Intraloop and Interloop Interactions in the Folded-G Quartet Structure of Oxytricha Telomeric Sesquence

The antiparallel intramolecular G quartet structure for the 3.5 copy Oxytricha telomeric sequence d(G(4)T(4))(3)G4 has been established using a combination of spectroscopic and chemical probing methods. In the presence of Naf ions, this sequence exhibits a circular dichroism spectrum with a positive band at 295 nm and a negative band around 265 nm, characteristic of an antiparallel G quartet structure. Further, we show that d(G(4)T(4))(3)G(4) adopts an antiparallel intramolecular G quartet structure even in K+ unlike d(G(4)T(4)G(4)). KMnO4 probing experiments indicated the existence of intra and interloop interactions in the Na+ induced structure. We have found that K+ not only increases the thermal stability of,G quartet structure but also binds to the loop region and disrupts stacking and interloop interactions. Biological consequences of such cation-dependent conformational micro-heterogeneity in the loop region of G quartet structures is also discussed.

Induction of Supramolecular Chirality in the Self-Assemblies of Lipophilic Pyrimidine Derivatives by Choice of the Amino Acid-Based Chiral Spacer

A new family of supramolecular organogelators, based on chiral amino acid derivatives of 2,4,6-trichloro-pyrimidine-5-carbaldehyde, has been synthesized. L-alanine was incorporated as a spacer between the pyrimidine core and long hydrocarbon tails to compare the effect of chirality and hydrogen bonding to that of the achiral analogue. The role of aromatic moiety on the chiral spacer was also investigated by introducing L-phenyl alanine moieties. The presence of intermolecular hydrogen-bonding leading to the chiral self-assembly was probed by concentration-dependent FTIR and UV/Vis spectroscopies, in addition to circular dichroism (CD) studies. Temperature and concentration-dependent CD spectroscopy ascribed to the formation of -sheet-type H-bonded networks. The morphology and the arrangements of the molecules in the freeze-dried gels were examined by scanning electron microscopy (SEM), transmission electron microscopy (TEM), atomic force microscopy (AFM), and X-ray diffraction (XRD) techniques. Calculation of the length of each molecular system by energy minimization in its extended conformation and comparison with the small-angle XRD pattern reveals that this class of gelator molecules adopts a lamellar organization. Polarized optical microscopy (POM) and differential scanning calorimetry (DSC) indicate that the solid state phase behavior of these molecules is totally dependent on the choice of their amino acid spacers. Structure-induced aggregation properties based on the H-bonding motifs and the packing of the molecule in three dimensions leading to gelation was elucidated by rheological studies. However, viscoelasticity was shown to depend only marginally on the H-bonding interactions; rather it depends on the packing of the gelators to a greater extent.

Interface characterization of Co2MnGe/Rh2CuSn Heusler multilayers

To address the amount of disorder and interface diffusion induced by annealing, all-Heusler multilayer structures, consisting of ferromagnetic Co2MnGe and nonmagnetic Rh2CuSn layers of varying thicknesses, have been investigated by means of hard x-ray photoelectron spectroscopy and x-ray magnetic circular dichroism. We find evidence for a 4 angstrom thick magnetically dead layer that, together with the identified interlayer diffusion, are likely reasons for the unexpectedly small magnetoresistance found for current-perpendicular-to-plane giant magnetoresistance devices based on this all-Heusler system. We find that diffusion begins already at comparably low temperatures between 200 and 250 degrees C, where Mn appears to be most prone to diffusion.

Biomimetic molecular organization of naphthalene diimide in the solid state: tunable (chiro-) optical, viscoelastic and nanoscale properties

The interfacing of aromatic molecules with biomolecules to design functional molecular materials is a promising area of research. Intermolecular interactions determine the performance of these materials and therefore, precise control over the molecular organization is necessary to improve functional properties. Herein we describe the tunable biomimetic molecular engineering of a promising n-type organic semiconductor, naphthalene diimide (NDI), in the solid state by introducing minute structural mutations in the form of amino acids with variable Ca-functionality. For the first time we could achieve all four possible crystal packing modes, namely cofacial, brickwork, herringbone and slipped stacks of the NDI system. Furthermore, amino acid conjugated NDIs exhibit ultrasonication induced organogels with tunable visco-elastic and temperature responsive emission properties. The amino acid-NDI conjugates self-assemble into 0D nanospheres and 1D nanofibers in their gel state while the ethylamine-NDI conjugate forms 2D sheets from its solution. Photophysical studies indicated the remarkable influence of molecular ordering on the absorption and fluorescence properties of NDIs. Interestingly, the circular dichroism (CD) and X-ray diffraction (XRD) studies revealed the existence of helical ordering of NDIs in both solution and solid state. The chiral amino acids and their conformations with respect to the central NDI core are found to influence the nature of the helical organization of NDIs. Consequently, the origin of the preferential handedness in the helical organization is attributed to transcription of chiral information from the amino acid to the NDI core. On account of these unique properties, the materials derived from NDI-conjugates might find a wide range of future interdisciplinary applications from materials to biomedicine.

