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1.
A method is described for the rapid analysis of DNA ligation products in the assembly of synthetic genes and gene fragments. The method is based on the simultaneous analysis of multiple ligation reactions where a single but different DNA oligomer is radiolabelled per ligation reaction. After each ligation the reaction mixture is electrophoresed on a denaturing, as well as a non-denaturing, polyacrylamide gel allowing one to monitor the ligation reaction products. In addition, a unique method for generating single stranded DNA sizing standards up to approximately 300 nucleotides in length is described. 相似文献
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M Smith 《Nucleic acids symposium series》1980,(7):387-395
The applications of synthetic oligodeoxyribonucleotides to problems in molecular biology described in this article are those where the oligodeoxyribonucleotide is a probe for a specific region of a nucleic acid. This includes the isolation of the iso-1-cytochrome c gene of yeast; the sequence determination of RNAs and DNAs including regions of double-stranded DNA; the introduction of defined site-specific point mutations into bacteriophage OX174 and in the in vitro selection of mutant DNA from a mixture with wild-type DNA. 相似文献
4.
Automated synthesis of oligodeoxyribonucleotides using in situ prepared methylchlorophosphite intermediates from amidine protected purine nucleosides is described. Phosphoramidite method using 1-methylimidazole trifluoromethanesulfonate as mediator is described. 相似文献
5.
Automated 3'-H-phosphonate synthesis of oligodeoxyribonucleotides using amidine protected purine synthons 总被引:1,自引:0,他引:1
Side reaction during phosphitylation of 5'-O-dimethoxytrityl-N2-isobutyryl-2'-deoxyguanosine was observed. As a suitable dG synthon, 5'-O-dimethoxytrityl-N2-dimethylaminomethyl-ene-3'-H-phosphonate was developed and used, along with 3'-H-phosphonates of 5'-O-dimethoxytrityl derivatives of dT, N4--benzoyl-dC and N6-dimethylaminoethylidene-dA, in automated synthesis of several oligodeoxyribonucleotides containing 30-40 bases. 相似文献
6.
Denis Scanlon Jim Haralambidis Christina Southwell Janice Turton Geoffrey Tregear 《Journal of chromatography. B, Analytical technologies in the biomedical and life sciences》1984,336(1)
Synthetic oligodeoxyribonucleotides rangin from 11 to 37 nucleotides in length and with varying base compositions, prepared by both the phosphotriester and phosphite procedures, have been purified by ion-exchange high-performance liquid chromatography on Whatman Partisil 10/SAX columns using phosphate buffer gradients. The effects of different buffer systems on elution times and resolution have been evaluated. Oligomer composition and length had a marked effect on the resolution achieved. In general the use of formamide buffers gave the best results, particularly in the case of 2′-deoxyguanosine-rich sequences. These methods have also been successfully applied to the purification of mixtures of synthetic oligodeoxynucleotides. 相似文献
7.
A method was developed for determination of the rate of undesired point mutations upon cloning of synthetic DNA. The method relies on cloning of an oligonucleotide(s) into the E. coli alkaline phosphatase gene inactivated due to a small deletion within the active site. The oligonucleotide adds back the deleted sequence, but simultaneously introduces a missense mutation at a critical position. The activity of the enzyme is restored only if there is a predefined sequence change within the codon specifying an essential residue of the active site. The clones carrying the reactivated gene are detected by colony color screening on plates. The method is fast and simple, does not require specialized equipment nor enzymatic reactions, although a separate oligonucleotide needs to be provided for each sequence change to be evaluated. The procedure allows for the use of crude extracts of oligonucleotides and distinguishes between different types of sequence changes. 相似文献
8.
Anna M. Banaszuk Ken V. Deugau Judy Sherwood Marek Michalak Bernard R. Glick 《Analytical biochemistry》1983,128(2):281-286
Modifications of the chemical method of DNA sequence analysis that permit rapid and reliable sequence determination of single-stranded oligodeoxyribonucleotides as short as 4 nucleotides in length are reported. The principal changes made were increasing the level of chemical modification and optimizing the conditions for recovery of the chemically modified oligodeoxyribonucleotides. This method includes two approaches to the removal of [γ-32P]ATP from 32P-labeled oligodeoxyribonucleotides and is especially useful in the determination of the sequence of chemically synthesized oligodeoxyribonucleotides, which are generally between 4 and 20 nucleotides in length. 相似文献
9.
N,O-protected 2'-deoxyribonucleotide-3'-H-phosphonates and 2-(p-nitrophenylethyl)-H-phosphonate were prepared and used in solid-phase synthesis of 5'-phosphorylated DNA. H-Phosphonate condensation is performed with 1:2 ratio of P-component to activator (pivaloyl chloride). Protection groups were removed either by sequential treatment with conc. NH3 and DBU or by combination of these reagents. 相似文献
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Fast methods for the removal of permanent amide exo-cyclic protective groups widely used in phosphoramidite-method DNA synthesis are desirable for many genomics and proteomics applications. In this communication, we present a method for the deprotection of a range of N-acyl deoxyribonucleosides (T, dA Bz, dC Bz, dC Ac, dG ibu, dG PAC) and synthetic oligodeoxyribonucleotides, ranging in length from 5-mer to 50-mer. Oligodeoxyribonucleotides were synthesized using standard amide protecting groups (dA Bz, dC Bz, dG ibu) and phosphoramidite chemistry on cis-diol solid phase support. This deprotection method utilizes 29% aqueous ammonia solution at 170 degrees C for 5 minutes under monomode microwave irradiation at a 20-nmole reaction scale. Reaction products were analyzed by TLC, RP-HPLC, CE, ESI-MS, real-time PCR, agarose gel electrophoresis, and by DNA uracil glycosylase (UDG) and phosphodiesterase I (PDE) enzymatic digestions. 相似文献
12.
