (ferromagnetic interaction) and the interaction of the adjacent spins of the nearest-neighbour layers is considered to be either positive or negative (ferromagnetic or anti-ferromagnetic interaction). The temperature dependence of the layer magnetizations of the system is examined to characterize the nature (continuous or discontinuous) of the phase transitions and obtain the phase transition temperatures. The system exhibits both second-and first-order phase transitions besides triple point (T P ), critical end point (E), multicritical point (A), isolated critical point (C) and reentrant behaviour depending on the interaction parameters. We have also studied the temperature dependence of the total magnetization to find the compensation points, as well as to determine the type of behaviour, and N-type behaviour in N′eel classification nomenclature existing in the system. The phase diagrams are constructed in eight different planes and it is found that the system also presents the compensation phenomena depending on the sign of the bilinear exchange interactions.     

Symmetries of electrostatic interaction between DNA molecules

A model for pair interaction U of DNA molecules generated by the discrete dipole moments of base-pairs and the charges of phosphate groups is studied. A noncommutative group of eighth order ℒ of symmetries that leave U invariant is found. The minima are classified with the use of group ℒ and numerical methods are employed for finding them. The minima may correspond to several cholesteric phases, as well as to phases formed by crosslike conformations of molecules at an angle close to 90°—the “snowflake phase.” The results depend on the effective charge Q of the phosphate group, which can be modified by the polycations or the ions of metals. The snowflake phase could exist for Q above the threshold Q _C. Below Q _C, there could be several cholesteric phases. Close to Q _C, the snowflake phase could change into the cholesteric one at constant distance between adjacent molecules. The text was submitted by the authors in English.     

Rare earth paramagnetism,as studied by μSR

Some recent result of muon spin relaxation measurements in rare earth metals and intermetallic compounds are reviewed. Special emphasis is put on measurements that relate to the properties of correlated regions of spins existing relatively far above the ordering temperature in the rare earth ions. As far as comparable data from paramagnetic neutron scattering exist, they will be discussed in the same framework. For each temperature the correlated regions (or short-lived magnetic clusters) are characterized by their size, possible anisotropy with respect to the crystalline axes and their lifetime. The actual form of the interaction between the rare earth spins themselves and with the crystal fields determine the temperature dependence of these properties; a strong dipole interaction can, for instance, be expected to change the critical behaviour nearT _c . Much of the time will be devoted to experiments on Gd-metal where there are experimental indications that several interesting phenomena occur: (1) a strong effect of a cross-over from a non-conserved dynamics (dipolar) regime to a conserved (exchange dominated) regime some 10 K aboveT _c , (2) an anisotropy of the magnetic clusters with respect to the hexagonalc-axis, and (3), a persistence of spin correlations far aboveT _c . Some attempts to correlate the rare earth spin relaxation times measured in this region with cluster lifetimes deduced from neutron scattering will be reviewed, as well as a model for understanding these lifetimes in terms of temperature dependent cluster wall motion, which is determined by exchange and magnetic anisotropy parameters. Effects of possible quantum correlations originating from the “spin system+bath” interaction will be mentioned.     

Locating of Nucleic Acid Intercalators in Yeast Cells by Image Analysis Combined Fluorescence Microscopy

Intracellular distribution in the intact (not fixed) Saccharomyces cerevisiae cells of the nucleic acid intercalators (NAI) was studied using fluorescence microscopy combined with computer image analysis (ImageJ software, NIH, USA). Three NAI—the anthracycline anticancer drug doxorubicin (DR) along with the nucleic acid dyes ethidium (E) and 4′,6-diamidino-2-phenylindole (DAPI)—were used. Staining pattern and ImageJ quantitative analysis data provided evidence that all three NAI were located in the nuclei and in the mitochondria. DR and E, in contrast to DAPI, may be bound to not only DNA, but to the mitochondrial membranes as well. Experiments on the combined application of DR+DAPI and E+DAPI have shown potential competition of DAPI with DR and E for binding sites in the nuclear and mitochondrial DNA. With the approach presented herein, the yeast cells of S. cerevisiae can be used as a model for locating intracellular sites of the fluorescing nucleic acid intercalators. This model may be of help in designing new DNA-targeted drugs and in preliminary studies of their interaction with eukaryotic cells.     

Structural phase transition and elastic properties of ZnSe at high pressure

We have evolved an effective interionic interaction potential to investigate the pressure-induced phase transitions from zinc blende (B3) to rock salt (B1) structure in II-VI [ZnSe] semiconductors. The elastic constants, including the long-range Coulomb and van der Waals (vdW) interactions and the short-range repulsive interaction of up to second-neighbor ions within the Hafemeister and Flygare approach, are deduced. Keeping in mind that both of the ions are polarisable, we employed the Slater-Kirkwood variational method to estimate the vdW coefficients. The estimated value of the phase transition pressure (P _t ) is higher than in the reported data, and the magnitude of the discontinuity in volume at the transition pressure is consistent with that data. The major volume discontinuity in the pressure-volume phase diagram identifies the structural phase transition from zinc blende to rock salt structure.

The variation of second-order elastic constants with pressure resembles that observed in some binary semiconductors. It is inferred that the vdW interaction is effective in obtaining the thermodynamic parameters such as the Debye temperature, the Gruneisen parameter, the thermal expansion coefficient and the compressibility. However, the inconsistency between the thermodynamic parameters as obtained from present model calculations and their experimental values is attributed to the fact that we have derived our expressions by assuming the overlap repulsion to be significant only up to the nearest second-neighbor ions, as well as neglecting thermal effects. It is thus argued that full analysis of the many physical interactions that are essential to binary semiconductors will lead to a consistent explanation of the structural and elastic properties of II–VI semiconductors.