A spectroscopic study of the fluorescence quenching interactions between biomedically important salts and the fluorescent probe merocyanine 540

Influence of Different Salts on the G-Quadruplex Structure Formed from the Reversed Human Telomeric DNA Sequence

G-rich telomeric DNA plays a major role in the stabilization of chromosomes and can fold into a plethora of different G-quadruplex structures in the presence of mono- and divalent cations. The reversed human telomeric DNA sequence (5′-(GGG ATT)4; RevHumTel) was previously shown to have interesting properties that can be exploited for chemical sensing and as a chemical switch in DNA nanotechnology. Here, we analyze the specific G-quadruplex structures formed by RevHumTel in the presence of K+, Na+, Mg2+ and Ca2+ cations using circular dichroism spectroscopy (CDS) and Förster resonance energy transfer (FRET) based on fluorescence lifetimes. CDS is able to reveal strand and loop orientations, whereas FRET gives information about the distances between the 5′-end and the 3′-end, and also, the number of G-quadruplex species formed. Based on this combined information we derived specific G-quadruplex structures formed from RevHumTel, i.e., a chair-type and a hybrid-type G-quadruplex structure formed in presence of K+, whereas Na+ induces the formation of up to three different G-quadruplexes (a basket-type, a propeller-type and a hybrid-type structure). In the presence of Mg2+ and Ca2+ two different parallel G-quadruplexes are formed (one of which is a propeller-type structure). This study will support the fundamental understanding of the G-quadruplex formation in different environments and a rational design of G-quadruplex-based applications in sensing and nanotechnology.

A novel fluorescent sensor based on electrosynthesized benzene sulfonic acid-doped polypyrrole for determination of Pb(II) and Cu(II)

To develop conducting organic polymers (COPs) as luminescent sensors for determination of toxic heavy metals, a new benzene sulfonic acid-doped polypyrrole (PPy-BSA) thin film was electrochemically prepared by cyclic voltammetry (CV) on flexible indium tin oxide (ITO) electrode in aqueous solution. PPy-BSA film was characterized by FTIR spectrometry, X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). The optical properties of PPy-BSA were investigated by ultraviolet (UV)-visible absorption and fluorescence spectrometry in dimethylsulfoxide (DMSO) diluted solutions. PPy-BSA fluorescence spectra were strongly quenched upon increasing copper(II) ion (Cu²⁺ ) and lead(II) ion (Pb²⁺ ) concentrations in aqueous medium, and linear Stern-Volmer relationships were obtained, which indicated the existence of a main dynamic fluorescence quenching mechanism. BSA-PPy sensor showed a high sensitivity for detection of both metallic ions, Cu²⁺ and Pb²⁺ , with very low limit of detection values of 3.1 and 18.0 nM, respectively. The proposed quenching-fluorimetric sensor might be applied to the determination of traces of toxic heavy metallic ions in water samples.

Molecular architecture of the N-type ATPase rotor ring from Burkholderia pseudomallei

The genome of the highly infectious bacterium Burkholderia pseudomallei harbors an atp operon that encodes an N‐type rotary ATPase, in addition to an operon for a regular F‐type rotary ATPase. The molecular architecture of N‐type ATPases is unknown and their biochemical properties and cellular functions are largely unexplored. We studied the B. pseudomallei N₁N_o‐type ATPase and investigated the structure and ion specificity of its membrane‐embedded c‐ring rotor by single‐particle electron cryo‐microscopy. Of several amphiphilic compounds tested for solubilizing the complex, the choice of the low‐density, low‐CMC detergent LDAO was optimal in terms of map quality and resolution. The cryoEM map of the c‐ring at 6.1 Å resolution reveals a heptadecameric oligomer with a molecular mass of ~141 kDa. Biochemical measurements indicate that the c₁₇ ring is H⁺ specific, demonstrating that the ATPase is proton‐coupled. The c₁₇ ring stoichiometry results in a very high ion‐to‐ATP ratio of 5.7. We propose that this N‐ATPase is a highly efficient proton pump that helps these melioidosis‐causing bacteria to survive in the hostile, acidic environment of phagosomes.

