Intracellular location of rabbit poxvirus nucleic acid within infected cells as determined by in situ hybridization.

The intracellular location of rabbit poxvirus DNA within cells during the course of infection has been determined by the hybridization in situ of labeled viral DNA probes to uninfected and infected cells under various conditions. Extensive control experiments were performed to demonstrate that DNA could be detected selectively and accurately within the cell. Our results suggest that rabbit poxvirus DNA is located only within the cytoplasm during the reproductive cycle, and we found no evidence that viral DNA enters the cell nucleus. The pattern of hybridization of viral DNA at early times (1 and 2 h postinfection) and in the presence of inhibitors of viral DNA synthesis suggests that there may be an association between the input viral DNA and some structural component of the host cell. A number of observations support the hypothesis that the host cell nucleus is required for a productive poxvirus infection. Our results are discussed in terms of the possible role of the nucleus in the replication of poxviruses.     

Genetic relatedness among mycoplasmas as determined by nucleic acid homology

Reich, Paul R. (National Institutes of Health, Bethesda, Md.), Norman L. Somerson, James A. Rose, and Sherman M. Weissman. Genetic relatedness among mycoplasmas as determined by nucleic acid homology. J. Bacteriol. 91:153-160. 1966.-A sensitive membrane filter method to detect nucleic acid homology was used to determine genetic relatedness among mycoplasma isolates. Deoxyribonucleic acid (DNA) was isolated from mycoplasmas and used as a primer for synthesis of tritium-labeled, complementary ribonucleic acid (RNA) by the enzyme RNA polymerase. DNA from each mycoplasma isolate tested was reacted separately with complementary RNA synthesized with homologous or heterologous DNA as primer. The quantity of DNA-RNA hybrids formed was assayed by the nitrocellulose membrane filter method. The amount of radioactivity bound to the membrane filter was used to measure the degree of homology between the nucleic acids. The three mycoplasma isolates from human oral cavities (DC 63, V2785, Botteicher) and the prototype strain PG21 placed in the Mycoplasma hominis type 1 group by gel diffusion and complement-fixation testing were investigated with this technique. Analysis of the data confirmed their immunological grouping with the M. hominis type 1 and their distinction from other human mycoplasmas. In contrast to the data from immunological studies, none of the four isolates tested appeared to be identical to any other. Preliminary experiments with DNA from four other mycoplasma isolates from tissue cultures inoculated with human material revealed them to be closely related, and possibly identical. The advantages of this nucleic acid homology technique for the study of relatedness among mycoplasmas are described.     

Lack of genetic relatedness among animal and plant acholeplasmas by nucleic acid hybridization

The present study compared the genetic characteristics of three previously unclassified acholeplasmas of plant origin with those of the eight established species ofAcholeplasma. A radiolabeled DNA probe was derived from the lemon (L1) strain acholeplasma by using the nick translation method and hybridized to the excess unlabeled DNA isolated from the eight established species ofAcholeplasma and three new isolates from plants. Nucleic acid hydridization and serological tests confirmed that the L1 acholeplasma was distinct from all eight established species ofAcholeplasma but closely related to strains isolated from the flowers of grapefruit trees (GF1) and powder puff plants (PP2). The results suggest that these new acholeplasmas isolated exclusively from plants may represent a new species ofAcholeplasma.     

Detection of Chlamydia trachomatis by nucleic acid sandwich hybridization

Abstract Chromosomal DNA fragments from Chlamydia trachomatis serotype L2 were shotgun-cloned into pBR322. A C. trachomatis -specific clone was further subcloned to produce specific DNA reagents for the identification of C. trachomatis by nucleic acid sandwich hybridization. The chosen DNA reagents from serotype L2 also hybridized with all the other chlamydial serotypes tested, but not with the DNA from 41 unrelated organisms. The sensitivity of the sandwich hybridization test was 10⁶ DNA molecules. The applicability of the test for routine diagnostic use was demonstrated by a pilot study in which C. trachomatis was directly detected from genital specimens.     

Acceleration of nucleic acid hybridization rate by polyethylene glycol

The addition of polyethylene glycol to filter-bound nucleic acid hybridization greatly increases the hybridization rate. With single-stranded probes, the increase obtained with polyethylene glycol is significantly greater than that obtained with dextran sulfate. Additionally, polyethylene glycol is easier to manipulate and less expensive than dextran sulfate.     

Detection of picogram amounts of nucleic acid by dot blot hybridization

An increasing number of human proteins isolated from cell sources are being produced for pharmaceutical use. Consequently, federal agencies have required the quantitative determination of residual nucleic acids that copurify with the potential protein products. We have conducted these assays in connection with our application for licensure of Alferon Injection. We report a sensitive dot blot hybridization assay that was used to quantitate picogram (or less) amounts of nucleic acids which copurified with human proteins isolated from recombinant (S. cerevisiae) or natural (leukocytes) sources.     

Topological constraints in nucleic acid hybridization kinetics

A theoretical examination of kinetic mechanisms for forming knots and links in nucleic acid structures suggests that molecules involving base pairs between loops are likely to become topologically trapped in persistent frustrated states through the mechanism of ‘helix-driven wrapping’. Augmentation of the state space to include both secondary structure and topology in describing the free energy landscape illustrates the potential for topological effects to influence the kinetics and function of nucleic acid strands. An experimental study of metastable complementary ‘kissing hairpins’ demonstrates that the topological constraint of zero linking number between the loops effectively prevents conversion to the minimum free energy helical state. Introduction of short catalyst strands that break the topological constraint causes rapid conversion to full duplex.     

