G-quadruplex aptamer selection using capillary electrophoresis-LED-induced fluorescence and Illumina sequencing.

One of the major difficulties that arises when selecting aptamers containing a G-quadruplex is the correct amplification of the ssDNA sequence. Can aptamers containing a G-quadruplex be selected from a degenerate library using non-equilibrium capillary electrophoresis (CE) of equilibrium mixtures (NECEEM) along with high-throughput Illumina sequencing? In this article, we present some mismatches of the G-quadruplex T29 aptamer specific to thrombin, which was PCR amplified and sequenced by Illumina sequencing. Then, we show the proportionality between the number of sequenced molecules of T29 added to the library and the number of sequences obtained in Illumina sequencing, and we find that T29 sequences from this aptamer can be detected in a random library of ssDNA after the sample is fractionated by NECEEM, amplified by PCR, and sequenced. Treatment of the data by the counting of double-stranded DNA T29 sequences containing a maximum of two mismatches reveals a good correlation with the enrichment factor (fE). This factor is the ratio of the number of aptamer sequences found in the collected complex sample divided by the total number of sequencing reads (aptamer and non-aptamer) plus the quantity of T29 molecules (spiked into a DNA library) injected into CE.

ssDNA degradation along capillary electrophoresis process using a Tris buffer.

Tris-Acetate buffer is currently used in the selection and the characterization of ssDNA by capillary electrophoresis (CE). By applying high voltage, the migration of ionic species into the capillary generates a current that induces water electrolysis. This phenomenon is followed by the modification of the pH and the production of Tris derivatives. By injecting ten times by capillary electrophoresis ssDNA (50 nM), the whole oligonucleotide was degraded. In this paper, we will show that the Tris buffer in the running vials is modified along the electrophoretic process by electrochemical reactions. We also observed that the composition of the metal ions changes in the running buffer vials. This phenomenon, never described in CE, is important for fluorescent ssDNA analysis using Tris buffer. The oligonucleotides are degraded by electrochemically synthesized species (present in the running Tris vials) until it disappears, even if the separation buffer in the capillary is clean. To address these issues, we propose to use a sodium phosphate buffer that we demonstrate to be electrochemically inactive.

Development of a near infrared protein nanoprobe targeting Thomsen-Friedenreich antigen for intraoperative detection of submillimeter nodules in an ovarian peritoneal carcinomatosis mouse model.

The epithelial ovarian cancer is one of the most lethal gynecological malignancy due to its late diagnostic and many relapses observed after first line of treatment. Once diagnose, the most important prognostic factor is the completeness of cytoreductive surgery. To achieve this goal, surgeons have to pinpoint and remove nodules, especially the smallest nodules. Recent advances in fluorescence-guided surgery led us to develop a recombinant lectin as a nanoprobe for the microscopic detection of nodules in the peritoneal cavity of tumor-bearing mice. This lectin has an intrinsic specificity for a carcinoma-associated glycan biomarker, the Thomsen-Friedenreich antigen. In this study, after its labelling by a near infrared dye, we first demonstrated that this nanoprobe allowed indirect detection of nodules already implanted in the peritoneal cavity, through tumor microenvironment targeting. Secondly, in a protocol mimicking the scattering of cells during surgery, we obtained a direct and long-lasting detection of tumor cells in vivo. This lectin as already been described as a nanocontainer able to do targeted delivery of a therapeutic compound to carcinoma cells. Future developments will focus on the combination of the nanoprobe and nanocontainer aspects in an intraperitoneal nanotheranostic approach.

Single-strand DNA translation initiation step analyzed by Isothermal Titration Calorimetry.

Is single-strand DNA translatable? Since the 60s, the question still remains whether or not DNA could be directly translated into protein. Some discrepancies in the results were reported about functional translation of single-strand DNA but all results converged on a similar behavior of RNA and ssDNA in the initiation step. Isothermal Titration Calorimetry method was used to determine thermodynamic constants of interaction between single-strand DNA and S30 extract of Escherichia coli. Our results showed that the binding was not affected by the nature of the template tested and the dissociation constants were in the same range when ssDNA (K(d)=3.62+/-2.1 x 10(-8)M) or the RNA corresponding sequence (K(d)=2.7+/-0.82 x 10(-8) M) bearing SD/ATG sequences were used. The binding specificity was confirmed by antibiotic interferences which block the initiation complex formation. These results suggest that the limiting step in translation of ssDNA is the elongation process.

A protein nanocontainer targeting epithelial cancers: rational engineering, biochemical characterization, drug loading and cell delivery.

