Escherichia coli Single-Stranded DNA-Binding Protein: NanoESI-MS Studies of Salt-Modulated Subunit Exchange and DNA Binding Transactions

Single-stranded DNA-binding proteins (SSBs) are ubiquitous oligomeric proteins that bind with very high affinity to single-stranded DNA and have a variety of essential roles in DNA metabolism. Nanoelectrospray ionization mass spectrometry (nanoESI-MS) was used to monitor subunit exchange in full-length and truncated forms of the homotetrameric SSB from Escherichia coli. Subunit exchange in the native protein was found to occur slowly over a period of hours, but was significantly more rapid in a truncated variant of SSB from which the eight C-terminal residues were deleted. This effect is proposed to result from C-terminus mediated stabilization of the SSB tetramer, in which the C-termini interact with the DNA-binding cores of adjacent subunits. NanoESI-MS was also used to examine DNA binding to the SSB tetramer. Binding of single-stranded oligonucleotides [one molecule of (dT)₇₀, one molecule of (dT)₃₅, or two molecules of (dT)₃₅] was found to prevent SSB subunit exchange. Transfer of SSB tetramers between discrete oligonucleotides was also observed and is consistent with predictions from solution-phase studies, suggesting that SSB-DNA complexes can be reliably analyzed by ESI mass spectrometry.      

MALDI‐MS detection of noncovalent interactions of single stranded DNA with Escherichia coli single‐stranded DNA‐binding protein

The Escherichia coli single‐stranded DNA binding protein (SSB) selectively binds single‐stranded (ss) DNA and participates in the process of DNA replication, recombination and repair. Different binding modes have previously been observed in SSB?ssDNA complexes, due to the four potential binding sites of SSB. Here, chemical cross‐linking, combined with high‐mass matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry (MS), is used to determine the stoichiometry of the SSB?ssDNA complex. SSB forms a stable homotetramer in solution, but only the monomeric species (m/z 19 100) can be detected with standard MALDI‐MS. With chemical cross‐linking, the quaternary structure of SSB is conserved, and the tetramer (m/z 79 500) was observed. We found that ssDNA also functions as a stabilizer to conserve the quaternary structure of SSB, as evidenced by the detection of a SSB?ssDNA complex at m/z 94 200 even in the absence of chemical cross‐linking. The stability of the SSB?ssDNA complex with MALDI strongly depends on the length and strand of oligonucleotides and the stoichiometry of the SSB?ssDNA complex, which could be attributed to electrostatic interactions that are enhanced in the gas phase. The key factor affecting the stoichiometry of the SSB?ssDNA complex is how ssDNA binds to SSB, rather than the protein‐to‐DNA ratio. This further suggests that detection of the complex by MALDI is a result of specific binding, and not due to non‐specific aggregation in the MALDI plume. Copyright © 2012 John Wiley & Sons, Ltd.     

Synthesis, crystal structures, DNA binding and cleavage studies of two oxovanadium(IV) complexes of 1,10-phenanthroline and Schiff bases derived from tryptophan

Two new V(IV) complexes, [VO(Naph?Ctrp)(phen)]·CH₃OH (1) and [VO(o-Van?Ctrp)(phen)]·CH₃OH·H₂O (2) (Naph?CTrp?=?Schiff base derived from 2-hydroxy-1-naphthaldehyde and l-tryptophan, o-Van?Ctrp?=?Schiff base derived from o-vanillin and l-tryptophan, phen?=?1,10-phenanthroline), have been synthesized and characterized by physicochemical methods. The V(IV) atoms in both complexes are six-coordinated in a distorted octahedral environment. In the crystals of complex 1, the C?CH···?? and ?ШC?? stacking interactions form a 1D chain structure, whereas for complex 2, hydrogen bonds connect the molecular units into a 2D plane structure. The DNA binding properties and cleavage efficiencies of the complexes have been investigated by spectroscopic methods, viscosity measurements and agarose gel electrophoresis. The results suggest that both complexes can bind to CT-DNA in an intercalative mode and can also cleave pBR322 DNA.     

