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E Taillandier

Publications and source records attributed to E Taillandier.

At least 37 records · Page 2Linked to original sources
PubMed1998

Triple helix-forming oligonucleotides which make imperfect Watson-Crick duplexes that compete with the creation of the triplex.

Because of the repetitive nature of the sequence, when titrating a G,A-rich, triple helix-forming oligonucleotide (TFO) with increasing concentrations of target duplex in order to obtain the dissociation constant of the complex, a duplex is sometimes first generated at intermediate concentrations of the target. This duplex is based on an imperfect Watson-Crick pairing of the TFO to the pyrimidine-rich strand of the target. An explanation is proposed for this duplex being obtained only in a certain domain of the titration range, before the triple helix becomes predominant.

Base Pairing↗
PubMed1998

Conformational study of DNA-RNA duplexes containing MMI substituted phosphodiester linkages by FTIR spectroscopy.

Six methylene(methylimino) (MMI, Bhat et al. J. Org. Chem., 61, 8186, 1996) linked oligonucleotides a-f (* = MMI linkage; 5'-GCGT*TT*TT*TT*TT*TGCG-3') containing various combinations of 2'-O-methyl and 2'-fluoro substituent were synthesized as a model to study the global conformational change upon hybridization to the complement RNA. Fourier transform infrared (FTIR) spectroscopic technique has been used to study and compare the influence of these modifications on the solution conformation of 2'-modified MMI DNA-RNA duplexes. FTIR analysis of the single-stranded RNA (5'-CGCAAAAAAAAAACGC-3') and the modified oligonucleotides a-f showed that all sugar residues adopted a C3'-endo conformation (North-type). Stable duplexes were formed when oligonucleotides a-f were hybridized to the complement RNA. These duplexes retained the original C3'-endo conformation for all sugar residues, hallmark of an A-form of duplex. We postulate that the observed preorganization of the sugar residues and oligonucleotides containing 2'-modified MMI modifications may play an important role in both improving the recognition of RNA target and enhancing the stability of duplex formation with RNA.

Carbohydrates↗
PubMed1997

Triple helix formation and homologous strand exchange in pyrene-labeled oligonucleotides.

The orientations of the symmetrical third strands (G3A4G3) and (G3T4G3) within the triplexes (C3T4C3) - (G3A4G3) x (G3A4G3) and (C3T4C3) - (G3A4G3) x (G3T4G3) were investigated by fluorescence spectroscopy and thermal denaturation using pyrene-labeled oligodeoxynucleotides. In the two triplex structures, both parallel and antiparallel orientations of the third strand with respects to the purine Watson-Crick one were identified by means of pyrene excimer formation. The pyrene labels do not modify the melting temperature of the (C3T4C3) - (G3A4G3) x (G3T4G3) triplex but somewhat stabilize the corresponding duplex against thermal denaturation. The absorption melting profiles of the (C3T4C3) - (G3A4G3) x (G3A4G3) triplex are monophasic in agreement with previous reports. In contrast, the melting of this structure, when monitored by the pyrene excimer band, reveals a biphasic behavior. These data, together with kinetics measurements, strongly suggest exchange mechanisms between the homologous oligomers (G3A4G3), Hoogsteen, and Watson-Crick strands.

DNA↗
PubMed1997

Hydration of the dTn.dAn x dTn parallel triple helix: a Fourier transform infrared and gravimetric study correlated with molecular dynamics simulations.

We present a comparative analysis of the water organization around the dTn.dAn x dTn triple helix and the Watson-Crick double helix dTn.dAn respectively by means of gravimetric measurements, infrared spectroscopy and molecular dynamics simulations. The hydration per nucleotide determined by gravimetric and spectroscopic methods correlated with the molecular dynamics simulations shows that at high relative humidity (98% RH) the triple helix is less solvated than the duplex (17 +/- 2 water molecules per nucleotide instead of 21 +/-1). The experimental desorption curves are different for both structures and indicate that below 81% RH the triplex becomes more hydrated than the duplex. At this RH the FTIR spectra show the emergence of N-type sugars in the adenosine strand of the triplex. When the third strand is bound in the major groove of the Watson-Crick duplex molecular dynamics simulations show the formation of a spine of water molecules between the two thymidine strands.

DNA↗
PubMed1997

A macrocyclic bis-acridine shifts the equilibrium from duplexes towards DNA hairpins.