The development of drug delivery and imaging tools is a major challenge in human health, in particular in cancer pathologies. This work describes the optimization of a protein nanocontainer, belonging to the lectin protein family, for its use in epithelial cancer diagnosis and treatment. Indeed, it specifically targets a glycosidic marker, the T antigen, which is known to be characteristic of epithelial cancers. Its quaternary structure reveals a large hydrated inner cavity able to transport small therapeutic molecules. Optimization of the nanocontainer by site directed mutagenesis allowed controlling loading and release of confined drugs. Doxorubicin confinement was followed, both theoretically and experimentally, and provided a proof of concept for the use of this nanocontainer as a vectorization system. In OVCAR-3 cells, a human ovarian adenocarcinoma cell line that expresses the T antigen, the drug was observed to be delivered inside late endosomes/lysosomes. These results show that this new type of vectorization and imaging device opens new exciting perspectives in nano-theranostic approaches.

Evidence for subdomain flexibility in Drosophila melanogaster acetylcholinesterase.

The catalytic domain of the acetylcholinesterases is composed of a single polypeptide chain, the folding of which determines two subdomains. We have linked these two subdomains by mutating two residues, I327 and D375, to cysteines, to form a disulfide bridge. As a consequence, the hydrodynamic radius of the protein was reduced, suggesting that there is some flexibility in the subdomain connection. In addition to the smaller size, the mutated protein is more stable than the wild-type protein. Therefore, the flexibility between the two domains is a weak point in terms of protein stability. As expected from the location of the disulfide bond at the rim of the active site, the kinetic studies show that it affects interactions with peripheral ligands and the entrance of some of the bulkier substrates, like o-nitrophenyl acetate. In addition, the mutations affect the catalytic step for o-nitrophenyl acetate and phosphorylation by organophosphates, suggesting that this movement between the two subdomains is connected with the cooperativity between the peripheral and catalytic sites.

Protein expression from synthetic genes: selection of clones using GFP.

Construction of synthetic genes is today the most elegant way to optimize the heterologous expression of a recombinant protein. However, the selection of positive clones that incorporate the correct synthetic DNA fragments is a bottleneck as current methods of gene synthesis introduce 3.5 nucleotide deletions per kb. Furthermore, even when all predictable optimizations for protein production have been introduced into the synthetic gene, production of the protein is often disappointing: protein is produced in too low amounts or end up in inclusion bodies. We propose a strategy to overcome these two problems simultaneously by cloning the synthetic gene upstream of a reporter gene. This permits the selection of clones devoid of frame-shift mutations. In addition, beside nucleotide deletion, an average of three non-neutral mutations per kb are introduced during gene synthesis. Using a reporter protein downstream of the synthetic gene, allows the selection of clones with random mutations improving the expression or the folding of the protein of interest. The problem of errors found in synthetic genes is then turned into an advantage since it provides polymorphism useful for molecular evolution. The use of synthetic genes appears as an alternative to the error-prone PCR strategy to generate the variations necessary in protein engineering experiments.

Effect of a fungal lectin from Xerocomus chrysenteron (XCL) on the biological parameters of aphids.

Aphids are important pests of crop plants in Europe. Increasing resistance of aphids to insecticides and their side effects on the environment and non target organism's including human's stimulated research on alterative methods of aphid control, including the use of entomotoxic proteins. Lectins are carbohydrate binding proteins that are widely distributed in nature; they have been isolated from microorganisms, fungi, plants and animals. Several of these proteins were tested for their potential biocide effect on plenty of pests. A fungal lectin, namely Xerocomus Chrysenteron lectin (XCL) was previously purified and was shown to be toxic for several pests including aphids. XCL was clearly the most toxic lectin against M. persicae. In this work, bioassays using artificial diets incorporating a broad range of XCL concentrations (from 10 microg x ml(-1) to 5000 microg x ml(-1)) were developed to assess the negative effects of XCL on the biological parameters (development duration, weight and fecundity) of M. persicae a polyphagous aphid found on more than 400 host plant species and transmitting more than 100 viral diseases. A significant mortality of aphids was observed, corresponding to the LC50 and LC90 of 0, 46 and 6, 02 mg/ml respectively after 24hrs. Significant differences of M. persicae weight, development duration and fecundity (P < 0.05) was observed between the tested XCL concentrations. Conavalia ensifomris lectin (ConA) was included as lectin reference on the bioassay experiments and was shown to be less toxic and induced lower negative changes in M. persicae biological parameters when compared with XCL.

Xerocomus chrysenteron lectin: identification of a new pesticidal protein.

Xerocomus chrysenteron is an edible mushroom with insecticidal properties. In an earlier work, we found that proteins are responsible for this toxicity. Here we describe the purification of a approximately 15 kDa lectin, named XCL, from the mushroom. Its cDNA and gDNA were cloned by PCR strategies and a recombinant form was expressed in Escherichia coli. Sequence alignments and sugar specificity showed that this protein is the third member of a new saline-soluble lectin family present in fungi. This protein, either purified from mushroom or expressed in vitro in E. coli, was found to be toxic to some insects, such as the dipteran Drosophila melanogaster and the hemipteran, Acyrthosiphon pisum. The lectin possesses a high insecticidal activity compared to lectin isolated from leguminosae (Lathyrus ochrus) or from the snowdrop (Galanthus nivalis).

