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‣ Voltammetric behaviour of oligonucleotide lipoplexes adsorbed onto glassy carbon electrodes

Piedade, J. A. P.; Mano, M.; Lima, M. C. Pedroso de; Oretskaya, T. S.; Oliveira-Brett, A. M.
Fonte: Universidade de Coimbra Publicador: Universidade de Coimbra
Tipo: Artigo de Revista Científica Formato: aplication/PDF
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The voltammetric behaviour of oligonucleotide lipoplexes (ODN-lipoplexes) prepared from short oligodeoxynucleotides (ODN), with different base compositions, and liposomes of the cationic lipid DOTAP, was studied by differential pulse voltammetry with a glassy carbon mini-electrode. It was found that the ODN base composition influences the ODN-lipoplex voltammetric response. Differential pulse voltammograms for ODN-lipoplexes of the ODN adenosine nucleotides present two different features when compared with the differential pulse voltammograms obtained for free ODN: a new peak appeared and the peak attributed to oxidation of adenosine diminished or was absent, depending on whether the ODN sequence had guanosine nucleotides or not. The presence of guanosine nucleotides in the ODN-lipoplex led to a peak due to guanosine oxidation with similar potential and current to the peak obtained for guanosine oxidation in free ODN. No detectable peaks were recorded in the voltammograms obtained with lipoplexes composed of ODN containing only pyrimidine bases. It was possible to show by voltammetry the occurrence of partial denaturation of short double helices of ODN when mixed with DOTAP liposomes to generate lipoplexes. The extent of denaturation was observed to increase with lipoplex (+/-) charge ratio as shown by the increase in the differential pulse voltammetry peak currents. The electrochemical characterisation of lipoplex properties at a charged interface can be important for understanding and development of these gene therapy vectors.; http://www.sciencedirect.com/science/article/B6TGB-4B4RVT3-2/1/80478920c615683b2439ef8a29808980

‣ Interaction of oligonucleotide-based amphiphilic block copolymers with cell membrane models

CASELI, L.; PASCHOLATI, C. P.; TEIXEIRA JR., F.; NOSOV, S.; VEBERT, C.; MUEELLER, A. H. E.; OLIVEIRA JUNIOR, Osvaldo Novais de
Fonte: ACADEMIC PRESS INC ELSEVIER SCIENCE Publicador: ACADEMIC PRESS INC ELSEVIER SCIENCE
Tipo: Artigo de Revista Científica
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Oligonucleotides have unique molecular recognition properties, being involved in biological mechanisms such as cell-surface receptor recognition or gene silencing. For their use in human therapy for drug or gene delivery, the cell membrane remains a barrier, but this can be obviated by grafting a hydrophobic tail to the oligonucleotide. Here we demonstrate that two oligonucleotides, one consisting of 12 guanosine units (G(12)), and the other one consisting of five adenosine and seven guanosine (A(5)G(7)) units, when functionalized with poly(butadiene), namely PB-G(12) and PB-A(5)G(7), can be inserted into Langmuir monolayers of dipalmitoyl phosphatidyl choline (DPPC), which served as a cell membrane model. PB-G(12) and PB-A(5)G(7) were found to affect the DPPC monolayer even at high surface pressures. The effects from PB-G(12) were consistently stronger, particularly in reducing the elasticity of the DPPC monolayers, which may have important biological implications. Multilayers of DPPC and nucleotide-based copolymers could be adsorbed onto solid supports, in the form of Y-type LB films, in which the molecular-level interaction led to lower energies in the vibrational spectra of the nucleotide-based copolymers. This successful deposition of solid films opens the way for devices to be produced which exploit the molecular recognition properties of the nucleotides. (C) 2010 Elsevier Inc. All rights reserved.; Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP); FAPESP; Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); CNPq; CAPES (Brazil); Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES); Swiss National Science Foundation (NSF)[200020-121822]; Swiss National Science Foundation (NSF)