Nucleic acids can undergo dynamic conformational changes associated with the regulation of biological processes. A molecule presenting larger affinities for alternative structures relative to a duplex is expected to modify such conformational equilibria. We have previously reported that macrocyclic bis-acridine binds preferentially to single-stranded regions, especially DNA hairpins, due to steric effects. Here, we show, using gel electrophoresis, fluorescence and melting temperature experiments, that the macrocycle bis-acridine shifts an equilibrium from a duplex towards the corresponding hairpins. Competition experiments enlighten the higher affinity of the macrocycle for hairpins compared with double-stranded DNA. The macrocycle bis-acridine destabilizes a synthetic polynucleotide, by the formation of premelted areas. By extrapolation, the macrocycle bis-acridine should be able to disrupt, at least locally, genomic DNA duplexes and to stabilize unpaired areas, especially palindromic ones forming hairpins. Such macrocyclic compounds may have potential applications in the therapy of diseases involving hairpins.

Acridines↗
PubMed1997

A physico-chemical study of triple helix formation by an oligodeoxythymidylate with N3'--> P5' phosphoramidate linkages.

Non-denaturing gel retardation assay, DNA melting experiments and FTIR spectroscopy were used to characterize the triple helix formed by a 15mer 2'-deoxythymidylate with N3'-->P5'phosphoramidate linkages with its target sequence. The results indicate that: (i) the pentadecadeoxythymidylate with phosphoramidate linkages [dT15(np)] is highly potent to form a triple helix with a dT15*dA15target duplex through Hoogsteenbase-pairing; (ii) it forms a dT15(np)*dA15xdT15(np) triplex with the single-stranded oligo-2'-deoxyadenylate (dA15) without detectable double-helical intermediate; (iii) it does not only form a triple helix on the dT15*dA15target duplex, but also partially displaces the dT15 strand from the dT15*dA15duplex to form a dT15(np)*dA15xdT15(np) complex.

DNA↗
PubMed1996

Parallel and antiparallel A*A-T intramolecular triple helices.

Intramolecular triple helices have been obtained by folding back twice oligonucleotides formed by decamers bound by non-nucleotide linkers: dA10-linker-dA10-linker-dT10 and dA10-linker-dT10-linker-dA10. We have thus prepared two triple helices with forced third strand orientation, respectively antiparallel (apA*A-T) and parallel (pA*A-T) with respect to the adenosine strand of the Watson-Crick duplex. The existence of the triple helices has been shown by FTIR, UV and fluorescence spectroscopies. Similar melting temperatures have been obtained in very different oligomer concentration conditions (micromolar solutions for thermal denaturation classically followed by UV spectroscopy, milimolar solutions in the case of melting monitored by FTIR spectroscopy) showing that the triple helices are intramolecular. The stability of the parallel triplex is found to be slightly lower than that of the antiparallel (deltaT(m) = 6 degrees C). The sugar conformations determined by FTIR are different for both triplexes. Only South-type sugars are found in the antiparallel triplex whereas both South- and North-type sugars are detected in the parallel triplex. In this case, thymidine sugars have a South-type geometry, and the adenosine strand of the Watson-Crick duplex has North-type sugars. For the antiparallel triplex the experimental results and molecular modeling data are consistent with a reverse-Hoogsteen like third-strand base pairing and South-type sugar conformation. An energetically optimized model of the parallel A*A-T triple helix with a non-uniform distribution of sugar conformations is discussed.

Carbohydrate Conformation↗
PubMed1996

Temporary ex vivo inhibition of the expression of the human oncogene HER2 (NEU) by a triple helix-forming oligonucleotide.

A 28-base phosphodiester triple helix-forming oligonucleotide, mostly G and A containing, targeted to a polypurine tract interrupted by a purine-pyrimidine inversion, situated upstream from the TATA box of the promoter of the human HER2 gene, was conceived by computer modeling. The "energetically best choice" was oligo 28(C), which formed the triple helix in vitro, as proved by gel retardation and Fourier transform infrared spectroscopy. When administered as a complex with lipofectin, fluorescence confocal microscopy and electrophoresis confirmed the delivery and persistence of this unprotected oligonucleotide inside MCF7 (breast cancer) cells. At a concentration of 2 microM, the oligonucleotide reduced within 6 h the HER2 mRNA level to 42% (Northern blot) but did not interfere with the transcription of a housekeeping gene, glyceraldehyde-3-phosphate dehydrogenase. During the first day of administration at 0.22 microM, it lowered to 59% the HER2 protein in treated, as compared to nontreated, cells (ELISA). The effect was sequence specific when compared to that of five different negative controls, and it was target selective when compared to the expression of a related, nontargeted protein, the epidermal growth factor receptor. By day 2, the inhibitory effect was overcome by replenishment reactions.

Base Sequence↗
PubMed1996

Ligand-induced formation of hoogsteen-paired parallel DNA.