Calcium binding properties of calcium dependent protein kinase 1 (CaCDPK1) from Cicer arietinum

Calcium plays a crucial role as a secondary messenger in all aspects of plant growth, development and survival. Calcium dependent protein kinases (CDPKs) are the major calcium decoders, which couple the changes in calcium level to an appropriate physiological response. The mechanism by which calcium regulates CDPK protein is not well understood. In this study, we investigated the interactions of Ca2+ ions with the CDPK1 isoform of Cicer arietinum (CaCDPK1) using a combination of biophysical tools. CaCDPK1 has four different EF hands as predicted by protein sequence analysis. The fluorescence emission spectrum of CaCDPK1 showed quenching with a 5 nm red shift upon addition of calcium, indicating conformational changes in the tertiary structure. The plot of changes in intensity against calcium concentrations showed a biphasic curve with binding constants of 1.29 mu M and 120 mu M indicating two kinds of binding sites. Isothermal calorimetric (ITC) titration with CaCl2 also showed a biphasic curve with two binding constants of 0.027 mu M and 1.7 mu M. Circular dichroism (CD) spectra showed two prominent peaks at 208 and 222 nm indicating that CaCDPK1 is a alpha-helical rich protein. Calcium binding further increased the alpha-helical content of CaCDPK1 from 75 to 81%. Addition of calcium to CaCDPK1 also increased fluorescence of 8-anilinonaphthalene-1-sulfonic acid (ANS) indicating exposure of hydrophobic surfaces. Thus, on the whole this study provides evidence for calcium induced conformational changes, exposure of hydrophobic surfaces and heterogeneity of EF hands in CaCDPK1. (C) 2015 Elsevier GmbH. All rights reserved.

In situ circular dichroic electrochemical study of bilirubin and bovine serum albumin complex

The electrooxidation of bilirubin (BR) and bovine serum albumin (BSA) complexes was studied by in situ circular dichroism (CD) spectroelectrochemistry. The result showed that the mechanism of the whole electrooxidation process of this complex corresponded to electrochemical processes (EE mechanism) in aqueous solution. Some parameters of the process were obtained by double logarithm method, differential method and nonlinear regression method. In visible region, CD spectra of the two enantiomeric components of the complex and their fraction distribution against applied potentials were obtained by singular value decomposition least-square (SVDLS) method. Meanwhile, the distribution of the five components of secondary structure was also obtained by the same method in far-UV region. The peak potential gotten from EE mechanism corresponds to a turning point for the component transition, beyond which the whole reaction reaches a new equilibrium. Under applied positive potentials, the enantiomeric equilibrium between M and P form is broken and M form transfers to its enantiomer of P, while the fraction of alpha-helix increases and that improves the transition to P form.

Carbon nanotubes selective destabilization of duplex and triplex DNA and inducing B-A transition in solution

Single-walled carbon nanotubes (SWNTs) have been considered as the leading candidate for nano-device applications ranging from gene therapy and novel drug delivery to membrane separations. The miniaturization of DNA-nanotube devices for biological applications requires fully understanding DNA-nanotube interaction mechanism. We report here, for the first time, that DNA destabilization and conformational transition induced by SWNTs are sequence-dependent. Contrasting changes for SWNTs binding to poly[dGdC]:poly[dGdC] and poly[dAdT]:poly[dAdT] were observed. For GC homopolymer, DNA melting temperature was decreased 40 degrees C by SWNTs but no change for AT-DNA. SWNTs can induce B-A transition for GC-DNA but AT-DNA resisted the transition. Our circular dichroism, competitive binding assay and triplex destabilization studies provide direct evidence that SWNTs induce DNA B-A transition in solution and they bind to the DNA major groove with GC preference.