Synthesis, crystal structure, and interaction with DNA of a novel coordination polymer: {[Cd(Pmal)(Bipy)] · 4H2O} n

A novel coordination polymer {[Cd(Pmal)(Bipy)] · 4H₂O} _n (I), where Bipy = 2,2??-Bipyridine, Pmal = phenethylmalonate, has been synthesized and characterized using IR, ¹H NMR, elemental analysis, and single-crystal X-ray diffractometry. The unit cell parameters for complex I: a = 12.3752(15), b = 6.8283(9), c = 13.4739(17) ?, ?? = 91.108(2)°, V = 1138.4(2) ?³, Z = 2, space group P2₁. The binding of complex I with fish sperm DNA (FS-DNA) was investigated by fluorescence spectroscopy, showing that the complex has the ability of interaction with DNA. Gel-electrophoresis assay demonstrates the ability of complex I to cleave the pBR322 plasmid DNA.     

Nucleic acid-binding comparative studies and cytotoxic properties of a Ru(II) complex

The comparative studies on the interaction of a ruthenium(II) complex [Ru(IP)₂DPBPD(NH₂)₂]²⁺ (1) {IP?=?imidazole[4,5-f] [1,10] phenanthroline, DPBPD(NH₂)₂?=?2,4,5,6-tetraaminopyrimidine-[3,2-a:2??,3??-c]-phenazine} with CT-DNA (calf thymus DNA) and yeast tRNA have been investigated by different spectrophotometric methods and viscosity measurements. The antitumor activities of complex 1 have been evaluated by MTT {MTT?=?(3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide} method. On the basis of the spectroscopic results, the binding mode of complex 1 to CT-DNA and yeast tRNA are intercalation, and RNA binding of complex 1 is stronger than DNA binding. Furthermore, complex 1 is a better candidate for an enantioselective binder to yeast tRNA than to CT-DNA. The results can be explained by the different structure and configuration between CT-DNA and yeast tRNA reasonably, suggesting that the configuration and structure of nucleic acids have significant effects on the binding behaviors of metal complexes. On the other hand, the complex demonstrates different antitumor activity against selected tumor cell lines in vitro.     

PHOTOSENSITIZATION OF SUPERCOILED DNA DAMAGE BY 5,6-DIHYDROXYINDOLE-2-CARBOXYLIC ACID, A PRECURSOR OF EUMELANIN

The photosensitizing or photoprotecting action of 5,6-dihydroxyindole-2-carboxylic acid (DICA), an intermediate in the biosynthesis of eumelanins, was investigated. Under irradiation at 313 nm, aqueous buffered solutions of DICA (22.5 μW) photosensitized the cleavage of phage φX174 DNA. The number of single strand breaks (SSB) depended on the dose of irradiation and was more important in the absence than in the presence of oxygen. In the presence of oxygen, the quantum yield of SSB was around 6′10 ⁷ (Φ_SSB) The influence of specific scavengers, such as mannitol, sodium azide or superoxide dismutase, indicated that hydroxyl radicals, superoxide anions and perhaps singlet oxygen were involved in these processes. The increase in SSB in D₂O was also indicative of the participation of singlet oxygen. Comparative experiments performed with indole-2-carboxylic acid (IC), a dehydrox-ylated analog of DICA, showed that this compound, although lacking a phenol group, also photosensitized DNA cleavage via a mechanism involving hydroxyl radicals. Various sources of these radicals were envisioned. Furthermore, under our conditions, DICA was not found to photoinduce the formation of DNA dimers: No increase in SSB was observed in DNA irradiated in the presence of DICA, after treatment by phage T4 endonuclease V (an enzyme that selectively cuts DNA at dimer sites), whereas, in contrast, a significant increase in SSB was detected after treatment of DNA irradiated alone. So it appears that DICA may both photosensitize DNA cleavage and reduce UV-induced DNA dimer formation.     