INTRODUCTION: Based on molecular modeling studies, a model has been proposed for intercalation of triple-helix-specific ligands (benzopyridoindole (BPI) derivatives) into triple helices, in which the intercalating compounds interact mainly with the Hoogsteen-paired strands of the triple helix. We set out to test this model experimentally using DNA duplexes capable of forming parallel Hoogsteen base-paired structures. RESULTS: We have investigated the possible formation of a parallel DNA structure involving Hoogsteen hydrogen bonds by thermal denaturation, FTIR spectroscopy and gel-shift experiments. We show that BPI derivatives bind to Hoogsteen base-paired duplexes and stabilize them. The compounds induce a reorganization from a non-perfectly matched antiparallel Watson- Crick duplex into a perfectly matched parallel Hoogsteen-paired duplex. CONCLUSIONS: These results suggest that preferential intercalation of BPI derivatives in triple helices is due to their ability to interact specifically with the Hoogsteen-paired bases. The results are consistent with a model proposed on the basis of molecular modeling studies using energy minimization, and they open a new field of investigations regarding the biological relevance of Hoogsteen base-pairing.

DNA↗
PubMed1995

Sugar conformations in DNA and RNA-DNA triple helices determined by FTIR spectroscopy: role of backbone composition.

We have studied the effect of the nature of the third-strand sugar (ribose or deoxyribose) on the geometry and stability of triple helices with a pyrimidine motif targeting the polypurine tract of the Friend murine retrovirus. Comparison between triplexes containing a third strand formed by a deoxy 13mer d(TCT5C6), the same oligomer but with C5-methylated cytosines d(T5meCT5(5me)C6), and an analogous modified 13mer RNA 2'Omer(UCU5C6) shows that the sugar conformations of the different triple helices, determined by FTIR spectroscopy, differ depending on nature of the third-strand sugar. Pyrimidine*purine-pyrimidine triple-helix formation with the third-strand RNA and the duplex as DNA appears to be associated with a conversion of the duplex part from a B-form secondary structure with S-type sugars to a geometry in which the polypurine strand sugars adopt an N-type conformation. Thermal dissociation of the triplexes was studied by UV absorbance spectroscopy. The most stable triple helix is obtained when the third strand contains 2'-O-methylated ribose sugars.

Base Sequence↗
PubMed1995

FTIR study of a nonclassical dT10*dA10-dT10 intramolecular triple helix.

Many early investigations on triple helices have been devoted to the study of the triplex formed by dT*dA-dT base triplets in which the third strand is oriented parallel to the dA strand. We now describe an intramolecular triple helix with dT*dA-dT base triplets in which the pyrimidine third strand is oriented antiparallel, formed by folding back twice the tridecamer dT10-linker-dA10-linker-dT10 (linker = pO(CH2CH2O)3p). Third-strand base pairing to the target strand, sugar conformation, and thermal denaturation of the triplex have been studied by Fourier transform infrared spectroscopy. Our results confirm than when the third-strand orientation is reversed from parallel to antiparallel with respect to the target strand, the third-strand hydrogen-bonding scheme is changed from Hoogsteen to reverse Hoogsteen. The sugar conformation in this triple helix is of the S type (C2'endo/anti, B family form) from all strands. Our results are discussed with respect to models for triplexes proposed as intermediates in homologous recombination [Zhurkin, V.B., Raghunathan, G., Ulyanov, N.B., Camerini-Otero, R.D., & Jernigan, R.L. (1994) J. Mol. Biol. 239, 181-200].

Animals↗
PubMed1995

Structural characterization of an intramolecular RNA triple helix by NMR spectroscopy.

A chemically synthesized 29-base RNA oligomer, designed to fold to form an intramolecular triple helix at acid pH, has been studied by NMR spectroscopy. The molecule consisted of seven U.A.U or C+.G.C base triples joined by two pyrimidine tetra-loops. The fold was such that the third strand was Hoogsteen base-paired in the major groove of a Watson-Crick paired double helix. The nature and size of the molecule required the use of an assignment strategy using two- and three-dimensional homonuclear methods, complemented by a natural abundance 13C correlation experiment. The assignment of the majority of the exchangeable and non-exchangeable resonances is presented. The data suggest a C3'-endo sugar puckering for all the nucleotides involved in base triples. A preliminary structural model consistent with the NMR data is presented.

Magnetic Resonance Spectroscopy↗
PubMed1995

Spectroscopic studies of chimeric DNA-RNA and RNA 29-base intramolecular triple helices.