‣ Interaction of cationic bilayer fragments with a model oligonucleotide

Rozenfeld, Julio Henrique Kravcuks; Oliveira, Tiago Ribeiro de; Lamy, Maria Teresa Moura; Ribeiro, Ana Maria Carmona
Fonte: ELSEVIER SCIENCE BV Publicador: ELSEVIER SCIENCE BV
Tipo: Artigo de Revista Científica
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The interaction between cationic bilayer fragments and a model oligonucleotide was investigated by differential scanning calorimetry, turbidimetry, determination of excimer to monomer ratio of 2-(10-(1-pyrene)-decanoyl)-phosphatidyl-choline in bilayer fragment dispersions and dynamic light scattering for sizing and zeta-potential analysis. Salt (Na(2)HPO(4)), mononucleotide (2`-deoxyadenosine-5`-monophosphate) or poly (dA) oligonucleotide (3`-AAA AAA AAA A-5`) affected structure and stability of dioctadecyldimethylammonium bromide bilayer fragments. Oligonucleotide and salt increased bilayer packing due to bilayer fragment fusion. Mononucleotide did not reduce colloid stability or did not cause bilayer fragment fusion. Charge neutralization of bilayer fragments by poly (dA) at 1:10 poly (dA):dioctadecyldimethylammonium bromide molar ratio caused extensive aggregation, maximal size and zero of zeta-potential for the assemblies. Above charge neutralization, assemblies recovered colloid stability due to charge overcompensation. For bilayer fragments/poly (dA), the nonmonotonic behavior of colloid stability as a function of poly (dA) concentration was unique for the oligonucleotide and was not observed for Na(2)HPO(4) or 2`-deoxyadenosine-5`-monophosphate. For the first time...

‣ Stable assemblies of cationic bilayer fragments and CpG oligonucleotide with enhanced immunoadjuvant activity in vivo

Rozenfeld, Julio H. K.; Silva, Sandriana dos Ramos; Raneia, Priscila A.; Faquim-Mauro, Eliana; Carmona-Ribeiro, Ana M.
Fonte: ELSEVIER SCIENCE BV; AMSTERDAM Publicador: ELSEVIER SCIENCE BV; AMSTERDAM
Tipo: Artigo de Revista Científica
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The cationic lipid dioctadecyldimethylammonium bromide (DODAB) and the CpG oligonucleotide (CpG) have been separately used as potent immunoadjuvants driving Th1 responses. Here DODAB bilayer fragments (BF) and CpG (5 -TTGACGTTCG-3) assemblies have their physical properties and immunoadjuvant activity determined using ovalbumin (OVA) as a model antigen. At 0.1 mg/mL OVA, the dependence of DODAB BF/OVA size and zeta-potential on time and [DODAB] establishes 0.1 mMDODAB as suitable for obtaining stable and cationic DODAB BF/OVA assemblies. At 0.1 mMDODAB, 0.1 mg/mL OVA and 0.006 mMCpG, the zeta-potential is zero. At [CpG]>0.006 mM, good colloidal stability for the anionic assemblies is due to charge overcompensation. At 0.020 mM CpG, these DODAB BF/OVA/CpG assemblies are highly effective in vivo generating responses similar to those elicited by the stable and cationic DODAB BF/OVA. The anti-OVA DTH reaction and the secretion of IFN-gamma and IL-12 are 6, 42 and 9 times larger for the DODAB BF/OVA/CpG-immunized mice than the same responses by OVA-immunized mice, respectively. This work shows for the first time that charge of small assemblies is not important to determine the immune response. (C) 2011 Elsevier B. V. All rights reserved.; FAPESP; CNPq

‣ Oligonucleotide Adsorption Affects Phase Transition but Not Interdigitation of diC14-Amidine Bilayers

Rozenfeld, Julio Henrique Kravcuks; Duarte, Evandro Luiz; Oliveira, Tiago Ribeiro de; Lamy, Maria Teresa Moura
Fonte: American Chemical Society; Washington Publicador: American Chemical Society; Washington
Tipo: Artigo de Revista Científica
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Oligonucleotides have been extensively used in basic research of gene expression and function, vaccine design, and allergy and cancer therapy. Several oligonucleotide-based formulations have reached the clinical trial phase and one is already on the market. All these applications, however, are dependent on suitable carriers that protect oligonucleotides against degradation and improve their capture by target cells. The cationic lipid diC14-amidine efficiently delivers nucleic acids to mammalian cells. It was recently shown that diC14-amidine bilayers present an interdigitated phase which strongly correlates with a potent fusogenic activity at low temperatures. Interdigitated phases correspond to very ordered gel phases where the two bilayer leaflets are merged; they usually result from perturbations at the interfacial region such as modifications of the polar headgroup area or dehydration of the bilayer. Interdigitation has been described for asymmetric lipids or mixed-chain lipids of different chain lengths and for lipids with large effective headgroup sizes. It has also been described for symmetric lipids under pressure modifications or in the presence of alcohol, glycerol, acetonitrile, polymyxin B, or ions like thiocyanate. Surprisingly...