Crystal structures, cyclic voltammetry and DNA binding of two mononuclear nickel(II) complexes

Two unsymmetrical complexes, [NiL¹]ClO₄ (1) and [NiL²]ClO₄ (2) have been synthesized and characterized by IR, UV, ES-MS and single crystal X-ray diffraction, where HL¹ and HL² are, respectively, the [1+1] condensation products of 2,6-diformyl-4-X-phenol (X = F or CH₃) with N ¹-(2-aminoethyl)-N ²-(4-nitrobenzyl) ethane-1,2-diamine. The coordination geometry of the metal in both complexes can be approximately described as square planar with a mean plane deviation of 0.032 Å in complex 1 and 0.027 Å in complex 2, respectively. The binding activities of the complexes toward calf-thymus DNA have been analyzed by spectroscopy and viscosity methods. The binding constants of 1 and 2 obtained from UV spectroscopic studies are 5.43 × 10⁵ and 1.83 × 10⁵ M^?1, respectively, while the linear Stern–Volmer quenching constants obtained from fluorescence spectroscopic studies are 0.83 × 10³ and 0.71 × 10³ M^?1, respectively. The cyclic voltammograms of the complexes show a pseudo-reversible electrochemical process.     

<Emphasis Type="Italic">Escherichia coli</Emphasis> single-strand binding protein–DNA interactions on carbon nanotube-modified electrodes from a label-free electrochemical hybridization sensor

An electrochemical hybridization biosensor based on the intrinsic oxidation signals of nucleic acids and proteins has been designed, that makes use of the unique binding event between Escherichia coli single-strand binding protein (SSB) and single-stranded DNA (ssDNA). The voltammetric signal from guanine oxidation significantly decreased upon binding of SSB to single-stranded oligonucleotides (probe), anchored on a single-walled carbon nanotube (SWCNT) -modified screen-printed carbon electrode (SPE). Simultaneously, oxidation of the tyrosine (Tyr) and tryptophan (Trp) residues of the SSB protein increased upon binding of the SSB protein to ssDNA and ss-oligonucleotides. After the hybridization, SSB did not bind to the double helix form, and the guanine signal could be observed along with the disappearance of the oxidation signal of the protein. The amplification of intrinsic guanine and protein oxidation signals by SWCNT, and a washing step with sodium dodecylsulfate, enabled the specific detection of a point mutation. Monitoring the changes in the guanine and protein signals upon hybridization greatly simplified the detection procedure. The detection limit of 0.15 g/ml target DNA can be applied to genetic assays. To the best of our knowledge, this is the first work that utilizes the monitoring of SSB–DNA interactions on a solid transducer for the electrochemical detection of DNA hybridization by using intrinsic oxidation signals.     

Label-free and sequence-specific DNA detection down to a picomolar level with carbon nanotubes as support for probe DNA

This study describes a simple and label-free electrochemical impedance spectroscopic (EIS) method for sequence-specific detection of DNA by using single-walled carbon nanotubes (SWNTs) as the support for probe DNA. SWNTs are confined onto gold electrodes with mixed self-assembly monolayers of thioethanol and cysteamine. Single-stranded DNA (ssDNA) probe is anchored onto the SWNT support through covalent binding between carboxyl groups at the nanotubes and amino groups at 5′ ends of ssDNA. Hybridization of target DNA with the anchored probe DNA greatly increases the interfacial electron-transfer resistance (R_et) at the double-stranded DNA (dsDNA)-modified electrodes for the redox couple of Fe(CN)₆^3−/4−, which could be used for label-free and sequence-specific DNA detection. EIS results demonstrate that the utilization of SWNTs as the support for probe DNA substantially increases the surface loading of probe DNA onto electrode surface and thus remarkably lowers the detection limit for target DNA. Under the conditions employed here, R_et is linear with the concentration of target DNA within a concentration range from 1 to 10 pM with a detection limit down to 0.8 pM (S/N = 3). This study may offer a novel and label-free electrochemical approach to sensitive sequence-specific DNA detection.     

Mutational analysis of human profilin I reveals a second PI(4,5)-P2 binding site neighbouring the poly(L-proline) binding site

Background

Profilin is a small cytoskeletal protein which interacts with actin, proline-rich proteins and phosphatidylinositol 4,5-bisphosphate (PI(4,5)-P₂). Crystallography, NMR and mutagenesis of vertebrate profilins have revealed the amino acid residues that are responsible for the interactions with actin and poly(L-proline) peptides. Although Arg88 of human profilin I was shown to be involved in PI(4,5)-P₂-binding, it was suggested that carboxy terminal basic residues may be involved as well.

