Bending and unwinding of nucleic acid by prion protein.

Nucleic acid induces conformational changes in the prion protein (23-231 amino acids) to a structure resembling its pathological isoform. The prion protein, in turn, facilitates DNA strand transfer and acts as a DNA chaperone which is modulated by the N-terminal unstructured basic segment of the protein. Here we have studied the prion protein induced conformational changes in DNA using oligonucleotides covalently labeled with the energy donor fluorescein and the acceptor rhodamine moieties by fluorescence resonance energy transfer (FRET) and by thermal stability of the unlabeled oligonucleotides. The protein induces a strong FRET effect in the oligonucleotides evidenced from the simultaneous quenching of fluorescence intensity of the donor and increase in the fluorescence intensity of the acceptor, which indicate bending of the oligonucleotides by the prion protein. The energy transfer efficiency induced by the protein is greater for the larger oligonucleotide. The prion protein also induces significant structural destabilization of the oligonucleotides observed from the lowering of their melting temperatures in the presence of the protein. The truncated globular prion protein 121-231 fragment neither induces FRET effect on the oligonucleotides nor destabilizes their structures, indicating that the N-terminal segment of the prion protein is essential for the DNA bending process. Equilibrium binding and kinetics of FRET show that the protein binding to the oligonucleotides and their bending occur simultaneously. The DNA structural changes observed in the presence of the prion protein are similar to those caused by proteins involved in initiation and regulation for protein synthesis.

Glycofection: facilitated gene transfer by cationic glycopolymers.

Mammalian cells express several types of lectins involved in intracellular trafficking, including endocytosis, interorganelle routing and putatively nuclear import. In order to enhance the gene transfer efficiency, glycosylated cationic polymers have been used as nonviral vectors. We developed a simple method to convert reducing saccharides into glycosynthons. Glycosynthons are used to synthesize cationic glycopolymers, called Glycofectins. Glycofectins interact with a plasmid to give a glycoplex, a compacted form of a polymer/DNA complex. The high glycoplex efficiency depends on the sugar involved in the uptake and in the intracellular trafficking of glycoplexes. The present paper deals with glycoplexes, with gene transfer into cystic fibrosis airway epithelial and gland serous cells, and with some of the problems that have to be solved before clinical trials.

Propynylated phosphodiester oligonucleotides inhibit ICAM-1 expression in A549 cells on electroporation.

Oligodeoxynucleotides (ODN) are used largely as either primers, antisense, or triplex-forming units. Phosphodiester ODN (PO-ODN), which are very rapidly degraded by exonucleases, must be protected at their ends. Even so, their life span inside cells is quite short. Phosphorothioate ODN (PS-ODN) are less sensitive to nucleases and are extensively used as antisense. Unfortunately, unlike PO-ODN, they interact with a number of molecules, including proteins, in addition to their specific nucleic acid targets. Their affinity for their target is lower than that of PO-ODN. PS-ODN containing propyne groups on C5 of pyrimidine have been shown to have a higher affinity toward their nucleic acid target. Here, we show that propynylated PO-ODN are more stable and much more efficient than their propyne-free counterparts. They are not efficient when they are used as lipoplexes, but they act as specific antisense on electroporation.

Delivery of oligonucleotides into mammalian cells by anionic peptides: comparison between monomeric and dimeric peptides.

The use of antisense oligonucleotides as putative therapeutic agents is limited by their poor delivery into the cytosol and/or the nucleus because they are not able to efficiently cross lipid bilayers. To circumvent this pitfall, anionic amphipathic peptides derived from the influenza virus fusogenic peptide have been used to destabilize membranes in an acidic environment. In this paper, we compare the ability of a monomeric and a dimeric peptide to introduce oligonucleotides into the cytosol and nuclei of several types of cultured cells. Cells incubated at pH 6.2 or at a slightly lower pH in the presence of the monomeric peptide but not the dimeric peptide were efficiently permeabilized. The location of fluorescent derivatives of peptides and of oligonucleotides was assessed by confocal microscopy. Both the peptides and oligonucleotides remained entrapped in vesicular compartments at neutral pH; at acidic pH, oligonucleotides in the presence of the monomeric peptide were mainly in the nucleus, while in the presence of the dimeric peptide they co-localized with the peptide into vesicles. The data are interpreted on the basis of the spectroscopic behaviour of monomeric and dimeric peptides in relation to the environmental pH.