‣ An oligonucleotide probe derived from kDNA minirepeats is specific for Leishmania (Viannia)

Fernandes,Octavio; Bozza,Marcelo; Pascale,Juan M; Miranda,Antonio B de; Lopes,Ulisses G; Degrave,Wim M
Fonte: Instituto Oswaldo Cruz, Ministério da Saúde Publicador: Instituto Oswaldo Cruz, Ministério da Saúde
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/06/1996 Português
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Sequence analysis of Leishmania (Viannia) kDNA minicircles and analysis of multiple sequence alignments of the conserved region (minirepeats) of five distinct minicircles from L. (V.) braziliensis species with corresponding sequences derived from other dermotropic leishmanias indicated the presence of a sub-genus specific sequence. An oligonucleotide bearing this sequence was designed and used as a molecular probe, being able to recognize solely the sub-genus Viannia species in hybridization experiments. A dendrogram reflecting the homologies among the minirepeat sequences was constructed. Sequence clustering was obtained corresponding to the traditional classification based on similarity of biochemical, biological and parasitological characteristics of these Leishmania species, distinguishing the Old World dermotropic leishmanias, the New World dermotropic leishmanias of the sub-genus Leishmania and of the sub-genus Viannia.

‣ Antitumor activity and pharmacokinetics of a mixed-backbone antisense oligonucleotide targeted to the RIα subunit of protein kinase A after oral administration

Wang, Hui; Cai, Qiuyin; Zeng, Xiaofei; Yu, Dong; Agrawal, Sudhir; Zhang, Ruiwen
Fonte: The National Academy of Sciences Publicador: The National Academy of Sciences
Tipo: Artigo de Revista Científica
Publicado em 23/11/1999 Português
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Overexpression of the RIα subunit of cAMP-dependent protein kinase (PKA) has been demonstrated in various human cancers. PKA has been suggested as a potential target for cancer therapy. The goal of the present study was to evaluate an anti-PKA antisense oligonucleotide (mixed-backbone oligonucleotide) as a therapeutic approach to human cancer treatment. The identified oligonucleotide inhibited the growth of cell lines of human colon cancer (LS174T, DLD-1), leukemia (HL-60), breast cancer (MCF-7, MDA-MB-468), and lung cancer (A549) in a time-, concentration-, and sequence-dependent manner. In a dose-dependent manner, the oligonucleotide displayed in vivo antitumor activity in severe combined immunodeficient and nude mice bearing xenografts of human cancers of the colon (LS174T), breast (MDA-MB-468), and lung (A549). The routes of drug administration were intraperitoneal and oral. Synergistic effects were found when the antisense oligonucleotide was used in combination with the cancer chemotherapeutic agent cisplatin. The pharmacokinetics of the oligonucleotide after oral administration of 35S-labeled oligonucleotide into tumor-bearing mice indicated an accumulation and retention of the oligonucleotide in tumor tissue. This study further provides a basis for clinical studies of the antisense oligonucleotide targeted to the RIα subunit of PKA (GEM 231) as a cancer therapeutic agent used alone or in combination with conventional chemotherapy.

‣ Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays

Kane, Michael D.; Jatkoe, Timothy A.; Stumpf, Craig R.; Lu, Jia; Thomas, Jeffrey D.; Madore, Steven J.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Publicado em 15/11/2000 Português
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To examine the utility and performance of 50mer oligonucleotide (oligonucleotide probe) microarrays, gene-specific oligonucleotide probes were spotted along with PCR probes onto glass microarrays and the performance of each probe type was evaluated. The specificity of oligonucleotide probes was studied using target RNAs that shared various degrees of sequence similarity. Sensitivity was defined as the ability to detect a 3-fold change in mRNA. No significant difference in sensitivity between oligonucleotide probes and PCR probes was observed and both had a minimum reproducible detection limit of ∼10 mRNA copies/cell. Specificity studies showed that for a given oligonucleotide probe any ‘non-target’ transcripts (cDNAs) >75% similar over the 50 base target may show cross-hybridization. Thus non-target sequences which have >75–80% sequence similarity with target sequences (within the oligonucleotide probe 50 base target region) will contribute to the overall signal intensity. In addition, if the 50 base target region is marginally similar, it must not include a stretch of complementary sequence >15 contiguous bases. Therefore, knowledge about the target sequence, as well as its similarity to other mRNAs in the target tissue or RNA sample...