Liposome-mediated conformation transition of DNA detected by molecular probe: methyl green

Recent studies have focused on the structural features of DNA-lipid assemblies. In this paper, we take methyl green (MG) as a probe molecule to detect the conformational change of DNA molecule induced by dimethyldioctadecylammonium bromide (DDAB) liposomes before the condensation process of DNA begins. DDAB-induced DNA topology changes were investigated by cyclic voltammetry (CV), circular dichroism (CD) and UV-VIS spectrometry. We find that upon binding to DNA, positively charged liposomes induce a conformational transition of DNA molecules from the native B-form to the C motif. Conformational transition in DNA results in the binding modes of MG to DNA, changing and being isolated from DNA to the solution. More stable complexes are formed between DNA and DDAB. That is also proved by the melting study of DNA.

Conformational transition of DNA in electroreduction studied by in situ UV and CD thin layer spectroelectrochemistry

Electrochemically induced three conformational transitions of calf thymus DNA from B-10.4 to Z(10.2)-DNA and from B-10.2 to B-10.4 and to C-DNA in 10 mM phosphate buffer solution (pH 7.21) at glassy carbon electrode are found and studied by in situ circular dichroism (CD) thin layer spectroelectrochemistry with singular value decomposition least square (SVDLS) analysis. It indicates that the so-called B-10.2 form and the C-form of DNA may be composed of B-10.4 and left-A DNA and of B-10.4 and right-A DNA, respectively. The irreversible electrochemical reduction of adenine and cytosine groups in the DNA molecule is studied by UV-Vis spectroelectrochemistry. Some electrochemical parameters alphan = 0.17, E-0' = -0.70 V (vs. Ag/AgCl), and the standard heterogeneous electron transfer rate constant, k(0) = 1.8 x 10(-5) cm s(-1) are obtained by double logarithmic analysis and non-linear regression. (C) 2000 Elsevier Science B.V. All rights reserved.

Electrochemistry and spectroscopy study on the interaction of microperoxidase-11 with lipid membrane

The interaction of microperoxidase-11 (MP11) with cationic lipid vesicles of didodecyldimethylammonium bromide (DDAB) induces an alpha -helical conformation from random coil conformations in solution and this change then makes heme macrocycle more distorted. DDAB-induced MP11 conformations were investigated by cyclic votammetry (CV), circular dichroism (CD) and UV-vis spectrometry. All results indicate that the binding of MP11 in solution to DDAB vesicles and the ordered structure formation are driven by mostly electrostatic interaction between negatively charged residues in the undecapeptide and positively charged lipid headgroups on the membrane surface. Upon binding to DDAB, its half-peak potential was also changed. The mechanism of the interaction between MP11 and DDAB was also discussed. (C) 2001 Elsevier Science B.V. All rights reserved.

Investigation of ergosterol in situ circular dichroic spectroelectrochemistry

In the present paper, the electrochemical behavior of ergosterol has been investigated by in situ circular dichroism (CD) spectroelectrochemistry with long path-length thin layer cell. E-0 (1.02V), alpha n(alpha) (0.302) of the electroxidation process of ergosterol were obtained from the CD spectroelectrochemical data. The mechanism of the electroxidation process of ergosterol is suggested.

Caractérisation du rôle de l’amyline (IAPP) dans le diabète de type 2 : études de dérivés peptidiques et de composés inhibiteurs de la formation d’amyloïde