Optimized synthesis of phosphorothioate oligodeoxyribonucleotides substituted with a 5'-protected thiol function and a 3'-amino group.

A new deprotection procedure enables a medium scale preparation of phosphodiester and phosphor-othioate oligonucleotides substituted with a protected thiol function at their 5'-ends and an amino group at their 3'-ends in good yield (up to 72 OD units/micromol for a 19mer phosphorothioate). Syntheses of 3'-amino-substituted oligonucleotides were carried out on a modified support. A linker containing the thioacetyl moiety was manually coupled in two steps by first adding its phosphor-amidite derivative in the presence of tetrazole followed by either oxidation or sulfurization to afford the bis-derivatized oligonucleotide bound to the support. Deprotection was achieved by treating the fully protected oligonucleotide with a mixture of 2,2'-dithiodipyridine and concentrated aqueous ammonia in the presence of phenol and methanol. This proced-ure enables (i) cleavage of the oligonucleotide from the support, releasing the oligonucleotide with a free amino group at its 3'-end, (ii) deprotection of the phosphate groups and the amino functions of the nucleic bases, as well as (iii) transformation of the 5'-terminal S -acetyl function into a dithiopyridyl group. The bis-derivatized phosphorothioate oligomer was further substituted through a two-step procedure: first, the 3'-amino group was reacted with fluorescein isothiocyanate to yield a fluoresceinylated oligo-nucleotide; the 5'-dithio-pyridyl group was then -quantitatively reduced to give a free thiol group which was then substituted by reaction with an N alpha-bromoacetyl derivative of a signal peptide containing a KDEL sequence to afford a fluoresceinylated peptide-oligonucleotide conjugate.

The sugar binding activity of MR60, a mannose-specific shuttling lectin, requires a dimeric state.

MR60 is an intracellular membrane protein which has been shown to act as a mannoside specific lectin and to be identical to ERGIC-53, a protein characteristic of the endoplasmic reticulum-Golgi apparatus-intermediate compartment, acting as a shuttle. According to its primary sequence, this MR60/ERGIC-53 protein contains a luminal domain including the carbohydrate recognition domain, a stem, a transmembrane segment and a cytosolic domain. The endogenous MR60/ERGIC-53 protein is spontaneously oligomeric, (dimers and hexamers). In this paper, we study the relationship between the oligomerization state and the sugar binding capacity by using recombinant proteins. The expression of the recombinant proteins was evidenced by immunocytochemistry and by immunoprecipitation followed by SDS-PAGE analysis. The full size recombinant protein binds mannosides and is oligomeric, up to the hexameric form. Two truncated proteins lacking the transmembrane and the cytosolic domains were prepared and characterized. A long one, containing the cysteine 466 close to the C-terminal end of the recombinant protein but lacking the cysteine 475, close to the C-terminal end of the native protein, does bind mannosides and forms dimers but no higher oligomeric forms. A shorter one, lacking both the cysteines 466 and 475, does not bind mannosides and does not form dimers or higher polymers. The two cysteines in the carbohydrate recognition domain (C190 and C230) are not involved in the stabilization of oligomers. In conclusion, this study shows that the luminal moiety of MR60/ERGIC-53 contains a device allowing both its oligomeric pattern and its sugar binding capability.

The nuclear export signal-dependent localization of oligonucleopeptides enhances the inhibition of the protein expression from a gene transcribed in cytosol.

Upon endocytosis, most oligodeoxynucleotides (ODNs) accumulate in vesicular compartments; a tiny number of them cross the vesicle membrane, reach the cytosol and by passive diffusion enter the nucleus where they are entrapped. So far, the compartment in which an antisense ODN interacts with its mRNA target has not been precisely characterized. In an attempt to answer this question, ODN-peptides were designed with the aim of maintaining them in the cytosol. This has been achieved by a short peptide sequence called the nuclear export signal (NES). Upon microinjection, ODN-NES peptide conjugates were efficiently and rapidly exported from the nucleus to the cytosol whereas ODN-peptides containing an inactive NES were found to be located in the nucleus. The inhibitory activity of antisense ODN was tested in a system allowing the specific transcription of a luciferase reporter gene in the cytosol. Antisense propynylated ODN-NES peptide conjugates, directed against the luciferase gene, efficiently inhibited (75%) the cytosolic expression of luciferase whereas at the same concentration the peptide-free propynylated ODN or the propynylated ODN-peptides containing an inactive NES were nearly inactive.

