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Tarashima N, Hayashi K, Terasaki M, Taniike H, Inagaki Y, Hirose K, Furukawa K, Matsuda A, Minakawa N. First synthesis of fully modified 4'-selenoRNA and 2'-OMe-4'-selenoRNA based on the mechanistic considerations of an unexpected strand break. Org Lett 2014; 16:4710-3. [PMID: 25181546 DOI: 10.1021/ol502077h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This study investigated oligonucleotide (ON) synthesis containing 4'-selenoribonucleoside(s) under standard phosphoramidite conditions. Careful operation using a manual ON synthetic system revealed that an unexpected strand break occurred to afford a C2-symmetric homodimer as a byproduct. In addition, this side reaction occurred during I2 oxidation. On the basis of these findings, the first synthesis of fully modified 4'-selenoRNA and 2'-OMe-4'-selenoRNA was achieved using tert-butyl hydroperoxide (TBHP) as the alternative oxidant.
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Affiliation(s)
- Noriko Tarashima
- Graduate School of Pharmaceutical Sciences, The University of Tokushima , Shomachi 1-78-1, Tokushima 770-8505, Japan
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Pon RT, Ogilvie KK. Automated Solid Phase Synthesis of Oligoribonucleotides. The Synthesis of a tRNA Anticodon Loop from Nucleoside-3'-chlorophosphite Derivatives. ACTA ACUST UNITED AC 2007. [DOI: 10.1080/07328318408081284] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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3
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Sinha ND, Biernat J, Köster H. Polymer Support Oligonucleotide Synthesis XVI: Synthesis of Oligonucleotides Using Suitably Protected Deoxynucleoside-N-morpholinophosphoramidites on Porous Glass Beads. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328318408079426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Aerschot AV, Herdewijn P, Vanderhaeghe H. Silica Gel Functionalised with Different Spacers as Solid Support for Oligonucleotide Synthesis. ACTA ACUST UNITED AC 1988. [DOI: 10.1080/07328318808068704] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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Chapter 10 Nucleic Acids, Polynucleotides and Oligonucleotides. ACTA ACUST UNITED AC 1988. [DOI: 10.1016/s0301-4770(08)61450-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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6
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Abstract
Treatment of 5'-end 32P-labeled oligodeoxyribonucleotides with 0.4 M aqueous piperidinium formate, pH 2, at 37 degrees C for 6 h, followed by treatment with 1 M aqueous piperidine at 90 degrees C for 6 h, produces, after electrophoresis through 27% polyacrylamide sequencing gels, one-dimensional distributions of radioactivity from which the base sequences can be deduced. The order of intensities for the bands signaling the various bases is G greater than A greater than C greater than T. The spacing from a given band to the next higher band in the ladder was base characteristic, the order of band spacings being G greater than T greater than or equal to A greater than C. In contrast to the one-cleavage one-lane DNA sequencing method reported earlier (B. J. B. Ambrose and R. C. Pless, 1985, Biochemistry 24, 6194-6200), which was based on treatment of end-labeled DNA with hot aqueous piperidine in the presence of sodium chloride, the present method produces a salt-free hydrolysate, thus minimizing electrophoretic irregularities in the fastest moving bands.
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Le Bouc Y, Dreyer D, Jaeger F, Binoux M, Sondermeyer P. Complete characterization of the human IGF-I nucleotide sequence isolated from a newly constructed adult liver cDNA library. FEBS Lett 1986; 196:108-12. [PMID: 2935423 DOI: 10.1016/0014-5793(86)80223-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A full-size cDNA sequence coding for insulin-like growth factor I (IGF-I) was isolated from a human liver library. For the construction of this bank, a new method was developed which anneals dG-tailed cDNA with a synthetic adaptor 5'-AATTCCCCCCCCCCC-3' followed by ligation into the EcoRI site of a lambda immunity-insertion vector. Based on the sequence analysis of the complete IGF-I messenger we concluded that the protein is synthesized as a precursor containing a signal peptide of 22 or 25 amino acid residues. In addition, the sequence extended in the 3'-direction and showed the presence of multiple polyadenylation sites in the IGF-I message.
