A laser Raman spectroscopic study of the interaction of calf-thymus DNA with Cu(II) and Pb(II) ions: metal ion binding and DNA conformational changes.

The interaction of calf-thymus DNA with Cu(II) and Pb(II) ions has been investigated in H2O and D2O solutions at physiological pH, using laser Raman spectroscopy. The results confirm the destabilizing effect of Cu2+ ions, which are shown to bind strongly to the guanine and cytidine bases, perturbing the A-T base pairs and disrupting the double-helical structure of DNA, whose conformation is markedly altered by these interactions. Earlier claims that Pb2+ ions destabilize DNA are not supported by the present study. These ions are found to interact only weakly with the nucleic bases, binding to the N7 position of the guanine bases and also interacting with the A-T pairs. Both types of ions are found to interact with the charged phosphate groups of DNA, although these sites are preferred over the nucleic bases by Pb2+ ions.     

Some aspects of the copper(II)-DNA interaction

The Cu(II) ion interaction with calf-thymus DNA was studied by means of differential pulse polarography and sweep voltammetry as well as chromatography and viscosimetry. Most of the complexes formed at high ionic strength (0.2 M) and lower Cu(II) concentrations are of a nondenaturing nature. Their formation has but a minor effect on unwinding process of the DNA double helix. The excess of Cu(II) (P = 5) leads, however, to distinct denaturation of the DNA structure. Metal ions have little effect on the denaturation induced by the polarographic reduction of DNA on the mercury electrode. This conclusion is consistent with the character of the polarographic process and with the fact that Cu(II) ions are not very effective in the interaction with AT pairs. Cupric ions have no renaturing ability towards thermally denatured DNA at 0.2 M ionic strength but distinct renaturation was observed at low ionic strength (0.05 M).     

Electrochemical behavior of neomycin at DNA-modified gold electrodes

Deoxyribonucleic acid (DNA) modified gold electrodes are prepared by the dry adsorptive method and the electrochemical behavior of neomycin and the influence of Pb(II) are studied by cyclic voltammetry, chronocoulometry, differential pulse voltammetry. It is found that in 0.01 M phosphate-buffered saline (PBS) buffer solutions (pH 7.3) at DNA/Au electrode neomycin exhibits an irreversible cathodic peak (E_p = 0.489 V), which is more positive and less sensitive compared with that at bare gold electrodes (E_p = 0.423 V). In the presence of Pb(II) the peak shifts toward positive with its height increasing. Moreover, the peak height is linear to neomycin concentration over the range of 0.15-57 μM. The interaction of Pb(II)-neomycin complex with calf thymus DNA is also studied by calculating the binding constants (K) of the Pb(II)-neomycin complex to DNA and binding site size (s) from voltammetric data (1.0 × 10⁷ M⁻¹ and 4 bp, respectively).     

Polyethyleneimine derivative for nucleic acid model

Water-soluble polyethyleneimine (PE) derivatives containing nucleic acid bases and hydrophilic amino acids such as homoserine (Hse) and serine were prepared by the activated ester method as nucleic acid models. From spectroscopic measurements, the polymers were found to interact with DNA accompanied by an induction of conformational change. Hypochromicity in UV spectra indicated that a stable polymer complex was formed between poly (A) with PEI-Hse-Ura by complementary hydrogen bonding with equimolar nucleic base units (adenine∶uracil=1∶1). The induced conformation of DNA by the interaction with the polymer containing uracil and homoserine (PEI-Hse-Ura) was concluded to be a super triple helical structure. The formation of the polymer complex, DNA:PEI-Hse-Ura, was found to be affected by the presence of metal ions such as Ca²⁺ and Cu²⁺.     

Role of the divalent cation in topoisomerase II mediated reactions

The effects of magnesium ions on interactions between Drosophila melanogaster topoisomerase II and its substrates were assessed by a number of kinetic and binding assays. Results indicated that the divalent cation plays two distinct functions in promoting enzyme-substrate interactions. One class of magnesium ions participates directly in enzyme-mediated DNA cleavage reactions. A second class of magnesium ions participates directly in topoisomerase II mediated ATPase reactions and functions by providing the enzyme with a magnesium-ATP substrate. In contrast, the divalent cation did not affect the quaternary structure of the enzyme, was not required for the site-specific binding of topoisomerase II to DNA, and did not affect the enzyme's ability to discern the topological state of its nucleic acid substrate.     