‣ Acid binding and detritylation during oligonucleotide synthesis.

Paul, C H; Royappa, A T
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 01/08/1996 Português
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Under the conditions normally used for detritylation in oligonucleotide synthesis, the haloacetic acid binds strongly to the oligonucleotide. Acetonitrile also forms a complex with the deblocking acid, in competition with the oligonucleotide, and drastically slows detritylation. Incomplete removal of acetonitrile during the deblock step may slow the kinetics enough to result in incomplete detritylation of the oligonucleotide. Acid binding to the growing oligonucleotide causes striking chromatographic effects in the presence of high oligonucleotide mass densities. In packed-bed column reactors, at low linear velocities, the acid binding almost completely depletes free acid from the deblocking solution. This results in an advancing zone within which the oligonucleotide is saturated with acid. Detritylation occurs mostly in a narrow band at the front of the advancing saturated zone. Increasing the DCA concentration in order to achieve quick saturation can give faster and more complete detritylation while minimizing the exposure time of the oligonucleotide to acid.

‣ Studies on the Formation of Transfer Ribonucleic Acid-Ribosome Complexes, XII. Phenylalanyl-Oligonucleotide Binding to E. coli Ribosomes: Necessity for a Free Amino Group

Hishizawa, Tokutaro; Lessard, James L.; Pestka, Sidney
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /06/1970 Português
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The binding of phenylalanyl-oligonucleotide, C-A-C-C-A-(Phe), to ribosomes requires the presence of a free amino group on the amino acid. Acetylation of the amino acid reduces the binding to ribosomes to about 1/20 of the binding observed with the intact Phe-oligonucleotide. Deacylation of the phenylalanyl-oligonucleotide eliminates binding of the free amino acid and markedly reduces the binding of the oligonucleotide (C-A-C-C-A). Neither 30S nor 50S subunits alone are sufficient for binding of the phenylalanyl-oligonucleotide; the presence of both subunits is necessary. The data suggest that phenylalanyl-oligonucleotide binding to ribosomes represents the binding of the aminoacyl-terminus of phenylalanyl-tRNA and that the presence of an amino acid with an unsubstituted amino group attached to the oligonucleotide (C-A-C-C-A) is required for binding to this potassium-dependent site. Furthermore, the ribosome itself has the capability of distinguishing between aminoacyl-oligonucleotides with N-substituted and unsubstituted amino acids-

‣ Oligonucleotide Sequence Analyses Indicate that Vesicular Stomatitis Virus Large Defective Interfering Virus Particle RNA Is Made by Internal Deletion: Evidence for Similar Transcription Polyadenylation Signals for the Synthesis of All Vesicular Stomatitis Virus mRNA Species

Clerx-Van Haaster, Corrie M.; Clewley, Jon P.; Bishop, David H. L.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /02/1980 Português
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RNase T1 oligonucleotide fingerprint analyses of three vesicular stomatitis virus Indiana serotype small defective interfering (DI) particle RNA species indicate that they only have oligonucleotides derived from the 5′ region of the viral genome. These studies also indicate that these three DI RNAs have partial L gene sequences as well as two 5′ viral oligonucleotides (59 and 70) that are not transcribed into L (or other) mRNA species (J. P. Clewley and D. H. L. Bishop, J. Virol. 30:116-123, 1979). Analyses of the large DI RNA (LT DI) reveal a different origin. The LT DI RNA has oligonucleotides derived from both the 3′ end of the genome (including all the large oligonucleotides identified for N, NS, M, and G genes), in addition to at least one of the 5′-proximal L gene oligonucleotides (47), as well as all seven oligonucleotides (3, 38, 42, 43, 44B, 59, and 70) that are not protected from nuclease digestion after the formation of mRNA-viral RNA duplexes (Clewley and Bishop). It appears therefore that the genesis of LT RNA involves a deletion of internal L gene sequences from the viral RNA. Oligonucleotide sequence analyses have been undertaken on several of the vesicular stomatitis viral RNA oligonucleotides, including all seven (3...