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Harvey RP, Degryse E, Stefani L, Schamber F, Cazenave JP, Courtney M, Tolstoshev P, Lecocq JP. Cloning and expression of a cDNA coding for the anticoagulant hirudin from the bloodsucking leech, Hirudo medicinalis. Proc Natl Acad Sci U S A 1986; 83:1084-8. [PMID: 3513162 PMCID: PMC323015 DOI: 10.1073/pnas.83.4.1084] [Citation(s) in RCA: 134] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Cloned cDNAs have been isolated that encode a variant of hirudin, a potent thrombin inhibitor that is secreted by the salivary glands of the medicinal leech, Hirudo medicinalis. This variant probably corresponds to a form that has been purified from leech heads but differs in amino acid sequence from the hirudin purified from whole leeches. There are at least three hirudin transcripts detectable in leech RNAs that are different in size, site of synthesis, inducibility by starvation, and relationship to hirudin activity. The new hirudin variant predicted by the cDNA and the heterodisperse transcription products suggest a hirudin protein family. The hirudin cDNA was expressed in Escherichia coli under the control of the bacteriophage lambda PL promoter. The recombinant product is biologically active, inhibiting the cleavage by thrombin of fibrinogen and a synthetic tripeptide substrate.
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Saffarini DA, Trewitt PM, Castro M, Wejksnora PJ, Bergtrom G. Deoxynucleotide sequence of an insect cDNA codes for an unreported member of the Chironomus thummi globin family. Biochem Biophys Res Commun 1985; 133:641-7. [PMID: 3841283 DOI: 10.1016/0006-291x(85)90953-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Synthetic oligonucleotides served as probes to isolate insect globin clones from a Chironomus thummi cDNA bank. The cDNA insert of one clone (pC-S9) was completely sequenced by the dideoxy termination procedure. Beginning at the 5' end of the coding region, the 584 base pair sequence encodes most of an N-terminal hydrophobic signal sequence and the complete sequence for a mature secreted globin, and contains a polyadenylation recognition site 3' to an appropriate stop codon. The inferred amino acid sequence is that of an unreported variant of hemoglobin VIIB. Based on the number of differences between Hb VIIB chains, the pC-S9 gene has been evolutionarily independent longer than the other (two) members of the globin VIIB subfamily.
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Piel N, Benseler F, Graeser E, McLaughlin LW. Synthesis of the oligodeoxyribonucleotide, d(CpTpGpGpApTpCpCpApG), and its substrate activity with the restriction endonuclease, BamHI. Bioorg Chem 1985. [DOI: 10.1016/0045-2068(85)90032-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kieny MP, Lathe R, Drillien R, Spehner D, Skory S, Schmitt D, Wiktor T, Koprowski H, Lecocq JP. Expression of rabies virus glycoprotein from a recombinant vaccinia virus. Nature 1984; 312:163-6. [PMID: 6548799 DOI: 10.1038/312163a0] [Citation(s) in RCA: 342] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Rabies is one of the oldest diseases know to man, but its successful control has remained elusive. Although effective vaccines of tissue culture origin against rabies do exist, such preparations are expensive. Live vaccinia virus (VV) recombinants expressing influenza or hepatitis B antigens have recently been used to immunize against these diseases. We have now used this approach to produce a novel rabies vaccine. We first altered the rabies glycoprotein cDNA by site-directed mutagenesis and removed the poly(dG) tail. We then aligned the modified cDNA with an early VV promoter sequence inserted within a cloned copy of the vaccinia thymidine kinase gene and transfected this plasmid into VV-infected cells. Recombination between the virus and the plasmid resulted in a recombinant virus harbouring the rabies glycoprotein cDNA. Inoculation of rabbits with the live recombinant virus induced high titres of rabies virus-neutralizing antibodies, and scarification with the recombinant VV protected mice against challenge with street rabies virus.