L’amyloïdose, une maladie progressive et incurable, implique une vaste panoplie de pathologies et de pathogénèses, qui est expliquée par la grande variabilité biologique et structurale des protéines responsables de la formation des dépôts d’amyloïde. L’amyline (polypeptide amyloïde des îlots pancréatiques, IAPP) est une protéine très susceptible de subir des changements de conformation impliquant les feuillets bêta et conférant aussi des propriétés physicochimiques distinctes. Cette protéine prend alors une forme fibrillaire et se dépose dans les îlots de Langerhans chez les humains atteints de diabète de type 2 ou d’insulinome. Ces dépôts d’amyloïde pancréatique (AIAPP) ont été décrits chez certaines espèces animales telles que les félins domestiques, les grands félins, le raton laveur et les primates non humains. La formation de dépôts d’amyloïde contribue à la pathogénèse du diabète de type 2, mais les mécanismes qui induisent la conversion de l’amyline (IAPP) en amyloïde (AIAPP) ne sont pas complètement compris. Les hypothèses du projet sont que certaines variations présentes dans les séquences peptidiques de l’IAPP provenant de différentes espèces animales jouent un rôle critique pour la formation de fibrilles et que plusieurs composés chimiques aromatiques/phénoliques sont capables d’abroger la formation de dépôts d’amyloïde. Le projet de recherche consiste donc à caractériser la propension des différentes isoformes animales d’IAPP à former de l’amyloïde in vitro afin d’identifier les acides aminés jouant un rôle clé dans cette transformation structurale et ultimement d’inhiber la formation d’amyloïde pancréatique. Le projet se divise en deux volets principaux. Le premier consiste à identifier les différentes séquences peptidiques de l’IAPP retrouvées chez les espèces animales. L’objectif est d’identifier les acides aminés jouant un rôle clé dans la formation d’amyloïde. Le gène de l’IAPP a été séquencé chez plus d’une quarantaine d’espèces. Le potentiel d’agrégation des séquences obtenues a été simulé à l’aide d’outils bioinformatique. Une librairie de 23 peptides a été commandée afin de procéder à des analyses physicochimiques in vitro permettant d’évaluer le potentiel amyloïdogénique (test fluorimétrique à la thioflavine T, essai de liaison au rouge Congo, dichroïsme circulaire, microscopie électronique à transmission) et cytotoxique (sur une lignée cellulaire provenant d’insulinome : INS-1). Les analyses effectuées à partir de la librairie constituée de 23 peptides ont permis d’identifier trois séquences ne formant pas d’amyloïde et qui proviennent des espèces animales suivantes : le tamarin lion doré (Leontopithecus rosalia), le grand dauphin (Tursiops truncatus) et l’alpaga (Vicugna pacos). Un site potentiellement critique est le segment 8-20 présentant le motif NFLVH qui ne forme plus d’amyloïde lorsqu’il est remplacé par le motif DFLGR ou KFLIR. Les acides aminés 29P, 14K et 18R sont également impliqués dans l’inhibition de la transformation structurale en fibrille. La dernière partie du projet consiste à inhiber la formation de l’amyloïde en utilisant des composés chimiques commercialisés (hypoglycémiants, anti-inflammatoires non stéroïdiens) ou nouvellement synthétisés dans notre laboratoire (les aryles éthyles urées). Un criblage d’une soixantaine de composés chimiques a été conduit dans cette étude. Leur efficacité a été testée sur l’IAPP humaine, qui possède un fort potentiel amyloïdogénique. Les techniques utilisées sont les mêmes que celles exploitées précédemment. L’essai de liaison croisée photo-induite ("photo-induced cross-linking of unmodified proteins", PICUP) a été réalisé afin d’étudier les formes intermédiaires (monomères, oligomères). Un total de 11 composés chimiques a démontré un potentiel à inhiber l’agrégation des fibrilles. Pour la classe des hypoglycémiants, le glyburide, le répaglinide et la troglitazone ont montré l’activité thérapeutique la plus élevée pour retarder et réduire la formation de fibrilles. Les anti-inflammatoires antiamyloïdogènes actifs incluaient le diclofenac, le méloxicam, le phénylbutazone, le sulindac et le ténoxicam. Les aryles étyles urées les plus intéressantes étaient la EU-362 et la EU-418. Tous ces composés ont conféré une protection cellulaire contre l’activité cytotoxique des fibrilles. Les molécules actives possèdent des éléments structuraux communs tels des substituants donneurs d’électrons (alcool, amine, halogène) sur un noyau benzène. En conclusion, ce projet de recherche a permis de caractériser l’IAPP chez diverses espèces animales, dont plusieurs chez lesquelles elle n’avait pas encore été décrite, de déterminer les sites jouant un rôle clé dans sa transformation en amyloïde et, ultimement, de tester le potentiel thérapeutique de nouveaux agents antiamyloïdogènes dans le diabète de type 2. Nous espérons que ce projet ouvrira ainsi la porte à de nouvelles stratégies de traitement.

DNA cleavage and antitumour activity of platinum(II) and copper(II) compounds derived from 4-methyl-2-N-(2-pyridylmethyl)aminophenol: spectroscopic, electrochemical and biological investigation