Utilization of heat-dried Pseudomonas aeruginosa biomass for voltammetric determination of Pb(II)

In this research, thermally dried Pseudomonas aeruginosa cells were used as a biological material for the construction of a microbial biosensor. The preparation, optimization and application of the developed microbial biosensor, which analyzed Pb(II), are presented. The method was based on stripping of adsorbed metal ions from the modified electrode surface. Modified carbon paste electrodes were preconcentrated at open circuit, and then electrochemically measured by using cyclic voltammetry (CV) and differential pulse stripping voltammetry (DPSV) techniques. It was found that the thermally dried cells were capable of adsorbing Pb(II) ions from aqueous solutions and could determine the ions prominently at optimum experimental conditions. Many important parameters to acquire the best electrochemical response were carried out, including effect of different electrolyte solutions, pH, deposition potential, deposition time, ionic strength, preconcentration time, and effect of interference ions. Finally, a calibration graph was obtained with a linear range from 1.0×10(-6) to 2.0×10(-5) M Pb(II) (R(2)=0.9916) and detection limit was found as 6.0×10(-7) M Pb(II) by using 3×S(b)/m formula. Other analytical properties of the developed microbial biosensor were also investigated. The suggested usage format of P. aeruginosa for the determination of Pb(II) does not require complicated immobilization procedure, easy to handle, and not time consuming.     

Simulation and modeling of nucleic acid structure, dynamics and interactions

In moving towards the simulation of larger nucleic acid assemblies over longer timescales that include more accurate representations of the environment, we are nearing the end of an era characterized by single nanosecond molecular dynamics simulation of nucleic acids. We are excited by the promise and predictability of the modeling methods, yet remain prudently cautious of sampling and force field limitations. Highlights include the accurate representation of subtle drug-DNA interactions, the detailed study of modified and unusual nucleic acid structures, insight into the influence of dynamics on the structure of DNA, and exploration of the interaction of solvent and ions with nucleic acids.     

Pb EXAFS studies on DNA quadruplexes: identification of metal ion binding site

Nucleic acid quadruplexes are composed of guanine quartets stabilized by specific metal ions. X-ray diffraction can provide high-resolution information on the structure and metal binding properties of quadruplexes, but only if they can be crystallized. NMR can provide detailed information on the solution structure of such quadruplexes but little quantitative data concerning the metal binding site. Here we apply extended X-ray absorption fine structure (EXAFS) measurements to characterize the metal ion binding site, in frozen solution, of the unimolecular quadruplex formed by the thrombin binding aptamer, d(G(2)T(2)G(2)TGTG(2)T(2)G(2)) (TBA), in the presence of Pb(2+) ions. The Pb L(III) -edge X-ray absorption spectrum of this metal-DNA complex is very similar to that we obtain for a Pb(2+)-stabilized quartet system of known structure constructed from a modified guanine nucleoside (G1). The Fourier transforms of the Pb(2+) complexes with both TBA and G1 show a first-shell interaction at about 2.6 A, and a weaker, broader shell at 3.5-4.0 A. Quantitative analysis of the EXAFS data reveals the following: (i) very close agreement between interatomic distances at the metal coordination site for the Pb(2+)-G1 complex determined by EXAFS and by X-ray crystallography; (ii) similarly close agreement between interatomic distances measured by EXAFS for the Pb(2+)-G1 and Pb(2+)-TBA complexes. These results provide strong evidence for binding of the Pb(2+) ion in the region between the two quartets in the Pb(2+)-TBA complex, coordinated to the eight surrounding guanine O6 atoms. The specific binding of Pb(2+) to DNA examined here may be relevant to the genotoxic effects of this environmentally important heavy metal. Furthermore, these results demonstrate the utility of EXAFS as a method for quantitative characterization of specific metal binding sites in nucleic acids in solution.     

Current aspects in metal genotoxicity

While carcinogenic metal ions are mostly non-mutagenic in bacteria, different types of cellular damage have been observed in mammalian cells, which may account for their carcinogenic potential. Two modes of action seem to be predominant: the induction of oxidative DNA damage, best established for chromium compounds, and the interaction with DNA repair processes, leading to an enhancement of genotoxicity in combination with a variety of DNA damaging agents. In the case of Cd(II), Ni(II), Co(II), Pb(II) and As(III), DNA repair processes are disturbed at low, non-cytotoxic concentrations of the respective metal compounds. Even though different steps in DNA repair are affected by the diverse metals, one common mechanism might be the competition with essential metal ions.     

