Dye-functionalized phosphate-binding macrocycles: from nucleotide to G-quadruplex recognition and "turn-on" fluorescence sensing.

A novel strategy to design "turn-on" fluorescent receptors for G-quadruplexes of DNA is presented, which relies on the connection of phosphate binding macrocycles (PBM) with naphthalimide dyes. A new PBM-dye family was synthesized and evaluated in terms of binding and detection of nucleotides and DNA G-quadruplexes of different topologies.

From Substrate to Fragments to Inhibitor Active against .

Antibiotic resistance is a worldwide threat due to the decreasing supply of new antimicrobials. Novel targets and innovative strategies are urgently needed to generate pathbreaking drug compounds. NAD kinase (NADK) is essential for growth in most bacteria, as it supports critical metabolic pathways.

Photoelectron spectroscopy of boron-containing reactive intermediates using synchrotron radiation: BH, BH, and BF.

Mass selected slow photoelectron spectra (SPES) of three boron-containing reactive species, BH, BH, and BF were recorded by double imaging photoion-photoelectron coincidence spectroscopy (iPEPICO) using synchrotron radiation. All species were generated in a flow reactor from the H-abstraction of BH by F atoms created in a F microwave discharge. The spectrum of BH exhibits a long bending mode progression with a 970 cm spacing due to the large geometry change from bent to linear upon ionization.

Identification of optimal fluorescent probes for G-quadruplex nucleic acids through systematic exploration of mono- and distyryl dye libraries.

A library of 52 distyryl and 9 mono-styryl cationic dyes was synthesized and investigated with respect to their optical properties, propensity to aggregation in aqueous medium, and capacity to serve as fluorescence "light-up" probes for G-quadruplex (G4) DNA and RNA structures. Among the 61 compounds, 57 dyes showed preferential enhancement of fluorescence intensity in the presence of one or another G4-DNA or RNA structure, while no dye displayed preferential response to double-stranded DNA or single-stranded RNA analytes employed at equivalent nucleotide concentration. Thus, preferential fluorimetric response towards G4 structures appears to be a common feature of mono- and distyryl dyes, including long-known mono-styryl dyes used as mitochondrial probes or protein stains.

State-Selected Reactivity of Carbon Dioxide Cations ( ) With Methane.

The reactivity of with CD has been experimentally investigated for its relevance in the chemistry of plasmas used for the conversion of CO in carbon-neutral fuels. Non-equilibrium plasmas are currently explored for their capability to activate very stable molecules (such as methane and carbon dioxide) and initiate a series of reactions involving highly reactive species (e.g.

Diborene: Generation and Photoelectron Spectroscopy of an Inorganic Biradical.

Diborenes, R-BB-R', are of current interest in inorganic chemistry because they offer the opportunity to tune the properties of a biradical by modifying the substituents of the diborene parent, HBBH. Here we synthesize the elusive diborene by H atom abstraction from diborane, BH, using fluorine atoms and report a vibrationally resolved photoelectron spectrum of the HBBH biradical. The spectrum is interpreted by comparison with high-level ab initio computations, taking into account the Renner-Teller splitting in the XΠ ionic ground state, which show an excellent agreement with the experimental spectrum.

Effects of collision energy and vibrational excitation of CH cations on its reactivity with hydrocarbons: But-2-yne CHCCCH as reagent partner.

The methyl carbocation is ubiquitous in gaseous environments, such as planetary ionospheres, cometary comae, and the interstellar medium, as well as combustion systems and plasma setups for technological applications. Here we report on a joint experimental and theoretical study on the mechanism of the reaction CH + CHCCCH (but-2-yne, also known as dimethylacetylene), by combining guided ion beam mass spectrometry experiments with ab initio calculations of the potential energy hypersurface. Such a reaction is relevant in understanding the chemical evolution of Saturn's largest satellite, Titan.

Communication: On the first ionization threshold of the CH radical.

The slow photoelectron spectrum of the ethynyl radical has been recorded for the first time by using the DESIRS beamline of the SOLEIL synchrotron facility. Ethynyl was generated using a microwave discharge flow tube. The observation of the XΠ3←XΣ+2 transition allowed the first direct measurement of the adiabatic ionization threshold of this radical (E = 11.

Synchrotron-based valence shell photoionization of CH radical.