Fourier transform infrared (FTIR), UV absorption and exchangeable proton NMR spectroscopies have been used to study the formation and stability of two intramolecular pH-dependent triple helices composed by a chimeric 29mer DNA-RNA (DNA double strand and RNA third strand) or by the analogous 29mer RNA. In both cases decrease of pH induces formation of a triple helical structure containing either rU*dA.dT and rC+*dG.dC or rU*rA.rU and rC+*rG.rC triplets. FTIR spectroscopy shows that exclusively N-type sugars are present in the triple helix formed by the 29mer RNA while both N- and S-type sugars are detected in the case of the chimeric 29mer DNA-RNA triple helix. Triple helix formation with the third strand RNA and the duplex as DNA appears to be associated with the conversion of the duplex part from a B-form secondary structure to one which contains partly A-form sugars. Thermal denaturation experiments followed by UV spectroscopy show that a major stabilization occurs upon formation of the triple helices. Monophasic melting curves indicate a simultaneous disruption of the Hoogsteen and Watson-Crick hydrogen bonds in the intramolecular triplexes when the temperature is increased. This is in agreement with imino proton NMR spectra recorded as a function of temperature. Comparison with experiments concerning intermolecular triplexes of identical base and sugar composition shows the important role played by the two tetrameric loops in the stabilization of the intramolecular triple helices studied.

Base Sequence↗
PubMed1995

Conformations of three-stranded DNA structures formed in presence and in absence of the RecA protein.

Using FTIR and UV spectroscopies, we have studied the structures of three-stranded DNA complexes (TSC) having two identical strands, containing all four bases, in parallel orientation. In the first system, an intermolecular TSC is formed by the addition of the third strand (ssDNA) previously coated with RecA protein to an hairpin duplex (dsDNA), in presence of ATP gamma S. In the second one, the formation of an intramolecular triplex is forced by folding back twice on itself an oligonucleotide. The sequences of the three strands are the same in both systems. The formation of the RecA-TSC, which accommodates all four bases, is evidenced by gel retardation assay, and by its biphasic melting profile observed by UV spectroscopy. Using FTIR spectroscopy, N-type sugars are detected in this structure. This shows that in the RecA-TSC studied in presence of the protein, the nucleic acid part adopts an extended form, in agreement with the model proposed by Zhurkin et al. (1,2) and electron microscopy observations (3-6). In contrast, the RecA-free intramolecular triplex in a non extended form has S-type sugars.

Base Sequence↗
PubMed1995

A triple helix obtained by specific recognition of all 4 bases in duplex DNA can adopt a collapsed or an extended form.

It has been proposed that during homologous recombination promoted by RecA DNA triple helices can be formed between a Watson Crick duplex and a homologous third strand without any sequence constraint. A triple helix, obtained by targeting the d(AGTTAGCATG) sequence containing all 4 bases, in which both homologous strands are oriented in a parallel direction with respect to each other, stabilized by addition of Mn2+ ions has been studied by UV and FTIR spectroscopies. We have characterized the sugar conformations of this triplex. All strands are found to contain S type sugars (C2'endo, B family form). Progressive addition of propidium iodide induces a complete reorientation of the sugar geometry to a N type conformation (C3'endo, A family form). This sugar repuckering is consistent with a conformational transition from a collapsed to an extended DNA triple helical structure.

Base Sequence↗
PubMed1994

Spectroscopic evidence for an intramolecular RNA triple helix.

A 29-base RNA oligomer has been chemically synthesized and shown to form an intramolecular triple helix in solution at acidic pH. Assignment of the majority of the exchangeable proton NMR resonances demonstrated the Watson-Crick and Hoogsteen base pairings consistent with folding to form pyrimidine-purine-pyrimidine base triplets. FTIR spectroscopy provided independent evidence of base triplet formation, and indicated a predominately C3'-endo sugar pucker. UV absorption as a function of temperature suggested monophasic melting behaviour, which was confirmed by NMR of the imino protons.

Acids↗
PubMed1994

Triple-helices targeted to the polypurine tract of a murine retrovirus.

The all-purine 13-mer oligodeoxyribonucleotide d(GGGGGGAAAAAGA), containing an unusually large block of contiguous guanines, was shown by electrophoresis and thermoelution to form a specific, 'antiparallel' complex with the duplex containing the polypurine tract of murine retroviruses. Fourier transform infra-red spectroscopy (FTIR) and molecular modeling indicated that the complex is based on reverse Hoogsteen G(GC) and A(AT) triplets, with anti orientations of the bases and with all the strands having S-type sugar conformations. This G + A-containing 13-mer and a G + T-containing 22-mer, d(TGTTTGTTTGGGGGGTTTTTGT), aimed at the same target, retarded in a sequence-specific manner the spreading of the Friend retrovirus in Dunni cells infected de novo, thus indicating that the polypurine tract of retroviruses may be a suitable target for anti-gene action.

Animals↗