A new lectin family with structure similarity to actinoporins revealed by the crystal structure of Xerocomus chrysenteron lectin XCL.

A newly defined family of fungal lectins displays no significant sequence similarity to any protein in the databases. These proteins, made of about 140 amino acid residues, have sequence identities ranging from 38% to 65% and share binding specificity to N-acetyl galactosamine. One member of this family, the lectin XCL from Xerocomus chrysenteron, induces drastic changes in the actin cytoskeleton after sugar binding at the cell surface and internalization, and has potent insecticidal activity. The crystal structure of XCL to 1.4 A resolution reveals the architecture of this new lectin family. The fold of the protein is not related to any of the several lectin folds documented so far. Unexpectedly, the structure similarity is significant with actinoporins, a family of pore-forming toxins. The specific structural features and sequence signatures in each protein family suggest a potential sugar binding site in XCL and a possible evolutionary relationship between these proteins. Finally, the tetrameric assembly of XCL reveals a complex network of protomer-protomer interfaces and generates a large, hydrated cavity of 1000 A3, which may become accessible to larger solutes after a small conformational change of the protein.

Determination of thermodynamic parameters of Xerocomus chrysenteron lectin interactions with N-acetylgalactosamine and Thomsen-Friedenreich antigen by isothermal titration calorimetry.

BACKGROUND: Lectins are carbohydrate-binding proteins which potentially bind to cell surface glycoconjugates. They are found in various organisms including fungi. A lectin from the mushroom Xerocomus chrysenteron (XCL) has been isolated recently. It shows insecticidal activity and has antiproliferative properties. RESULTS: As the monosaccharide binding specificity is an important determinant of lectin function, we determined the affinity of XCL for the galactose moiety. Isothermal titration calorimetry studies revealed a dissociation constant Kd of 5.2 microM for the XCL:N-acetylgalactosamine interaction at 27 degrees C. Higher affinities were observed at lower temperatures and higher osmotic pressures. The dissociation constant was five hundred times higher for the disaccharide beta-D-Gal(1-3)-D-GalNAc, Thomsen-Friedenreich (TF) antigen (Kd of 0.94 microM). By using fetuin and asialofetuin in interaction with the XCL, we revealed its ability to recognize the Thomsen-Friedenreich motif on glycoproteins. CONCLUSION: The XCL antiproliferative effect and the TF antigen specificity presented in this work suggest that XCL and ABL may have similar binding mechanisms. The recent structure determination of these two proteins lead us to analyse these interactions in the light of our thermodynamic data. The understanding of this type of interaction may be a useful tool for the regulation of cell proliferation.

Fungal lectin, XCL, is internalized via clathrin-dependent endocytosis and facilitates uptake of other molecules.

The lectin isolated from Xerocomus chrysenteron (XCL) displays a toxic activity towards insects. In order to assess its possible mode of action and to gather useful data for its potential use in insect-resistant transgenic plants, we investigated the effects of XCL at the cellular level. Immunofluorescence microscopy studies revealed that XCL is rapidly internalized into small endocytic vesicles that further coalesce in the perinuclear region. We show that XCL is endocytosed by the clathrin-dependent pathway, and is delivered to late endosome/lysosome compartments. The internalization of XCL seems to be general since it occurs in different cell types such as insect (SF9) or mammalian (NIH-3T3 and Hela) cell lines. In the presence of XCL, the uptake of GFP and BSA is greatly enhanced, demonstrating that XCL facilitates endocytosis. Thus, XCL could serve as a delivery agent to facilitate the endocytosis of proteins that do not enter the cell alone.

Proteins as active compounds involved in insecticidal activity of mushroom fruitbodies.

Many mushrooms are toxic to insects. To identify the chemicals involved in insecticidal activity, the toxicity of 14 species has been studied for water solubility, thermolability, and dialysis. The data strongly suggest that proteins are responsible for most of the insecticidal activity of mushroom fruitbodies and may be a source of genes available for plant protection against insects. Among proteins, lectins and hemolysins were good insecticide candidates because the toxicities were not affected by protease.

Direct validation of aptamers as powerful tools to image solid tumor.