Modular assembly of synthetic proteins that span the plasma membrane in mammalian cells

Background

To achieve synthetic control over how a cell responds to other cells or the extracellular environment, it is important to reliably engineer proteins that can traffic and span the plasma membrane. Using a modular approach to assemble proteins, we identified the minimum necessary components required to engineer such membrane-spanning proteins with predictable orientation in mammalian cells.

Results

While a transmembrane domain (TM) fused to the N-terminus of a protein is sufficient to traffic it to the endoplasmic reticulum (ER), an additional signal peptidase cleavage site downstream of this TM enhanced sorting out of the ER. Next, a second TM in the synthetic protein helped anchor and accumulate the membrane-spanning protein on the plasma membrane. The orientation of the components of the synthetic protein were determined through measuring intracellular Ca²⁺ signaling using the R-GECO biosensor and through measuring extracellular quenching of yellow fluorescent protein variants by saturating acidic and salt conditions.

Conclusions

This work forms the basis of engineering novel proteins that span the plasma membrane to potentially control intracellular responses to extracellular conditions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-016-0320-7) contains supplementary material, which is available to authorized users.

Fluorescence Quenching of Two Coumarin-3-carboxylic Acids by Trivalent Lanthanide Ions

The effects of various trivalent lanthanide ions (acetates of Ce³⁺, Er³⁺, Eu³⁺, Nd³⁺) on the electronic absorption and fluorescence spectra of un-substituted coumarin-3-carboxylic acid (CCA) and 7-N,N-diethylamino-coumarin-3-carboxylic acid (DECCA) have been investigated in dimethylsulfoxide (DMSO) at room temperature. Depending on the lanthanide ion nature and concentration, significant spectral changes of absorption bands occurred for both coumarin derivatives. These spectral changes were attributed to the formation of ground-state complexes between the coumarin carboxylate derivatives and lanthanide ions. The fluorescence quenching of CCA and DECCA upon increasing the lanthanide ion concentration was studied. Different quantitative treatments, including the Stern-Volmer equation, the Perrin equation and a polynomial equation, were applied and compared in order to determine the nature of the quenching mechanisms for both coumarin derivatives. The results suggested the contribution of both dynamic and static quenching. Significant differences of CCA and DECCA fluorescence quenching efficiency were also observed, depending on the lanthanide ion. DECCA fluorescence lifetime measurements, performed in the absence and in the presence of Ln³⁺, confirmed a contribution of static quenching.

Merocyanine 540 adsorbed on polyethylenimine-functionalized graphene oxide nanocomposites as a turn-on fluorescent sensor for bovine serum albumin

We suggest a simple, fast, sensitive and selective BSA sensor designed by assembling MC540 molecules on PEI–GO nanocomposites.

A Simple Fluorescence Probe Based on Aggregation-Induced Emission (AIE) Property for the Detection of Mg(2+) Ions

A simple aggregation-induced emission-based fluorescence probe (1) for Mg(2+) was synthesized by condensation of benzene-1, 2-diamine with 5-bromo-2-hydroxybenzaldehyde, This compound shows favourable character of the AIE-active molecules. More importantly, after addition of Mg(2+) to probe (1) in acetonitrile, the solution changed from colorless to yellow colour solution under ultraviolet (UV) radiation obtained from hand-held UV lamp, this finding suggested that probe (1) can be used to detect Mg(2+) by colorimetric detection. Detection limit can reach 2.31 × 10(-5) M(-1). The practical value of the selective and sensitive fluorescence indicators was confirmed by its application to detection of magnesium ion in acetonitrile.

Insights into the structural stability of nuclear matrix ribonucleoprotein, LMG160: thermodynamic and spectroscopic analysis

Low-mobility group nonhistone chromatin protein, LMG160, is a nuclear matrix ribonucleoprotein particle (RNP) which has a RNA molecule with approximately 300 bases. In this study, structural stability of the intact LMG160 (I-LMG160) was investigated at different ionic strength and in the absence of its RNA moiety (T-LMG160) employing spectroscopic and thermodynamic techniques. The UV absorption spectra showed hypochromicity and red shift under increasing ionic strength for both forms of LMG160 but in different extents. The fluorescence emission intensity was decreased as ionic strength was increased and the Stern-Volmer quenching constant (Ksv) for T-LMG160 was 3.7 times less than for I-LMG160. In the absence of sodium chloride, I-LMG160 exhibited a very stable structure against the temperature change compared to T-LMG160. The thermodynamic parameters showed that the positive values of ΔHm and ΔSm increased by increasing ionic strength in both forms of LMG160. Removal of the RNA moiety altered secondary structure: as T-LMG160 showed more helical content than I-LMG160. From the results, it is concluded that I-LMG160 is more sensitive to alteration of environment and the RNA has an important role in this RNP conformation. Also, interaction of both I- and T-LMG160 with sodium chloride is entropy driven and is usually accompanied by surface hydrophobicity.