Results

Using site directed mutagenesis we have refined the PI(4,5)-P₂ binding site of human profilin I. For each mutant we assessed the stability and studied the interactions with actin, a proline-rich peptide and PI(4,5)-P₂ micelles. We identified at least two PI(4,5)-P₂-binding regions in human profilin I. As expected, one region comprises Arg88 and overlaps with the actin binding site. The second region involves Arg136 in the carboxy terminal helix and neighbours the poly(L-proline) binding site. In addition, we show that adding a small protein tag to the carboxy terminus of profilin strongly reduces binding to poly(L-proline), suggesting local conformational changes of the carboxy terminal α-helix may have dramatic effects on ligand binding.

Conclusions

The involvement of the two terminal α-helices of profilin in ligand binding imposes important structural constraints upon the functions of this region. Our data suggest a model in which the competitive interactions between PI(4,5)-P₂ and actin and PI(4,5)-P₂ and poly(L-proline) regulate profilin functions.     

UV-absorption studies of interaction of karanjin and karanjachromene with ds. DNA: Evaluation of binding and antioxidant activity

Two flavonoids, karanjin (Kj) and karanjachromene (Kc) have been investigated spectrophotometrically for their mode of interactions with double stranded (ds)-DNA at blood (7.4) and stomach (4.7) pH and at human body temperature (37°C). Benesi-Hildebrand equation was used to evaluate the binding constants, K _b . Binding constants at both pH values and at body temperature showed stronger binding of both the flavonoids and formation of 1:1 flavonoid-DNA complex via intercalative mode. However, K _b values for karanjin were evaluated to be comparatively greater than karanjachromene at both pH values. The highest value of binding constant (1.32×10⁵ M^?1) for karanjin at blood pH (7.4) demonstrated its comparatively stronger binding and greater effectiveness at this pH. Standard Gibbs free energy changes (ΔG) of flavonoid-DNA complexes were calculated as negative values and indicative of spontaneity of their binding. Both flavonoids showed significant DNA protection activity.      

The reaction of ammonium tetra(isothiocyanato)diamminechromate(III) with ?-caprolactam in aqueous solution. Revised refinement of the structure of (HCpl2)3[Cr(NCS)6]

A reaction of ammonium tetra(isothiocyanato)diamminechromate(III) (ammonium reineckate) with ?-caprolactam in aqueous solution at different pH values gave the novel complexes (NH₄)[Cr(NH₃)₂(NCS)₄] · 7Cpl (I), (NH₄)[Cr(NH₃)₂(NCS)₄] · 2.5Cpl · 0.5(H₂O) (II), and (HCpl₂)[Cr(NH₃)₂(NCS)₄] (III), where Cpl is ?-caprolactam (?-C₆H₁₁NO). The crystals of complexes I?CIII are triclinic, space group $P\bar 1$ ; I: a = 12.7058(4) ?, b = 13.2544(4) ?, c = 19.4487(7) ?, ?? = 105.2360(10)°, ?? = 106.6410(10)°, ?? = 91.5290(10)°, V = 3009.37(17) ?³, ??_calc = 1.245 g/cm³, Z = 2; II: a = 12.3144(5) ?, b = 12.6518(5) ?, c = 23.3300(8) ?, ?? = 75.4580(10)°, ?? = 80.0760(10)°, ?? = 61.0830(10)°, V = 3074.1(2) ?³, ??_calc = 1.358 g/cm³, Z = 4; III: a = 6.4701(4) ?, b = 12.5973(9) ?, c = 16.5556(12) ?, ?? = 108.769(2)°, ?? = 98.543(2)°, ?? = 90.345(2)°, V = 1261.36(15) ?³, ??_calc = 1.437 g/cm³, Z = 2. The structure refinement for (HCpl₂)₃[Cr(NCS)₆] (IV) was revised. Like complex III, complex IV contains the cation (HCpl₂)⁺ stabilized by a strong hydrogen bond between the O atoms of the ?-caprolactam molecules; the cation was structurally characterized for the first time.     