Vladimir A. Khripach Vladimir N. Zhabinskii Galina V. Ivanova Dmitrii V. Tsavlovskii Bernd Schneider 《Steroids》2010,75(1):27-33
Preparation of partially protected brassinosteroids is achieved through the reaction of the source material (24-epicastasterone and 24-epibrassinolide) with diol-specific reagents (2,2-dimethoxypropane and methylboronic acid). The obtained products were shown to be useful synthetic intermediates for further preparation of minor representatives of this class of natural phytohormones (such as 3,24-diepicastasterone and 3-dehydro-24-epibrassinolide). 相似文献
13.
Synthesis of mixed oligodeoxyribonucleotides following the solid phase method. 总被引:3,自引:4,他引:3
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A method for the synthesis of mixed dimers, trimers and oligonucleotides on a solid support using monomeric protected nucleoside phosphochloridites (1a-d) has been developed and the different nucleoside reagents, and the results show that yields of different oligomers in a mixture could be directly correlated to the concentration of the four reagents. Separation of mixed oligomers on a reversed phase C18 column has also been studied. 相似文献
14.
Murphy PA Barua K Hauck CC 《Journal of chromatography. B, Analytical technologies in the biomedical and life sciences》2002,777(1-2):129-138
Acetonitrile is superior to acetone, ethanol and methanol in extracting the 12 phytoestrogenic soy isoflavone forms found in foods. At 53% organic solvent in water, raw soy flour, tofu, tempeh, textured vegetable protein and soy germ were evaluated for isoflavone extraction efficiency. The efficiency of acetonitrile extraction was demonstrated in mass balance evaluations of toasting of soy flour and soymilk heating. 相似文献
15.
Antiviral activity of conjugates between poly(L-lysine) and synthetic oligodeoxyribonucleotides 总被引:10,自引:0,他引:10
J P Leonetti B Rayner M Lemaitre C Gagnor P G Milhaud J L Imbach B Lebleu 《Gene》1988,72(1-2):323-332
Short (14 to 20-mer range) synthetic oligodeoxyribonucleotides (oligos) allow to modulate specifically viral or cellular gene expression at various stages thus providing a versatile tool for fundamental studies and a rational approach to antiviral chemotherapy. Several problems, such as metabolic stability and efficient cell internalization of oligos, still limit this approach appreciably, as briefly discussed here. We demonstrate here that the conjugation of 15-mer (beta)-anomeric oligos to poly(L-lysine) allows a specific protection of various cell lines against vesicular stomatitis virus infection at concentrations lower than 1 microM. This can be achieved with oligos complementary to the viral N-protein mRNA initiation site or to viral intergenic sequences, i.e., to untranscribed regions. No antiviral activity can be obtained with (alpha)-anomeric oligos directed against the same targets, although such analogues are much more resistant to nuclease degradation and form stable hybrids, at least in cell-free experiments. 相似文献
16.
A solvent extraction method was developed to concentrate lacidin from the culture of Lactobacillus acidophilus OSU133. The new method concentrates the bacteriocin at the interface between chloroform and the aqueous culture of the producing bacterium. Compared with other extraction procedures, the new method effectively recovers higher bacteriocin yield and results in relatively clean preparations. Recovery of lacidin by the chloroform extraction procedure, compared with ammonium sulphate precipitation and cell acidification methods, was >10-fold and about 100-fold greater, respectively. The new extraction procedure saves time and is easy to perform. This method is also effective in recovering subtilin, bacillicin, pediocin and nisin from cultures of Bacillus subtilis ATCC 6633, B. subtilis OSY1115/C, Pediococcus acidilactici PO2 and Lactococcus lactis ATCC 11454, respectively. 相似文献
17.