We report the first experimental observations of X(+) (1)Σ(+)←X (2)Π and a(+) (3)Π←X (2)Π single-photon ionization transitions of the CH radical performed on the DESIRS beamline at the SOLEIL synchrotron facility. The radical was produced by successive hydrogen-atom abstractions on methane by fluorine atoms in a continuous microwave discharge flow tube. Mass-selected ion yields and photoelectron spectra were recorded as a function of photon energy using a double imaging photoelectron/photoion coincidence spectrometer.

Selective Generation of the Radical Cation Isomers [CH3CN](•+) and [CH2CNH](•+) via VUV Photoionization of Different Neutral Precursors and Their Reactivity with C2H4.

Experimental and theoretical studies have been carried out to demonstrate the selective generation of two different C2H3N(+) isomers, namely, the acetonitrile [CH3CN](•+) and the ketenimine [CH2CNH](•+) radical cations. Photoionization and dissociative photoionization experiments from different neutral precursors (acetonitrile and butanenitrile) have been performed using vacuum ultraviolet (VUV) synchrotron radiation in the 10-15 eV energy range, delivered by the DESIRS beamline at the SOLEIL storage ring. For butanenitrile (CH3CH2CH2CN) an experimental ionization threshold of 11.

Highly efficient radiosensitization of human glioblastoma and lung cancer cells by a G-quadruplex DNA binding compound.

Telomeres are nucleoprotein structures at the end of chromosomes which stabilize and protect them from nucleotidic degradation and end-to-end fusions. The G-rich telomeric single-stranded DNA overhang can adopt a four-stranded G-quadruplex DNA structure (G4). Stabilization of the G4 structure by binding of small molecule ligands enhances radiosensitivity of tumor cells, and this combined treatment represents a novel anticancer approach.

Binding of calcium, magnesium, and target peptides to Cdc31, the centrin of yeast Saccharomyces cerevisiae.

Cdc31, the Saccharomyces cerevisiae centrin, is an EF-hand calcium-binding protein essential for the cell division and mRNA nuclear export. We used biophysical techniques to investigate its calcium, magnesium, and protein target binding properties as well as their conformations in solution. We show here that Cdc31 displays one Ca(2+)/Mg(2+) mixed site in the N-terminal domain and two low-affinity Ca(2+) sites in the C-terminal domain.

Scherffelia dubia centrin exhibits a specific mechanism for Ca(2+)-controlled target binding.

Centrins are calcium binding proteins that belong to the EF-hand (or calmodulin) superfamily, which are highly conserved among eukaryotes. Herein, we report the molecular features and binding properties of the green alga Scherffelia dubia centrin (SdCen), a member of the Chlamydomonas reinhardtii centrin (CrCen) subfamily. The Ca(2+) binding capacity of SdCen and its isolated N- and C-terminal domains (N-SdCen and C-SdCen, respectively) was investigated using flow dialysis and isothermal titration calorimetry.

Threshold photoelectron spectroscopy of the methyl radical isotopomers, CH3, CH2D, CHD2 and CD3: synergy between VUV synchrotron radiation experiments and explicitly correlated coupled cluster calculations.

Threshold photoelectron spectra (TPES) of the isotopomers of the methyl radical (CH(3), CH(2)D, CHD(2), and CD(3)) have been recorded in the 9.5-10.5 eV VUV photon energy range using third generation synchrotron radiation to investigate the vibrational spectroscopy of the corresponding cations at a 7-11 meV resolution.

What determines the degree of compactness of a calcium-binding protein?

The EF-hand calcium-binding proteins may exist either in an extended or a compact conformation. This conformation is sometimes correlated with the function of the calcium-binding protein. For those proteins whose structure and function are known, calcium sensors are usually extended and calcium buffers compact; hence, there is interest in predicting the form of the protein starting from its sequence.

Profiling lipids across Caucasian and Afro-American hair transverse cuts, using synchrotron infrared microspectrometry.

Synchrotron-based infrared microscopic measurements have been performed on various hair transverse sections, sampled either from the heads of Caucasian or Afro-American subjects. Lipid content of various virgin hair transverse sections was established, with an unprecedented resolution. The variations in shape and intensity of the CH(2), CH(3), amide I and amide II bands, before and after lipid removal by solvent extraction, were profiled, showing clearly that Caucasian hair often contains lipids localized inside the medulla and to a lesser extent inside the cuticle.