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Marugg JE, Piel N, McLaughlin LW, Tromp M, Veeneman GH, van der Marel GA, van Boom JH. Polymer supported DNA synthesis using hydroxybenzotriazole activated phosphotriester intermediates. Nucleic Acids Res 1984; 12:8639-51. [PMID: 6095205 PMCID: PMC320404 DOI: 10.1093/nar/12.22.8639] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Phosphorylation of N-acyl-5'-O-DMTr-d-nucleosides, or similarly protected DNA-dimers having a free 3'-OH group, with 2-chlorophenyl-0,0-bis(1-benzotriazolyl)phosphate affords reactive 3'-phosphotriester derivatives. The latter intermediates can be used, without further purification, for the synthesis of DNA-fragments on the controlled pore glass/long chain alkylamine support. Further, 2-cyano-1,1-dimethylethoxy dichlorophosphine proved to be very suitable for the preparation of 5'-phosphorylated DNA-fragments on the same type of solid support.
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Tessier LH, Sondermeyer P, Faure T, Dreyer D, Benavente A, Villeval D, Courtney M, Lecocq JP. The influence of mRNA primary and secondary structure on human IFN-gamma gene expression in E. coli. Nucleic Acids Res 1984; 12:7663-75. [PMID: 6093047 PMCID: PMC320192 DOI: 10.1093/nar/12.20.7663] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Parameters influencing the efficiency of expression of the human immune interferon (IFN-gamma) gene in E. coli were studied by comparing a series of eight in vitro-derived gene variants. These contained all possible combinations of silent mutations in the first three codons of the mature IFN-gamma polypeptide coding sequence. Expression levels varied up to 50-fold among the different constructions. Comparison of messenger RNA secondary structure models for each variant suggested that the presence of stem-loop structures blocking the translation initiation signals could drastically decrease the efficiency of IFN-gamma synthesis. With variants displaying no stable mRNA secondary structure in the region, a C----U transition at position +11 after the AUG resulted in a 5-fold increase in expression indicating that RNA primary structure also plays an important role in expression. In addition we demonstrate that, in this system, a spacing of 8 nucleotides between the Shine-Dalgarno region and AUG was optimal for gene expression and that the steady-state production level of IFN-gamma rose exponentially with increasing rate of synthesis.
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Chollet A, Ayala E, Kawashima EH. Improved Synthesis of Oligodeoxyribonucleotides by Solid-Phase Phosphotriester Method UtilizingO6-[2-(p-Nitrophenyl)ethyl]-2?-deoxyguanosine Derivatives. Helv Chim Acta 1984. [DOI: 10.1002/hlca.19840670521] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Matthes HW, Zenke WM, Grundström T, Staub A, Wintzerith M, Chambon P. Simultaneous rapid chemical synthesis of over one hundred oligonucleotides on a microscale. EMBO J 1984; 3:801-5. [PMID: 16453516 PMCID: PMC557430 DOI: 10.1002/j.1460-2075.1984.tb01888.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An inexpensive, extremely rapid manual method for simultaneous synthesis of large numbers of oligodeoxyribonucleotides on 50 or 150 nanomole scale is described. The oligonucleotides are assembled in parallel by the phosphotriester method on small cellulose paper disks in a simple gas pressure-controlled continuous-flow system. For each addition of a nucleotide the disks are sorted into four sets which are placed in four columns for addition of A, C, G and T, respectively. During one 2-week period, three rounds of synthesis by this method yielded 254 oligomers (8- to 22-mers), many of which were also purified during this time. Using 50 nanomole scale reactions the yields for 17-mers, for example, were in the range of 0.5 O.D.(260) units ( 5 nmol, i.e., 10% yield), an amount sufficient for most purposes. The equipment required is relatively inexpensive and for the most part usually already available in molecular biology laboratories. All chemicals are commercially available and the current reagent cost per oligonucleotide (25 mug, average length 17-mer) is 3 US dollars.