功能核酸DNA水凝胶的制备与组装

功能核酸DNA水凝胶是一种以DNA为构建单元通过化学反应或物理缠结自组装而成的新型柔性材料,其构建单元中包含1种或多种能够形成功能核酸的特定序列。功能核酸是通过碱基修饰和DNA分子之间的相互作用力组合的一类特定核酸结构,包括核酸适配体、DNA核酶、G-四联体(G-quadruplex,G4)和i-motif结构等。传统上,高浓度的长DNA链是制备DNA水凝胶的必要条件,而核酸扩增方法的引入为DNA水凝胶的组装方式提供了新的可能。因此,对常用于制备DNA水凝胶的多种功能核酸以及核酸的提取、合成和扩增手段进行了详细的介绍。在此基础上,综述了通过化学或物理交联方式组装功能核酸DNA水凝胶的制备方法。最后,提出了DNA纳米材料的组装所面临的挑战和潜在的发展方向,以期为开发高效组装的功能核酸DNA水凝胶提供参考。     

Dissecting the metal ion dependence of DNA binding by PvuII endonuclease.

Divalent cations can provide an effective means of modulating the behavior of nucleic acid binding proteins. As a result, there is strong interest in understanding the role of metal ions in the function of both nucleic acid binding proteins and their enzymes. We have applied complementary fluorescence spectroscopic and nitrocellulose filter binding assays to quantitate the role of metal ions in mediating DNA binding and sequence specificity by the representative PvuII endonuclease. At pH 7.5 in the presence of the catalytically nonsupportive Ca(II), this enzyme binds the PvuII target sequence with a K(d) of 50 pM. Under strict metal-free conditions, the enzyme exhibits a K(d) of only 300 nM for the cognate sequence, an affinity which is weak relative to those measured for other systems in the absence of metal ions. This represents a 6000-fold increase in PvuII affinity for cognate DNA upon the addition of Ca(II). The pH dependences of both metal ion-dependent and metal ion-independent DNA binding are remarkably shallow throughout the physiological range; other characterized restriction enzymes exhibit more pronounced pH dependences of DNA binding even in the absence of metal ions. Similar measurements with noncognate sequences indicate that divalent metal ions are not important to nonspecific DNA binding; K(d) values are approximately equal to 200 nM throughout the physiological pH range, a behavior shared with other endonucleases. While some of these results extend somewhat the range of expected behavior for restriction enzymes, these results indicate that PvuII endonuclease shares with other characterized systems a mechanism by which cognate affinity and sequence discrimination are most effectively achieved in the presence of divalent metal ions.     

Synthesis and DNA binding studies of Mg(II) complex of Schiff base derived from vanillin and L-tryptophan

The Mg(II) complex of Schiff base (K[HL]) derived from vanillin and L-tryptophan could bind with herring sperm DNA. The binding behaviors between them in physiological pH environment (pH 7.40) have been studied by spectroscopy, cyclic voltammetry and viscosity methods. Binding ratios of n(Mg(II)): n(K[HL])?= 1:1 and n(Mg(II)L): n(DNA)?= 5:1 were confirmed. The obtained thermodynamic parameters suggest that the interaction between Mg(II)L and DNA is driven mainly by entropy. Combined with fluorimeteric studies, cyclic voltammetry, CD spectroscopy and viscosity methods, the results indicate the interaction modes between Mg(II)L and DNA are mainly with intercalation and involving some electrostatic interaction.     

Interaction of Pb(II) ions with C-phycocyanin from Spirulina platensis: effect of ionic strength

The effect of Pb(II) ions on C-phycocyanin from Spirulina platensis was studied by the method of fluorescence spectroscopy. The efficiency of quenching was analyzed using the Stern-Volmer relation. Isotherms of adsorption were constructed, and the constants of binding of Pb(II) ions to C-phycocyanin in solutions of varying ionic strength were determined by equilibrium dialysis and atomic absorption spectroscopy. The constants of binding of Pb(II) ions to C-phycocyanin in 2, 20, and 50 mM NaN03 solutions were estimated to be 4.79 x 10(5), 3.63 x 10(5) and 2.82 x 10(5), respectively. It was found that the interaction of Pb(II) ions with C-phycocyanin has a cooperative character at all values of ionic strengths studied.     