Intracellular localization of oligonucleotides: influence of fixative protocols.

In many studies reporting the use of antisense oligonucleotides (ODN), the intracellular localization was investigated by using fluorescent-labeled oligonucleotides (F-ODN). More often, cells were fixed on uptake of F-ODN before microscopic analysis. We report here the influence of various methods of cell fixation on the intracellular localization of ODN. By confocal microscopy, we show that with unfixed cells, endocytosed peptides, oligonucleotides (Mr around 10,000), and endocytosed proteins were mainly localized in vesicular compartments. On mild fixation with paraformaldehyde, an identical intracellular localization was observed repeatedly after fixation, from immediately up to several days. In contrast, with methods based on the use of strong fixatives, such as methanol or acetone, the small molecules diffuse into the cytosol and in the case of oligonucleotides into the nucleus. These results point out the importance of the fixation protocol in the study of intracellular localization of ODN and their derivatives.

Optimized conditions to couple two water-soluble biomolecules through alkylamine thiolation and thioetherification.

A simple method for introducing, in buffered saline, a reactive sulfhydryl group on water-soluble molecules bearing an alkyl-amino group is described. This method is based on the use of two water-soluble reagents: 2-iminothiolane and 6,6'-dithiodinicotinic acid. The first one is open upon reaction with an amino group, and the generated thiol group is immediately protected by action of the second reagent. The optimal conditions were determined by taking into account the stability and the reactivity of both reagents with regards to pH and temperature. This method was validated through two applications, the substitution of bovine serum albumin with a bromoacetyl peptide and the substitution of an amino link at the 5' end of an oligonucleotide by reaction with either a fluorescent tag, iodoacetamidofluorescein, or a bromoacetyl peptide, upon reduction of the protected disulfide bridge with a third water-soluble reagent, namely tris(2-carboxyethyl)phosphine.

Intradermal DNA immunization: antisera specific for the membrane lectin MR60/ERGIC-53.

The trafficking of intracellular membrane proteins in Golgi apparatus, endoplasmic reticulum or intermediate compartment has not yet been fully elucidated. The human MR60/ ERGIC-53 and the rat p58 proteins are one such protein; and to study them in cell-free and in situ systems, high quality monospecific antisera are required. Highly specific antisera have been obtained after immunization of mice with plasmids containing a gene encoding either the full length or a truncated protein. The best results were obtained after intradermal injections of a plasmid encoding a truncated protein comprising both the luminal carbohydrate recognition domain and the stem down to a cysteine residue close to the C-terminal end, but neither the transmembrane nor the cytosolic domains. Such antisera have a very high titer and are very efficient tools to visualize the MR60 protein in situ or to selectively precipitate the MR60 proteins from a whole cell lysate.

Glycotargeting: influence of the sugar moiety on both the uptake and the intracellular trafficking of nucleic acid carried by glycosylated polymers.

Nucleic acids (plasmids as well as oligonucleotides) used to specifically express or modulate the expression of a gene, must reach the cytosol and/or the nucleus. Several systems have been developed to increase their uptake and their efficiency. Glycosylated polylysines have been shown to specifically help nucleic acids to be taken up in cells expressing a given cell surface membrane lectin. However, it appeared that the efficiency of the imported nucleic acid was not directly related to the extent of the uptake. Indeed, some glycosylated polylysines bearing sugar moities which are poor ligands of the cell surface lectins of a given cell were found to be more efficient than those bearing better sugar ligands. The interpretation of this paradoxal result is discussed with regards to the nature of the compartment allowing the nucleic acid to cross the membrane and to be delivered in the cytosol on the one hand, and to the presence of intracellular lectins on the other hand.

Glycotargeting: the preparation of glyco-amino acids and derivatives from unprotected reducing sugars.