The biological interpretation of metabolomic data can be misled by the extraction method used 总被引:1,自引:0,他引:1
Xavier Duportet Raphael Bastos Mereschi Aggio Sónia Carneiro Silas Granato Villas-B?as 《Metabolomics : Official journal of the Metabolomic Society》2012,8(3):410-421
The field of metabolomics is getting more and more popular and a wide range of different sample preparation procedures are in use by different laboratories. Chemical extraction methods using one or more organic solvents as the extraction agent are the most commonly used approach to extract intracellular metabolites and generate metabolite profiles. Metabolite profiles are the scaffold supporting the biological interpretation in metabolomics. Therefore, we aimed to address the following fundamental question: can we obtain similar metabolomic results and, consequently, reach the same biological interpretation by using different protocols for extraction of intracellular metabolites? We have used four different methods for extraction of intracellular metabolites using four different microbial cell types (Gram negative bacterium, Gram positive bacterium, yeast, and a filamentous fungus). All the quenched samples were pooled together before extraction, and, therefore, they were identical. After extraction and GC?CMS analysis of metabolites, we did not only detect different numbers of compounds depending on the extraction method used and regardless of the cell type tested, but we also obtained distinct metabolite levels for the compounds commonly detected by all methods (P-value?<?0.001). These differences between methods resulted in contradictory biological interpretation regarding the activity of different metabolic pathways. Therefore, our results show that different solvent-based extraction methods can yield significantly different metabolite profiles, which impact substantially in the biological interpretation of metabolomics data. Thus, development of alternative extraction protocols and, most importantly, standardization of sample preparation methods for metabolomics should be seriously pursued by the scientific community. 相似文献
18.
The structure of an oligodeoxyribonucleotide may be determined by a simple two-dimensional separation on a polyethyleneimine-cellulose thin layer sheet. Chromatography in the first dimension fractionates by chain length a nested set of fragments that are generated by subjecting the oligomer to partial spleen phosphodiesterase degradation and then labelling their non-common ends with 32P using polynucleotide kinase. A subsequent in situ treatment with nuclease Bal 31 produces labelled mononucleotides, and these are identified by chromatography in the second dimension. Since the method does not identify the 3' terminal nucleotide, a convenient procedure involving 3' end labelling followed by enzymatic digestion to monomers has been developed for this purpose. This approach to sequence analysis also has the advantage of permitting assignment of the identity and location of any modified or unusual bases within the oligonucleotide. 相似文献
19.
Construction of viable and lethal mutations in the origin of bacteriophage 'phi' X174 using synthetic oligodeoxyribonucleotides 总被引:11,自引:0,他引:11
P D Baas W R Teertstra A D van Mansfeld H S Jansz G A van der Marel G H Veeneman J H van Boom 《Journal of molecular biology》1981,152(4):615-639
Six different synthetic deoxyhexadecamers complementary to the origin of bacteriophage φX174, corresponding to nucleotides 4299 to 4314, except for one preselected nucleotide change were used as primers for DNA synthesis on wild-type φX2 DNA as a template. DNA synthesis was performed with Escherichia coli DNA polymerase I (Klenow fragment) in the presence of DNA ligase. Heteroduplex RFIV DNA was isolated and, after limited digestion with DNAase I, complementary strands containing the mutant primers were isolated. The biological activity of these complementary strands was assayed in spheroplasts. Spheroplasts were made from E. coli K58 ung? (uracil N-glycosylase) to prevent degradation of the complementary strands caused by uracil incorporation (Baas et al., 1980a).Using (5′-32P) end-labeled primers, it was shown that all tested DNA polymerase preparations, including phage T4 DNA polymerase, contained variable amounts of 5′ → 3′ exonuclease activity. This nick translation activity may result in removal of the mutation in the primers, and therefore in isolation of wild-type complementary DNA instead of mutant complementary DNA.Restriction enzyme analysis of completed RFIV DNA showed that the primers can initiate DNA synthesis at more than one place on the φX174 genome. These complications result in a mixed population of complementary strand DNAs synthesized in vitro. Nevertheless, the desired mutants were picked up with high frequency using a selection test that is based on the difference in ultraviolet light sensitivity of homoduplex and heteroduplex φX174 RF DNA. Heteroduplex φX174 RF DNA is two to three times more sensitive to ultraviolet light irradiation than is homoduplex φX174 RF DNA (Baas &; Jansz, 1971,1972). Phage DNA derived from single plaque lysates of two of the six mutant complementary strand DNA preparations yielded, after annealing with wild-type complementary strand DNA, heteroduplex DNA with high frequency. DNA sequence analysis in the origin region of RF DNA obtained from these two phage preparations revealed the presence of the expected mutation. RFI DNA of these two origin mutants was nicked by φX174 gene A protein in the same way as wild-type φX174 RFI DNA.Phage DNA derived from single plaque lysates of the other four mutant complementary strand DNA preparations yielded exclusively homoduplex DNA after annealing with wild-type complementary strand DNA. It is concluded that priming with these deoxyhexadecamers resulted in the synthesis of complementary φX174 DNA with lethal mutations. The implications of these results, the construction of two silent, viable φX174 origin mutants and the failure to detect four others, for the initiation mechanism of φX174 RF DNA replication are discussed. 相似文献
20.
Efficient methods for attaching non-radioactive labels to the 5'' ends of synthetic oligodeoxyribonucleotides. 总被引:3,自引:31,他引:3
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The syntheses are described of two types of linker molecule useful for the specific attachment of non-radioactive labels such as biotin and fluorophores to the 5' terminus of synthetic oligodeoxyribonucleotides. The linkers are designed such that they can be coupled to the oligonucleotide as a final step in solid-phase synthesis using commercial DNA synthesis machines. Increased sensitivity of biotin detection was possible using an anti-biotin hybridoma/peroxidase detection system. 相似文献