The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins

Using sensitive structure similarity searches, we identify a shared alpha+beta fold, RAGNYA, principally involved in nucleic acid, nucleotide or peptide interactions in a diverse group of proteins. These include the Ribosomal proteins L3 and L1, ATP-grasp modules, the GYF domain, DNA-recombination proteins of the NinB family from caudate bacteriophages, the C-terminal DNA-interacting domain of the Y-family DNA polymerases, the uncharacterized enzyme AMMECR1, the siRNA silencing repressor of tombusviruses, tRNA Wybutosine biosynthesis enzyme Tyw3p, DNA/RNA ligases and related nucleotidyltransferases and the Enhancer of rudimentary proteins. This fold exhibits three distinct circularly permuted versions and is composed of an internal repeat of a unit with two-strands and a helix. We show that despite considerable structural diversity in the fold, its representatives show a common mode of nucleic acid or nucleotide interaction via the exposed face of the sheet. Using this information and sensitive profile-based sequence searches: (1) we predict the active site, and mode of substrate interaction of the Wybutosine biosynthesis enzyme, Tyw3p, and a potential catalytic role for AMMECR1. (2) We provide insights regarding the mode of nucleic acid interaction of the NinB proteins, and the evolution of the active site of classical ATP-grasp enzymes and DNA/RNA ligases. (3) We also present evidence for a bacterial origin of the GYF domain and propose how this version of the fold might have been utilized in peptide interactions in the context of nucleoprotein complexes.     

Analysing DNA complexes by circular and linear dichroism

The application of linear and circular dichroism (LD and CD) in nucleic acid research id illustrated by recent results aimed at answering specific structural problem in the interaction of DNA with molecules of biological importance. We first consider the circumstances under which ligands, such as DAPI (4′, 6-diamidino-2-phenylindole), change their preferred binding mode in the minor groove to major groove binding or intercalation. As an extension of this problem we refer to the switch between groove binding and intercalation of structurally similar ligands such as ellipticines and trigonal ruthenium complexes. We also explore the use of LD and CD in the determination of the structure of the complex formed between the polynucleotide poly(dA) and the novel ‘peptide nucleic acid’, consisting of nucleic acid bases joined by a polyamide homomorphous with the deoxyribose-phosphate backbone of DNA. Finally, the structure and interaction of the recombination enzyme RecA with DNA is discussed, in particular the influence of the presence of the intercalators, groove binders or covalent DNA adducts.     

Constants of binding of Pb(II) ions with DNA at various ionic strength]

The energetics of Pb(II) ion binding to DNA was determined from their binding isotherms by equilibrium dialysis and atomic absorption spectroscopy at different ionic strengths. Two types of binding of Pb(II) ions to DNA at different NaCl concentrations were observed.     

Nucleic acid binding and chaperone properties of HIV-1 Gag and nucleocapsid proteins

The Gag polyprotein of HIV-1 is essential for retroviral replication and packaging. The nucleocapsid (NC) protein is the primary region for the interaction of Gag with nucleic acids. In this study, we examine the interactions of Gag and its NC cleavage products (NCp15, NCp9 and NCp7) with nucleic acids using solution and single molecule experiments. The NC cleavage products bound DNA with comparable affinity and strongly destabilized the DNA duplex. In contrast, the binding constant of Gag to DNA was found to be ~10-fold higher than that of the NC proteins, and its destabilizing effect on dsDNA was negligible. These findings are consistent with the primary function of Gag as a nucleic acid binding and packaging protein and the primary function of the NC proteins as nucleic acid chaperones. Also, our results suggest that NCp7's capability for fast sequence-nonspecific nucleic acid duplex destabilization, as well as its ability to facilitate nucleic acid strand annealing by inducing electrostatic attraction between strands, likely optimize the fully processed NC protein to facilitate complex nucleic acid secondary structure rearrangements. In contrast, Gag's stronger DNA binding and aggregation capabilities likely make it an effective chaperone for processes that do not require significant duplex destabilization.     

Nature of active sites during complex formation of DNA and Pt (II) compounds]

Quantitative estimation of the binding of Pt (II) with DNA and its derivatives is carried out and the selectivity of this reaction is studied. Absorption spectra and binding curves of Pt (II) with GC- and AT-enriched DNA fractions, apurinic and apyrimidinic acids, poly A and deoxyribonucleotides are studied. The strongest Pt (II) binding was observed in cytosine-containing nucleic acid components. The reduction of Pt (II) to Pt (O) took place only in the presence of cytosine. Adenine component was found to form 1 : 1 complex with chloroplatinit. A model of Pt (II) : DNA complex is proposed, in which a metal ion is bound with cytosine cycle through N3 atom. A complex is formed due to a high electron-acceptor capacity of cytosine cycle, the charge being transferred between platinum and DNA base. Thus, complex-bound platinum is capable of oxidating platinum ions in the solution.