A new type of proton coordination in an F(1)F(o)-ATP synthase rotor ring

The high-resolution structure of the rotor ring from alkaliphilic Bacillus pseudofirmus OF4 reveals a new type of ion binding in F₁F_o-ATP synthases.

We solved the crystal structure of a novel type of c-ring isolated from Bacillus pseudofirmus OF4 at 2.5 Å, revealing a cylinder with a tridecameric stoichiometry, a central pore, and an overall shape that is distinct from those reported thus far. Within the groove of two neighboring c-subunits, the conserved glutamate of the outer helix shares the proton with a bound water molecule which itself is coordinated by three other amino acids of outer helices. Although none of the inner helices contributes to ion binding and the glutamate has no other hydrogen bonding partner than the water oxygen, the site remains in a stable, ion-locked conformation that represents the functional state present at the c-ring/membrane interface during rotation. This structure reveals a new, third type of ion coordination in ATP synthases. It appears in the ion binding site of an alkaliphile in which it represents a finely tuned adaptation of the proton affinity during the reaction cycle.

Like the wind turbines that generate electricity, the F₁F_o-ATP synthases are natural “ion turbines” each made up of a stator and a rotor that turns, when driven by a flow of ions, to generate the cell's energy supply of ATP. The F_o motor rotates by reversible binding and release of coupling ions that flow down the electrochemical ion gradient across the cytoplasmic cell membrane (in the case of bacteria) or intracellular organelle membranes (in the case of eukaryotic cells). Here, we present the structure of a rotor (c-)ring from a Bacillus species (B. pseudofirmus OF4) determined at high-resolution by X-ray crystallography. This bacterium prefers alkaline environments where the concentration of protons (H⁺) is lower outside than inside the cell – the inverse of the situation usually found in organisms that prefer neutral or acidic environments. The amino acid sequence of the protein subunits in this rotor, nevertheless, has features common to an important group of ATP synthases in organisms from bacteria to man. The structure reveals a new type of ion binding in which a protonated glutamate residue in the protein associates with a water molecule. This finding raises the possibility considered by Nobel laureate Paul Boyer several decades ago that a hydronium ion (a protonated water molecule, H₃O⁺), rather than a proton alone, might be the coupling species that energizes ATP synthesis. Also, it demonstrates the finely tuned adaptation of ATP synthase rotor rings and their ion-binding sites to the specific requirements of different organisms.

Natural terpenes: Self-assembly and membrane partitioning

Monoterpenes (MTs) are highly hydrophobic substances present in essential oils. They cover a wide spectrum of biological effects with a membrane interaction as a common point. Here we studied the surface activity of camphor, cineole, thymol, menthol and geraniol, and their ability to reach and incorporate into model membranes affecting some features of their dynamic organization. All the MTs studied self-aggregated in water with critical micellar concentrations (CMC) between 3 and 8 microM. Their octanol-water and membrane-water partition coefficients were correlated with one another. They all penetrated in monomolecular layers of dipalmitoyl-phosphatildylcholine at the air-water interface, even at surface pressures (pi) above the equilibrium lateral pressure of bilayers; thymol exhibited the highest (61.3 mN/m) and camphor the lowest (37 mN/m) pi(cut-off) value. They affected the self-aggregation of Triton X-100, increasing its CMC from 0.16 mM in the absence of MTs up to 0.68 mM (e.g. for geraniol), and the topology of sPC vesicles, increasing its surface curvature, suggesting their location at the polar head group region of the membrane. The latter was supported by their ability to increase differentially the polarity of the membrane environment sensed by two electrochromic dyes. Dipole moment values (between 1.224 and 2.523 D) and solvation areas (between 80 and 97 A(2)) were calculated from their energy-minimized structures. The relative contribution of each experimental, theoretical and structural property to determine MTs' effects on membrane dynamics were evaluated by a principal component analysis.