The reaction of the redox-active ligand, Hpyramol (4-methyl-2-N-(2-pyridylmethyl)aminophenol) with K2PtCl4 yields monofunctional square-planar [Pt(pyrimol)Cl], PtL-Cl, which was structurally characterised by single-crystal X-ray diffraction and NMR spectroscopy. This compound unexpectedly cleaves supercoiled double-stranded DNA stoichiometrically and oxidatively, in a non-specific manner without any external reductant added, under physiological conditions. Spectro-electrochemical investigations of PtL-Cl were carried out in comparison with the analogue CuL-Cl as a reference compound. The results support a phenolate oxidation, generating a phenoxyl radical responsible for the ligand-based DNA cleavage property of the title compounds. Time-dependent in vitro cytotoxicity assays were performed with both PtL-Cl and CuL-Cl in various cancer cell lines. The compound CuL-Cl overcomes cisplatin-resistance in ovarian carcinoma and mouse leukaemia cell lines, with additional activity in some other cells. The platinum analogue, PtL-Cl also inhibits cell-proliferation selectively. Additionally, cellular-uptake studies performed for both compounds in ovarian carcinoma cell lines showed that significant amounts of Pt and Cu were accumulated in the A2780 and A2780R cancer cells. The conformational and structural changes induced by PtL-Cl and CuL-Cl on calf thymus DNA and phi X174 supercoiled phage DNA at ambient conditions were followed by electrophoretic mobility assay and circular dichroism spectroscopy. The compounds induce extensive DNA degradation and unwinding, along with formation of a monoadduct at the DNA minor groove. Thus, hybrid effects of metal-centre variation, multiple DNA-binding modes and ligand-based redox activity towards cancer cell-growth inhibition have been demonstrated. Finally, reactions of PtL-Cl with DNA model bases (9-Ethylguanine and 5'-GMP) followed by NMR and MS showed slow binding at Guanine-N7 and for the double stranded self complimentary oligonucleotide d(GTCGAC)(2) in the minor groove.

Self-assembly of a modified amyloid peptide fragment: pH-responsiveness and nematic phase formation

The self-assembly of peptide YYKLVFFC based on a fragment of the amyloid beta (A) peptide, A beta 16-20, KLVFF has been studied in aqueous solution. The peptide is designed with multiple functional residues to examine the interplay between aromatic interactions and charge on the self-assembly, as well as specific transformations such as the pH-induced phenol-phenolate transition of the tyrosine residue. Circular dichroism (CD) and Fourier-transform infrared (FTIR) spectroscopies are used to investigate the conditions for beta-sheet self-assembly and the role of aromatic interactions in the CD spectrum as a function of pH and concentration. The formation of well-defined fibrils at pH 4.7 is confirmed by cryo-TEM (transmission electron microscope) and negative stain TEM. The morphology changes at higher pH, and aggregates of short twisted fibrils are observed at pH 11. Polarized optical microscopy shows birefringence at a low concentration (1 wt.-%) of YYKLVFFC in aqueous solution, and small-angle X-ray scattering was used to probe nematic phase formation in more detail. A pH-induced transition from nematic to isotropic phases is observed on increasing pH that appears to be correlated to a reduction in aggregate anisotropy upon increasing pH.

Influence of end-capping on the self-assembly of model amyloid peptide fragments

The influence of charge and aromatic stacking interactions on the self-assembly of a series of four model amyloid peptides has been examined. The four model peptides are based on the KLVFF motif from the amyloid Beta peptide, ABeta(16-20) extended at the N terminus with two Beta-alanine residues. We have studied NH2-BetaABetaAKLVFF-COOH (FF), NH2-BetaABetaAKLVFCOOH (F), CH3CONH-BetaABetaAKLVFF-CONH2 (CapF), and CH3CONH-BetaABetaAKLVFFCONH2 (CapFF). The former two are uncapped (net charge plus 2) and differ by one hydrophobic phenylalanine residue; the latter two are the analogous capped peptides (net charge plus 1). The self-assembly characteristics of these peptides are remarkably different and strongly dependent on concentration. NMR shows a shift from carboxylate to carboxylic acid forms upon increasing concentration. Saturation transfer measurements of solvent molecules indicate selective involvement of phenylalanine residues in driving the self-assembly process of CapFF due presumably to the effect of aromatic stacking interactions. FTIR spectroscopy reveals beta-sheet features for the two peptides containing two phenylalanine residues but not the single phenylalanine residue, pointing again to the driving force for self-assembly. Circular dichroism (CD) in dilute solution reveals the polyproline II conformation, except for F which is disordered. We discuss the relationship of this observation to the significant pH shift observed for this peptide when compared the calculated value. Atomic force microscopy and cryogenic-TEM reveals the formation of twisted fibrils for CapFF, as previously also observed for FF. The influence of salt on the self-assembly of the model beta-sheet forming capped peptide CapFF was investigated by FTIR. Cryo-TEM reveals that the extent of twisting decreases with increased salt concentration, leading to the formation of flat ribbon structures. These results highlight the important role of aggregation-induced pKa shifts in the self-assembly of model beta-sheet peptides.