‣ Hybridization of Escherichia coli producing Shiga-like toxin I, Shiga-like toxin II, and a variant of Shiga-like toxin II with synthetic oligonucleotide probes.

Brown, J E; Sethabutr, O; Jackson, M P; Lolekha, S; Echeverria, P
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /09/1989 Português
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Synthetic oligonucleotides, constructed from the nucleotide sequences of genes coding for the A subunit of Shiga-like toxin (SLT) I and the B subunit of SLT-II, were used as probes at different degrees of stringency to identify Escherichia coli producing different types of SLTs. At 45 degrees C, the A-I oligonucleotide probe hybridized with E. coli producing SLT-I, SLT-II, and variant of SLT-II (SLT-IIv). At 53 degrees C, only SLT-I-producing E. coli hybridized with this probe. At 45 degrees C, the B-II oligonucleotide probe hybridized with SLT-II- and SLT-IIv-producing E. coli. At 53 degrees C, this probe hybridized with only SLT-II-producing E. coli. The A-I and B-II oligonucleotide probes were subsequently tested for hybridization with 73 SLT-producing E. coli and 49 non-SLT-producing E. coli isolated in Asia and Canada. At 45 degrees C, the A-I oligomer had a sensitivity of 97% and a specificity of 100% in identifying SLT-producing E. coli. At 53 degrees C, the A-I oligonucleotide probe had a sensitivity of 92% and a specificity of 91% in identifying E. coli containing genes encoding SLT-I. At 45 degrees C, the B-II oligonucleotide had a 100% sensitivity and 97% specificity in identifying E. coli that hybridized with the SLT-II probe. Of 17 E. coli that hybridized only with the SLT-II probe...

‣ Oligonucleotide Chip for Detection of Lamivudine-Resistant Hepatitis B Virus

Jang, Hyunjung; Cho, Mong; Heo, Jeong; Kim, Hyunghoi; Jun, Hongki; Shin, Woowon; Cho, Byungman; Park, Heekyung; Kim, Cheolmin
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /09/2004 Português
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Hepatitis B virus (HBV) is one of the major causes of liver disease worldwide. It is important to conduct antiviral therapy against chronic hepatitis B to minimize the amount of liver damage. Lamivudine has been known to be an effective antiviral agent for the treatment of HBV infection. However, the emergence of viral mutants resistant to lamivudine is the main concern during the treatment of HBV-infected patients. Therefore, the detection of lamivudine-resistant mutants is of clinical importance. We have developed an oligonucleotide chip for the detection of lamivudine-resistant HBV which is rapid and accurate. The oligonucleotide chip consists of quality control probes, negative control probes, and specific oligonucleotide probes for the detection of lamivudine-resistant HBV. The specific probes consist of five probes for the detection of wild-type rtL180, rtM204, and rtV207 sequences and seven probes for the detection of HBV mutations. We tested 123 serum samples from patients with chronic HBV infection who had received lamivudine therapy. Eighty samples contained mutants with YMDD mutations. Among these, 17 contained rtM204V (YVDD), 24 contained rtM204I3 (YIDD3), 3 contained rtM204I2 (YIDD2), and 36 contained mixed types. We compared the results obtained with our oligonucleotide chip with those obtained by PCR-restriction fragment length polymorphism (RFLP) analysis and sequencing. The rate of concordance between the assay with the oligonucleotide chip and PCR-RFLP analysis for detection of the YMDD motif was 96.7%. The rate of concordance between the results obtained with the oligonucleotide chip for the detection of rtL180 and rtV207 and the results obtained by sequencing was 100%. Thus...

‣ Induction of endogenous γ-globin gene expression with decoy oligonucleotide targeting Oct-1 transcription factor consensus sequence