The carboxy-terminal domain of xeroderma pigmentosum complementation group C protein, involved in TFIIH and centrin binding, is highly disordered.

Xeroderma pigmentousum group C protein (XPC) is involved in the first step of nucleotide excision repair, with multiple functional roles including DNA damage recognition and recruitment of the repair machinery. This human protein of 940 residues forms a strong heterotrimeric complex with Rad23B and centrin 2. The structure of XPC is actually not known, and lack of significant sequence homology with proteins from structural data bases precludes any relevant prediction.

Radiative relaxation and fragmentation dynamics of S 2p-excited hydrogen sulfide.

Radiative relaxation of S 2p-excited hydrogen sulfide (H(2)S) is investigated by dispersed ultraviolet and visible fluorescence spectroscopies. We observe distinct changes in the fluorescence spectra as a function of excitation energy. Excitation to Rydberg states below the S 2p ionization threshold yields intense fluorescence from neutral and ionic atomic fragments (H, S(+), and S(2+)).

Binding of human centrin 2 to the centrosomal protein hSfi1.

hSfi1, a human centrosomal protein with homologs in other eukaryotic organisms, includes 23 repeats, each of 23 amino acids, separated by 10 residue linkers. The main molecular partner in the centrosome is a small, calcium-binding EF-hand protein, the human centrin 2. Using isothermal titration calorimetry experiments, we characterized the centrin-binding capacity of three isolated hSfi1 repeats, two exhibiting the general consensus motif and the third being the unique Pro-containing human repeat.

Time-resolved study of the oxidation of ethanol by cerium(IV) using combined quick-XANES, UV-vis, and Raman spectroscopies.

Time-resolved X-ray absorption spectroscopy (Quick-XANES) has been combined with UV-vis and Raman spectroscopies to study the in situ reduction of Ce4+ to Ce3+ in ethanolic solution with a time resolution of ca. 4-5 s. For this purpose, a cam-driven oscillating double-crystal monochromator with a channel-cut crystal was combined with two spectrometers for UV-vis and Raman spectroscopies in a specialized cell which allows one to fit the optical pathways for all three spectroscopies individually.

Propagation of statistical errors across EXAFS extraction and Fourier filtering.

A statistical model for estimating the error bars on the EXAFS signal is developed. The average can be calculated at the beginning of the analysis, with the estimation of the error bars made directly on the individual measurements; the error bars are then propagated across the EXAFS extraction. Furthermore, this model also allows the estimation of the error bars on the Fourier transformation of the EXAFS signal, and on the filtered EXAFS spectrum after the inverse Fourier transform.

SFG study of the ethanol in an acidic medium--Pt(110) interface: effects of the alcohol concentration.

Ethanol in an acidic solution-Pt(110) interface was studied by SFG spectroscopy (between 1820 and 2325 cm(-1)) to explore primarily the effects of the alcohol concentration. Stretching bands of H-Pt (ca. 1970 or 2050 cm(-1)) and CO (ca.

Flexibility and plasticity of human centrin 2 binding to the xeroderma pigmentosum group C protein (XPC) from nuclear excision repair.

Human centrin 2 is a component of the nucleotide excision repair system, as a subunit of the heterotrimer including xeroderma pigmentosum group C protein (XPC) and hHR23B. The C-terminal domain of centrin (C-HsCen2) binds strongly a peptide from the XPC protein (P1-XPC: N(847)-R(863)). Here, we characterize the solution Ca(2+)-dependent structural and molecular features of the C-HsCen2 in complex with P1-XPC, mainly using NMR spectroscopy and molecular modeling.

The N-terminal domain of human centrin 2 has a closed structure, binds calcium with a very low affinity, and plays a role in the protein self-assembly.

Centrins are well-conserved calcium binding proteins from the EF-hand superfamily implicated in various cellular functions, such as centrosome duplication, DNA repair, and nuclear mRNA export. The intrinsic molecular flexibility and the self-association tendency make difficult the structural characterization of the integral protein. In this paper we report the solution structure, the Ca2+ binding properties, and the intermolecular interactions of the N-terminal domain of two human centrin isoforms, HsCen1 and HsCen2.