Lectins are present on the surface of many cells. Many lectins actively recycle from membrane to endosomes and efficiently take up glycoconjugates in a sugar-dependent manner. On this basis, glycoconjugates, specially those obtained by chemical means, are good candidates as carriers of drugs, oligonucleotides or genes. In this paper, we present a panel of methods suitable to transform unprotected reducing oligosaccharides into glycosynthons designed to be easily linked to therapeutic agents. All the glycosynthons presented here are glycosylamines or derivatives, mainly glyco-amino acids or glycopeptides. Glycosylamines are easy to obtain, but they are very labile in slightly acidic or neutral medium; they must be stabilized, by acylation for instance. The coupling efficiency of a reducing sugar with ammonia as well as an alkylamine or an arylamine is higher at high temperature, however, because of the Amadori rearrangement, special conditions have to be selected to prepare the expected glycosylamine derivative with a high yield. Glycosylamines are easily acylated by N-protected amino acids, or by halogeno acids which can then be transformed into amino acids. Alternatively, unprotected reducing oligosaccharides may very efficiently be transformed into N-glycosyl-amino acids and then protected by N-acylation. With a glutamyl derivative having both the alpha-amino and the gamma-carboxylic groups free, the coupling and the acylation, which is intramolecular, are roughly quantitative. N-oligosaccharyl-amino acid derivatives are interesting glycosynthons, because their sugar moiety bears the specificity towards membrane lectins while the amino acid part has the capacity to easily substitute a therapeutic agent.

Novel glycosynthons for glycoconjugate preparation: oligosaccharylpyroglutamylanilide derivatives.

The reducing sugar of an oligosaccharide reacting with the alpha-amino group of an amino acid is converted to an N-oligosaccharylamino acid which can then be stabilized by N-acylation. Oligosaccharides in solution in N,N-dimethylformamide reacted with alpha-glutamyl-p-nitroanilide at 50 degrees C for a few hours, leading to an N-oligosaccharylglutamyl-p-nitroanilide. Then, the gamma-carboxylic group of the glutamyl moiety, activated by adding (benzotriazol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate (BOP), reacted with the substituted alpha-amino group of the glutamyl residue, leading to an N-oligosaccharylpyroglutamyl-p-nitroanilide within 0.5 h. Such a one-pot two-step reaction was shown to be very efficient in the case of a disaccharide such as lactose, or pentasaccharides such as lacto-N-fucopentaoses, Lewis(a) or Lewis(x). The glycosynthons were characterized by chromatography (HPAEC and HPLC); their molecular mass was determined by electrospray ionization mass spectrometry, and the glycosylamides were shown to have a beta-anomeric configuration on the basis of their proton NMR. The N-oligosaccharylpyroglutamyl-p-nitroanilides are quite stable at room temperature over a large pH range. They are easily converted to N-oligosaccharylpyroglutamyl-p-isothiocyanatoanilides which can be used to prepare glycoconjugates such as cationic glycosylated polylysines suitable for specifically delivering genes or oligonucleotides in a sugar-dependent manner.

Cytosolic and nuclear delivery of oligonucleotides mediated by an amphiphilic anionic peptide.

Antisense oligonucleotides (ODN) were easily introduced into the cytosol of mammalian cells on permeabilization of the plasma membrane by an amphiphilic anionic peptide. The E5CA peptide (GLFEAIAEFIEGGWEGLIEGCA) is an E5 peptide analog derived from the N-terminal segment of the HA2 subunit of influenza virus hemagglutinin. This peptide undergoes a conformational change when the pH shifts from neutral to around 6.0, inducing a transient permeabilization of the plasma membrane. In the presence of the E5CA peptide at pH close to 6.0, fluoresceinylated ODN were rapidly taken up by cells and diffused into the nucleus. The uptake of ODN was dependent on the E5CA peptide concentration and on the duration of the incubation at low pH, as shown by confocal microscopy and flow cytometry analyses. This procedure is suitable for loading adherent cells as well as nonadherent cells with single-stranded or double-stranded ODN. Under optimal conditions, a high percentage of cells were nuclei loaded, and the viability was not affected. This method makes use of a well-defined chemical product without the requirement of any special equipment. It will be useful to study the interactions of single-stranded or double-stranded ODN used as antisense, antigenes, or decoys.

Intracellular routing and inhibitory activity of oligonucleopeptides containing a KDEL motif.