Cobalt(II) coordination polymers built on isomeric dipyridyl triazole ligands with pyromellitic acid: Synthesis, characterization and their effects on the thermal decomposition of ammonium perchlorate

Three new cobalt(Ⅱ) coordination compounds,[Co(3,3’-Hbpt)2(H2pm)(H2O)2]·2H2O(1),[Co(4,4’-Hbpt)(pm)0.5(H2O)]·3H2O (2) and [Co(3,4’-Hbpt)(pm) 0.5 (H2O)3]·2H2O(3)(3,3’-Hbpt=3,5-bis(3-pyridyl)-1H-1,2,4-triazole;4,4’-bpt=3,5-bis(4-pyridyl)1H-1,2,4-triazole,3,4’-Hbpt=3-(3-pyridyl)-5-(4’-pyridyl)-1H-1,2,4-triazole and H4pm=pyromellitic acid) have been synthesized by hydrothermal reactions.Single-crystal X-ray diffraction reveals that compound 1 has a one-dimensional (1D) chain network,2 exhibits a four-connected three-dimensional (3D) structure with 1D open channels encapsulated by water molecules,while 3 displays a regular two-dimensional (2D) architecture connected through 1D metal helical chains.In addition,the efficacy of compounds 1-3 as additives to promote the thermal decomposition of ammonium perchlorate (AP) is explored by differential scanning calorimetry (DSC).     

Syntheses and crystal structures of oxovanadium(V) complexes derived from N′-[1-(2-hydroxynaphthyl)ethylidene]-4-nitrobenzohydrazide and 2-hydroxy-N′-[1-(2-hydroxynaphthyl)ethylidene]benzohydrazide

Reactions of bis(acetylacetonato)oxovanadium(IV) with N??-[1-(2-hydroxynaphthyl)ethylidene]-4-nitrobenzohydrazide (H₂HNB) and 2-hydroxy-N??-[1-(2-hydroxynaphthyl)ethylidene]benzohydrazide (H₂HHB), respectively, product two oxovanadium(V) species with the formulas [VO(OMe)(HNB)]₂ (I) and [VO(OMe)(HHB)] (II). The complexes I and II have been characterized by elemental analysis, IR spectra, and single crystal X-ray diffraction. The crystal of I is monoclinic: space group P2₁/n, a = 8.208(2), b = 14.528(3), c = 16.418(3) ?, ?? = 97.887(3)°, V = 1939.3(7) ?³, Z = 2. The crystal of II is triclinic: space group P $P\bar 1$ a = 8.334(2), b = 10.236(2), c = 11.337(2) ?, ?? = 80.91(3)°, ?? = 75.41(3)°, ?? = 75.63(3)°, V = 902.0(3) ?³, Z = 2. Complex I is a methoxide-bridged dimeric oxovanadium(V) complex, and complex II is a mononuclear oxovanadium(V) complex. The V atom in I is in an octahedral coordination, and that in II is in a square pyramidal coordination.     

Selection and identification of ssDNA aptamers recognizing zearalenone

Zearalenone (ZEN) is a nonsteroidal estrogenic mycotoxin produced by Fusarium graminearum on maize and barley. Because most current methods of ZEN detection rely on the use of low-stability antibodies or expensive equipment, we sought to develop a rapid, low-cost determination method using aptamers instead of antibodies as the specific recognition ligands. This work describes the isolation and identification of single-stranded DNA (ssDNA) aptamers recognizing ZEN using the modified systematic evolution of ligands by exponential enrichment methodology based on magnetic beads. After 14 rounds of repeated selection, a highly enriched ssDNA library was sequenced and 12 representative sequences were assayed for their affinity and specificity. The best aptamer, 8Z₃₁, with a dissociation constant (K _d) of 41?±?5 nM, was successfully applied in the specific detection of ZEN in binding buffer and in real samples based on a magnetic separation/preconcentration procedure. This analytical method provided a linear range from 3.14?×?10^?9 to 3.14?×?10^?5 M for ZEN, and the detection limit was 7.85?×?10^?10 M. The selected aptamers are expected to be used in the potential development of affinity columns, biosensors, or other analytical systems for the determination of ZEN in food and agricultural products.