Visualization of cancer cells requires distinguishing malignant from normal cells by objective criteria with high specificity. For several years, tumor markers expressed on the surface of cancer cells have been characterized as cancer signatures, and their labeling with specific imaging probes has revolutionized cancer diagnosis. This specific labeling is also an important tool in surgery tumor ablation. The present study considers the tumor labeling potential of an aptamer that specifically recognizes the epithelial cancer biomarker mucin1 (MUC1). This anti-MUC1 aptamer was investigated in vitro in a three-dimensional (3D) environment and compared to an anti-MUC1 antibody for its capacity to visualize cancer cells. Multicellular spheroids of breast cancer MCF-7 cells were used as tumor models and anti-MUC1 fluorescent aptamer and antibody were visualized by fluorescence imaging. Results showed that the antibodies interacted only with cells located on the surface of the spheroid, whereas the anti-MUC1 aptamers were able to penetrate inside these 3D tumor models and thereafter internalized into the cancer cells. Due to their lack of immunogenicity and their facility to be chemically modified, aptamers may replace advantageously the use of antibodies in diagnosis based on imaging setup thanks to their specific detection of cancer cells without invasive surgical procedures or during clinical intraoperative intervention.

α,ß-D-constrained nucleic acids are strong terminators of thermostable DNA polymerases in polymerase chain reaction.

(S(C5'), R(P)) α,ß-D- Constrained Nucleic Acids (CNA) are dinucleotide building blocks that can feature either B-type torsional angle values or non-canonical values, depending on their 5'C and P absolute stereochemistry. These CNA are modified neither on the nucleobase nor on the sugar structure and therefore represent a new class of nucleotide with specific chemical and structural characteristics. They promote marked bending in a single stranded DNA so as to preorganize it into a loop-like structure, and they have been shown to induce rigidity within oligonucleotides. Following their synthesis, studies performed on CNA have only focused on the constraints that this family of nucleotides introduced into DNA. On the assumption that bending in a DNA template may produce a terminator structure, we investigated whether CNA could be used as a new strong terminator of polymerization in PCR. We therefore assessed the efficiency of CNA as a terminator in PCR, using triethylene glycol phosphate units as a control. Analyses were performed by denaturing gel electrophoresis and several PCR products were further analysed by sequencing. The results showed that the incorporation of only one CNA was always skipped by the polymerases tested. On the other hand, two CNA units always stopped proofreading polymerases, such as Pfu DNA polymerase, as expected for a strong replication terminator. Non-proofreading enzymes, e.g. Taq DNA polymerase, did not recognize this modification as a strong terminator although it was predominantly stopped by this structure. In conclusion, this first functional use of CNA units shows that these modified nucleotides can be used as novel polymerization terminators of proofreading polymerases. Furthermore, our results lead us to propose that CNA and their derivatives could be useful tools for investigating the behaviour of different classes of polymerases.

Fluorescence imaging agents in cancerology.

BACKGROUND: One of the major challenges in cancer therapy is to improve early detection and prevention using novel targeted cancer diagnostics. Detection requests specific recognition. Tumor markers have to be ideally present on the surface of cancer cells. Their targeting with ligands coupled to imaging agents make them visible/detectable. CONCLUSIONS: Fluorescence imaging is a newly emerging technology which is becoming a complementary medical method for cancer diagnosis. It allows detection with a high spatio-temporal resolution of tumor markers in small animals and in clinical studies. In this review, we focus on the recent outcome of basic studies in the design of new approaches (probes and devices) used to detect tumor cells by fluorescence imaging.

Stabilization of liposomes through enzymatic polymerization of DNA.

Combining supramolecular self-assembly of lipids with enzymatic triggered DNA interfacial polymerization allows construction of composite nanocapsules. Covalent grafting of oligonucleotides functionalizes the surface of liposomes. Subsequent addition of an enzyme called terminal deoxynucleotidyl transferase elongates the single-stranded DNA. The elongated DNA hybridizes, creating a random network. The short segments of double-stranded DNA provides a substrate for the Klenow fragment of E. coli DNA polymerase, which synthesizes a double-strand DNA, reinforcing the network. Alternate action of both enzymes leads to a three-dimensional network anchored on the liposome surface.

Inhibitory action of a new lectin from Xerocomus chrysenteron on cell-substrate adhesion.

Lectins are carbohydrate-binding proteins which potentially link to cell surface glycoconjugates and affect cell proliferation. We investigated the effect of a new lectin from the mushroom Xerocomus chrysenteron (XCL) on cell proliferation using adherent and suspension cell lines. XCL caused a dose-dependent inhibition of proliferation of the adherent cell lines NIH-3T3 and HeLa. Several experiments suggest that disruption of cell-substrate adhesion is the main factor affecting cell growth inhibition. (i) No antiproliferative effect was observed on the SF9 cell line, which does not require to be attached to grow. (ii) XCL was shown to affect the adherence of cells following their suspension by trypsin treatment. (iii) XCL was localized on the cell surface where it would act as a coating agent. (iv) XCL induced morphological changes from well spread to rounded cells and disrupted the actin cytoskeleton. By contrast, flow cytometric analysis showed that XCL does not interfere with the cell cycle, and does not induce apoptosis.