On internalization, oligonucleotides (ODN) remain mostly sequestered in endocytic compartments. To increase their delivery into the cytosol and/or nucleus, which contain their targets, we attempted to guide them into compartments containing the KDEL receptor. Antisense ODN, phosphodiester protected at both ends, that are complementary to the AUG initiation site of gagHIV-1 mRNA (odn) were linked to a peptide ending with the Lys-Asp-Glu-Leu (KDEL) motif in a carboxyl-terminal position (odn-p-KDEL) or with the Lys-Asp-Glu-Ala (odn-p-KDEA) as a control. The effect of odn substitution with a peptide was examined with regard to its accumulation, subcellular location, and activity in HepG2 cells. Although odn-p-KDEL was internalized 4-fold less than the corresponding peptide-free odn, it was 5-fold more efficient in inhibiting gagHIV-1 gene expression in HepG2 cells. The internalization of odn-p-KDEA was as low as that of odn-p-KDEL, but its biological activity was lower, close to that of the peptide-free odn. On endocytosis at 37 degrees, both conjugates as well as the peptide-free odn were found in a neutral environment. However, the substitution of an odn with a KDEL motif altered its intracellular trafficking; most of the odn-p-KDEL was found in the endoplasmic reticulum and in the intermediate compartment as identified by colabeling with either anti-ERGIC-53 or anti-KDEL receptor antibodies. Conversely, odn-p-KDEA and peptide-free odn were localized in vesicular compartments not labeled with these antibodies. In addition, pulse-chase experiments showed that odn-p-KDEL and odn-p-KDEA had a lower efflux than peptide-free odn. Therefore, the large increase in efficiency was due to the KDEL motif.

The reduction of the positive charges of polylysine by partial gluconoylation increases the transfection efficiency of polylysine/DNA complexes.

A polylysine partially substituted with polyhydroxyalkanoyl residues and specially with gluconoyl residues was developed in order to increase the transfection efficiency by decreasing the strength of the electrostatic interactions between the DNA and the cationic polymer. Partially gluconoylated polylysine/DNA complexes were more easily dissociated in solution and their transfection efficiency in the presence of chloroquine, evaluated with HepG2 cells, a human hepatocarcinoma line, was higher when 43 +/- 4% of the epsilon-amino groups of polylysine were blocked with gluconoyl residues. Partially gluconoylated polylysine/plasmid complexes were efficient in transfecting different adherent as well as non-adherent cell lines. Partially gluconoylated polylysine formed highly soluble (above 100 micrograms/ml in DNA) complexes with DNA plasmids. In addition, partially gluconoylated polylysine bearing few lactosyl residues increased the transfection efficiency of HepG2 cells which express a galactose-specific membrane lectin.

Enhanced biological activity of antisense oligonucleotides complexed with glycosylated poly-L-lysine.

We sought to exploit glycosylated poly-L-lysine (pLK) to increase the uptake and biological antisense activity of a phosphorothioate oligonucleotide (pt-odn) [pt-odn complementary to the 3' noncoding region of intercellular adhesion molecule-1 (ICAM-1) (odn(ICAM-1))] complementary to the 3'-noncoding region of ICAM-1 in A549 cells. Dose-dependent inhibition of ICAM-1 expression was obtained (IC50 = 500 nM) through treatment of cells with odn(ICAM-1) complexed with pLK carrying fucose residues in the presence of 100 microM chloroquine. Alteration in the charge ratio between fucosylated pLK and pt-odn had a significant effect on the efficacy of inhibition (optimal conditions, charge ratio = 1.1). This effect was also dependent on the number of fucose moieties per pLK. Free pt-odn or pt-odn complexed with nonglycosylated pLK gave no inhibition at concentrations of < or = 2 microM. Two control pt-odn (one was targeted against an unrelated gene not present in these cells, gag(HIV), and the other had a randomized sequence) gave no inhibition of ICAM-1 expression in the presence or absence of pLK carrying fucose residues at concentrations of < or = 2 microM. When complexed with pLK carrying 100 fucose residues, the amount of cell-associated pt-odn was increased by 15-fold compared with the free pt-odn. Nongycosylated pLK also increased the amount of cell-associated pt-odn by >10 fold but did not alter the biological activity. These results demonstrate clearly the potential of glycosylated pLK as a pt-odn transporter.