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Affiliation(s)
- H W Matthes
- Laboratoire de Génétique Moléculaire des Eucaryotes du CNRS, Unité 184 de Biologie Moléculaire et de Génie Génétique de 1'INSERM, Faculté de Médecine, 11 Rue Humann, 67085 Strasbourg Cedex, France
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Courtney M, Buchwalder A, Tessier LH, Jaye M, Benavente A, Balland A, Kohli V, Lathe R, Tolstoshev P, Lecocq JP. High-level production of biologically active human alpha 1-antitrypsin in Escherichia coli. Proc Natl Acad Sci U S A 1984; 81:669-73. [PMID: 6322161 PMCID: PMC344896 DOI: 10.1073/pnas.81.3.669] [Citation(s) in RCA: 100] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A cDNA clone containing the complete human alpha 1-antitrypsin sequence was isolated from a human liver cDNA bank by screening with a chemically synthesized oligonucleotide probe. DNA sequences encoding the alpha 1-antitrypsin mature polypeptide were inserted into an Escherichia coli expression vector that allows transcription from the efficient leftward promoter of bacteriophage lambda (PL) and initiation of translation at the lambda cII gene ribosome-binding site. This construction resulted in the induction of a 45-kilodalton protein at a level of approximately 15% of total cell protein. The polypeptide produced was recognized by antisera raised against human alpha 1-antitrypsin protein and displayed normal biological activity in an in vitro antielastase assay.
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Alder L, Rosenthal A, Cech D. Mass spectrometric monitoring of solid phase phosphate triester synthesis of DNA fragments. Nucleic Acids Res 1983; 11:8431-41. [PMID: 6672769 PMCID: PMC326593 DOI: 10.1093/nar/11.23.8431] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A new and convenient pyrolysis mass spectrometric approach for monitoring solid phase phosphate triester synthesis of oligodeoxyribonucleotides in 5'-3' direction has been developed. The base-typical fragment ions produced by pyrolysis at 280 degrees C of the polymer-bound oligonucleotide triesters in the mass spectrometer permit the analytical monitoring of DNA chain growth, using simple mathematical operations. The base composition can be determined directly from the polymer. In addition, minor nucleosides can easily be detected.
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Abstract
A new pair of cloning and sequencing vectors based on bacteriophage M13mp7 has been developed. These vectors (M13tg130 and M13tg131) contain, in addition to the EcoRI, BamHI, HindIII, SmaI, SalI and PstI sites present in other vectors [cf., M13mp8 and M13mp9, Messing and Vieira, Gene 19 (1982) 269-276], unique restriction recognition sequences for the enzymes EcoRV, KpnI, SphI, SstI and XbaI. A restriction site for the enzyme BglII has been incorporated into the polylinker region of one of the vector pair to permit rapid discrimination between the two vectors.
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Kume A, Sekine M, Hata T. FURTHER IMPROVEMENTS OF OLIGODEOXYRIBONUCLEOTIDES SYNTHESIS: SYNTHESIS OF TETRADEOXYADENYLATE ON A NEW SILICA GEL SUPPORT USINGN6-PHTHALOYLDEOXYADENOSINE. CHEM LETT 1983. [DOI: 10.1246/cl.1983.1597] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Jaye M, de la Salle H, Schamber F, Balland A, Kohli V, Findeli A, Tolstoshev P, Lecocq JP. Isolation of a human anti-haemophilic factor IX cDNA clone using a unique 52-base synthetic oligonucleotide probe deduced from the amino acid sequence of bovine factor IX. Nucleic Acids Res 1983; 11:2325-35. [PMID: 6687940 PMCID: PMC325887 DOI: 10.1093/nar/11.8.2325] [Citation(s) in RCA: 140] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A unique 52mer oligonucleotide deduced from the amino acid sequence of bovine Factor IX was synthesized and used as a probe to screen a human liver cDNA bank. The Factor IX clone isolated shows 5 differences in nucleotide and deduced amino acid sequence as compared to a previously isolated clone. In addition, precisely one codon has been deleted.Images
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22
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Sproat B, Bannwarth W. Improved synthesis of oligodeoxynucleotides on controlled pore glass using phosphotriesther chemistry and a flow system. Tetrahedron Lett 1983. [DOI: 10.1016/s0040-4039(00)94197-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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