Xu, Xiaoxin S; Hong, Xin; Wang, Gan
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em 27/03/2009 Português
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Human β-globin disorders are relatively common genetic diseases cause by mutations in the β-globin gene. Increasing the expression of the γ-globin gene has great benefits in reducing complications associated with these diseases. The Oct-1 transcription factor is involved in the transcriptional regulation of the γ-globin gene. The human γ-globin genes (both Aγ and Gγ-globin genes) carry three Oct-1 transcription factor consensus sequences within their promoter regions. We have studied the possibility of inducing γ-globin gene expression using decoy oligonucleotides that target the Oct-1 transcription factor consensus sequence. A double-stranded 22 bp decoy oligonucleotide containing the Oct-1 consensus sequence was synthesized. The results obtained from our in vitro binding assay revealed a strong competitive binding of the decoy oligonucleotide for the Oct-1 transcription factor. When K562 human erythroleukemia cells were treated with the Oct-1 decoy oligonucleotide, significant increases in the level of the γ-globin mRNA were observed. The results of our western blots further demonstrated significant increases of the fetal hemoglobin (HbF, α2γ2) in the Oct-1 decoy oligonucleotide-treated K562 cells. The results of our immunoprecipitation (IP) studies revealed that the treatment of K562 cells with the Oct-1 decoy oligonucleotide significantly reduced the level of the endogenous γ-globin gene promoter region DNA co-precipitated with the Oct-1 transcription factor. These results suggest that the decoy oligonucleotide designed for the Oct-1 transcription factor consensus sequence could induce expression of the endogenous γ-globin gene through competitive binding of the Oct-1 transcription factor...

‣ Electrophoresis for genotyping: temporal thermal gradient gel electrophoresis for profiling of oligonucleotide dissociation.

Day, I N; O'Dell, S D; Cash, I D; Humphries, S E; Weavind, G P
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 11/07/1995 Português
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Traditional use of an oligonucleotide probe to determine genotype depends on perfect base pairing to a single-stranded target which is stable to a higher temperature than when imperfect binding occurs due to a mismatch in the target sequence. Bound oligonucleotide is detected at a predetermined single temperature 'snapshot' of the melting profile, allowing the distinction of perfect from imperfect base pairing. In heterozygotes, the presence of the alternative sequence must be verified with a second oligonucleotide complementary to the variant. Here we describe a system of real-time variable temperature electrophoresis during which the oligonucleotide dissociates from its target. In 20% polyacrylamide the target strand has minimal mobility and released oligonucleotide migrates extremely quickly so that the 'freed' rather than the 'bound' is displayed. The full profile of oligonucleotide dissociation during gel electrophoresis is represented along the gel track, and a single oligonucleotide is sufficient to confirm heterozygosity, since the profile displays two separate peaks. Resolution is great, with use of short track lengths enabling analysis of dense arrays of samples. Each gel track can contain a different target or oligonucleotide and the temperature gradient can accommodate oligonucleotides of different melting temperatures. This provides a convenient system to examine the interaction of many different oligonucleotides and target sequences simultaneously and requires no prior knowledge of the mutant sequence(s) nor of oligonucleotide melting temperatures. The application of the technique is described for screening of a hotspot for mutations in the LDL receptor gene in patients with familial hypercholesterolaemia.

‣ Investigation of the intracellular stability and formation of a triple helix formed with a short purine oligonucleotide targeted to the murine c-pim-1 proto-oncogene promotor.

Svinarchuk, F; Debin, A; Bertrand, J R; Malvy, C
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 15/01/1996 Português
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In our previous work we have shown that the oligonucleotide 5'-GGGGAGGGGGAGG-3' gives a very stable and specific triplex with the promoter of the murine c-pim-1 proto-oncogene in vitro[Svinarchuk, F., Bertrand, J.-R. and Malvy, C.(1994)Nucleic Acids Res., 22, 3742-3747]. In the present work, we have tested triplex formation with some derivatives of this oligonucleotide which are designed to be degradation-resistant inside the cells, and we show that phosphorothioate and the oligonucleotide with a 3' terminal amino group are still able to form triplexes. Moreover these oligonucleotides, like the 13mer oligonucleotide of similar composition [Svinarchuk, F., Paoletti, J., and Malvy, C. (1995) J. Biol. Chem., 270, 14068-14071], are able to stabilize the targeted duplex. In vivo DMS footprint analysis after electroporation of the pre-formed triplex into the cell have shown the presence of the triple helix inside the cells. This triplex structure partially blocks c-pim-1 promotor activity as shown by transient assay with a c-pim-1 promoter-luciferase gene construct. To our knowledge these data are the first direct evidence that conditions inside cells are favorable for triplex stability with non-modified oligonucleotides. However we were unable to show triplex formation inside living cells using various methods of oligonucleotide delivery. We suppose that this may be due to the oligonucleotide being sequestered by cellular processes or proteins. Further work is needed to find oligonucleotide derivatives and ways of their delivery to overcome the problem of triplex formation inside the cells.