Electrochemical detection of DNA binding by tumor suppressor p53 protein using osmium-labeled oligonucleotide probes and catalytic hydrogen evolution at the mercury electrode

In this paper, we present an electrochemical DNA–protein interaction assay based on a combination of protein-specific immunoprecipitation at magnetic beads (MBIP) with application of oligonucleotide (ON) probes labeled with an electroactive oxoosmium complex (Os,bipy). We show that double-stranded ONs bearing a dT₂₀ tail labeled with Os,bipy are specifically recognized by the tumor suppressor p53 protein according to the presence or absence of a specific binding site (p53CON) in the double-stranded segment. We demonstrate the applicability of the Os,bipy-labeled probes in titration as well as competition MBIP assays to evaluate p53 relative affinity to various sequence-specific or structurally distinct unlabeled DNA substrates upon modulation of the p53-DNA binding by monoclonal antibodies used for the immunoprecipitation. To detect the p53-bound osmium-labeled probes, we took advantage of a catalytic peak yielded by Os,bipy-modified DNA at the mercury-based electrodes, allowing facile determination of subnanogram quantities of the labeled oligonucleotides. Versatility of the electrochemical MBIP technique and its general applicability in studies of any DNA-binding protein is discussed. Figure

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Reversibility of electrosurface transfer through eutectic interfaces of MeWO4|WO3 (Me ? Ca, Sr, Ba)

It is found that electrosurface transition (EST) through eutectic interfaces of (?/+)WO₃|MeWO₄(+/?) induced by electric field is a reversible process. In the case of the (?/+) polarity, nominally, in the ??direct experiment??, macro amounts of WO₃ from a W ₃ ^(?) brick are drawn in the (+) direction onto the inner surface of MeWO₄ forming a two-phase {ie1070-1} composite. Simultaneously, nonequivalent countertransport of Me ²⁺ within the W ₃ ^(?) brick occurs, which changes the color of W ₃ ^(?) from the natural hue to dark-green. Intercalation of Me ²⁺ into W ₃ ^(?) is proved by several spectroscopic methods. The key role in the EST phenomenon belongs to a nonautonomous electrolytic phase of MeW-s formed on the contact interface with WO₃|MeWO₄. The composition of MeW-s is close to W/Me ?? 2. As a result of EST, the cell acquires a more complicated structure: {fx1070-1} where |///| are interface regions occupied by the MeW-s phase. At the cathodic boundary of subcell {fx1070-2} the following process occurs: {fx1070-3}, The process at the anodic boundary is: {fx1070-4}. Ultimately, WO₃ is transported in the (+) direction (into the composite) and Me ²⁺ penetrates under the effect of the gradient in chemical potential into W ₃ ^(?) forming a dark-green Me _x WO₃ phase with its front reaching the (?) Pt electrode. After the end of the ??direct experiment??, the cell polarity was changed to (+/?) and the ??reverse experiment?? was carried out. Now, on the cathodic boundary | ₄ of subcell {fx1070-5} anions (WO₄)^2? are generated that are discharged on boundary ₃ | to oxide WO₃ that is intercalated into the right boundary of MeWO_{4 ? (3)}, where the rightmost composite region {ie1070-2} is formed. Thus, the mass of W ₃ ^(?) decreases; it becomes dark-green (see above) and the mass of the MeWO₄ disk continues growing and now its structure is as follows {ie1070-3}. It is important that the left W ₃ ⁽⁺⁾ disk that was dark-green after the ??direct experiment?? gradually becomes lighter in the ??reverse experiment?? up to its natural pale green color, i.e., Me ²⁺ is deintercalated from it: Me ²⁺: Me _x WO₃ + 1/2O₂ ?? xMe ²⁺ + 2e + WO₃. It is found that dependences of variations of disk masses ??m(Q) practically coincide for the ??direct?? and ??reverse?? experiments.