‣ Detection of proopiomelanocortin mRNA by in situ hybridization with an oligonucleotide probe.

Lewis, M E; Sherman, T G; Burke, S; Akil, H; Davis, L G; Arentzen, R; Watson, S J
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /08/1986 Português
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Synthetic oligonucleotide probes can be easily obtained and used, in contrast to cDNA cloning to develop probes, and thus the present study was carried out to determine whether such probes could also be useful for in situ hybridization. A 24-base synthetic oligonucleotide complementary to part of the alpha-melanocyte-stimulating hormone (alpha-MSH) coding region of proopiomelanocortin (POMC) mRNA was 5'-end-labeled by using [gamma-32P]ATP with T4 polynucleotide kinase or was 3' tailed by using [alpha-32P]dATP or [3H]dCTP with terminal deoxynucleotidyltransferase. Blot analysis of pituitary poly(A)+ RNA showed that the oligonucleotide hybridized to a single species with a molecular size of approximately 1200 nucleotides, consistent with that determined previously for POMC mRNA. The oligonucleotide, regardless of labeling method, hybridized to cells in the pituitary intermediate lobe, but not in the posterior lobe. Only the 3H-labeled probe gave resolution of individual pituitary anterior lobe cells. The specificity of the hybridization was determined by showing that the intermediate lobe signal was blocked by prehybridization of the tissue with unlabeled alpha-MSH oligonucleotide probe. Furthermore, the hybridized probe exhibited a sharp sigmoid curve when melted off. Finally...

‣ Adsorption models of hybridization and post-hybridization behaviour on oligonucleotide microarrays

Burden, Conrad; Pittelkow, Yvonne; Wilson, Susan
Fonte: Institute of Physics Publishing Publicador: Institute of Physics Publishing
Tipo: Artigo de Revista Científica
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Analysis of data from an Affymetrix Latin Square spike-in experiment indicates that measured fluorescence intensities of features on an oligonucleotide microarray are related to spike-in RNA target concentrations via a hyperbolic response function, genera

‣ Fast comparison of DNA sequences by oligonucleotide profiling

Arnau, Vicente; Gallach, Miguel; Marín, Ignacio
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artículo Formato: 157639 bytes; 412519 bytes; application/pdf; application/pdf
Português
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Provisional abstact and full-text PDF files correspond to the article as it appeared upon acceptance. Fully formatted PDF and final abstract will be made available soon.; Technical Note; [Background] The comparison of DNA sequences is a traditional problem in genomics and bioinformatics. Many new opportunities emerge due to the improvement of personal computers, allowing the implementation of novel strategies of analysis.; [Findings] We describe a new program, called UVWORD, which determines the number of times that each DNA word present in a sequence (target) is found in a second sequence (source), a procedure that we have called oligonucleotide profiling. On a standard computer, the user may search for words of a size ranging from k = 1 to k = 14 nucleotides. Average counts for groups of contiguous words may also be established. The rate of analysis on standard computers is from 3.4 (k = 14) to 16 millions of words per second (when k = 1 - 8). This makes feasible the fast screening of even the longest known DNA molecules.; [Discussion] We show that the combination of the ability of analyzing words of relatively long size, which occur very rarely by chance, and the fast speed of the program allows to perform novel types of screenings...

‣ Sensitivity and specificity of five abundance estimators for high-density oligonucleotide microarrays

James, Andrew; Veitch, Jim; Zareh, Ali; Triche, Timothy
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Português
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Motivation: A number of algorithms have been proposed for the processing of feature-level data from high-density oligonucleotide microarrays to give estimates of transcript abundance. Performance in the common task of detecting differential expression between samples can be quantified by the statistical concepts of sensitivity and specificity, and represented by the use of receiver operating characteristic curves. These have been previously presented for small numbers of genes known to be differentially present in spiked-in samples. We present here a study of performance over a large number (thousands) of transcripts for which there is strong evidence of differential expression, with corresponding false positive rates controlled by comparisons between replicates. Results: The straight-line regression analysis of a mixture series with replicates by five estimation algorithms produces a consensus set of 4462 transcripts with differential expression of agreed direction and high significance (p < 0.01) according to all algorithms. The more difficult task of two-sample tests between adjacent mixture levels produces performance curves of fraction true positive detected against significance level. Performance varies significantly between algorithms: at the p < 0.01 level...