Amplified detection of nucleic acid by G-quadruplex based hybridization chain reaction

A protein-free, isothermal, self-amplified nucleic acid sensing system which was a G-quadruplex integrated hybridization chain reaction (GQ-HCR) system was developed. The G-quadruplex was closed two-thirds in the loop and one-third in the stem of one of the GQ-HCR hairpin probes. In the absence of the target molecule, the GQ-HCR probes stayed as inactive meta-stable hairpin structures and the G-quadruplex was inert. Reversely, the GQ-HCR probes could be cross-opened to start a hybridization chain reaction and the closed G-quadruplex could be released to be free when the GQ-HCR probes came across the target molecule. The GQ-HCR nucleic acid sensing system could detect as low as 7.5nM ssDNA or RNA by the colorimetric method and 4nM ssDNA by the fluorometric method. Less than 10 copies of dsDNA template could also be detected when PCR was combined with the GQ-HCR system (PCR+GQ-HCR). Because of these advantages, the GQ-HCR system was also studied for application in visual chip detection to obtain a satisfactory repeatable and specific result.     

Membrane-based hybridization capture of intracellular peptide nucleic acid

Peptide nucleic acid (PNA) is a chimeric oligonucleotide with nucleotide-derived bases and a peptide backbone. Compared with natural nucleotides, PNA has several advantages, including improved stability and high sequence discrimination during duplex formation. Despite its potential for therapeutic application, analysis technologies have not been generalized, mainly due to ambiguous physiochemical properties resembling those of nucleic acids as well as protein. Here we present a PNA detection method: sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) followed by electrotransfer to a Western blotting membrane and then hybridization with a radiolabeled oligonucleotide probe. This method is useful for evaluating the quality of synthetic PNA and determining its intracellular localization.     

Use of bioluminescence in nucleic acid hybridization reactions

Luminescence reactions can be used to detect specific nucleic acid sequences hybridized with a nucleic probe. Different labels such as cytidine sulphone, fluorescein, and biotin can be incorporated into DNA or oligonucleotide molecules and detected by antibody or avidin conjugates coupled to glucose-6P dehydrogenase. On supports such as nitrocellulose filters, sensitivity is not greatly increased using luminescence, but detection is rapid and easy to perform using polaroid film. Moreover, hybridization can be performed with different labelled probes on the same sample. In solution, luminescence can be used to monitor sandwich reactions. The method is less sensitive than detection on filters but can easily be automated. The performance of these assays can be increased considerably by enzymatic amplification of the target catalysed by a thermostable polymerase.     

DNA hybridization detection in a microfluidic channel using two fluorescently labelled nucleic acid probes

A conceptually new technique for fast DNA detection has been developed. Here, we report a fast and sensitive online fluorescence resonance energy transfer (FRET) detection technique for label-free target DNA. This method is based on changes in the FRET signal resulting from the sequence-specific hybridization between two fluorescently labelled nucleic acid probes and target DNA in a PDMS microfluidic channel. Confocal laser-induced microscopy has been used for the detection of fluorescence signal changes. In the present study, DNA hybridizations could be detected without PCR amplification because the sensitivity of confocal laser-induced fluorescence detection is very high. Two probe DNA oligomers (5'-CTGAT TAGAG AGAGAA-TAMRA-3' and 5'-TET-ATGTC TGAGC TGCAGG-3') and target DNA (3'-GACTA ATCTC TCTCT TACAG GCACT ACAGA CTCGA CGTCC-5') were introduced into the channel by a microsyringe pump, and they were efficiently mixed by passing through the alligator teeth-shaped PDMS microfluidic channel. Here, the nucleic acid probes were terminally labelled with the fluorescent dyes, tetrafluororescein (TET) and tetramethyl-6-carboxyrhodamine (TAMRA), respectively. According to our confocal fluorescence measurements, the limit of detection of the target DNA is estimated to be 1.0 x 10(-6) to 1.0 x 10(-7)M. Our result demonstrates that this analytical technique is a promising diagnostic tool that can be applied to the real-time analysis of DNA targets in the solution phase.     

利用RAPD技术对葱属品种遗传关系的分析

利用随机扩增多态性DNA(RAPD)技术分析了我国栽培的几个主要葱属品种。所用的20个引物,有11个能扩增出重现性好且稳定的谱带,10个品种共扩增出102条带,其中68条具多态性。根据DNA谱带计算的10个品种相似系数范围为0.571～0.947。对10个品种的UPGMA聚类分析表明,章丘大葱(Allium fistulosum var. gigantum cv. Zhangqiu Welsh onion)、天津五叶齐（A. fistulosum var.gigantum cv. Tianjin Wuyeqi Welsh onion）、上海分葱（A. fistulosum var. caepitosum cv.Shanghai Spring onion）、南京冬葱（A. fistulosum var. caepitosum cv. Nanjing Winter onion）和韩国大葱（A. fistulosum var .gigantum cv. Korea Welsh onion）关系较近。根据聚类结果,将章丘大葱、天津五叶齐、上海分葱、南京冬葱、韩国大葱、细香葱（A. schoenoprasum）以及楼葱（A. fistulosum var. viviparum）归为葱组;而将胡葱（A. ascalonicum）、洋葱（A. cepa）及洋葱和大葱的杂交种归为洋葱组。最后根据RAPD标记,讨论了各品种之间的亲缘关系。     

Recombination between endogenous and exogenous RNA tumor virus genes as analyzed by nucleic acid hybridization.

Certain chicken cells that do not spontaneously release virus particles have been shown to produce a subgroup E avian RNA tumor virus, Rous-associated virus 60 (RAV-60), after infection with viruses of other subgroups. The nucleic acids of RAV-60 were analyzed for sequence homologies with the viral nucleic acids contained in the uninfected cell and with those of RAV-2, the exogenous virus used for the preparation of this particular RAV-60 isolate. In addition, these nucleic acids were compared with those of RAV-0, an endogenous virus spontaneously released from line 100 chicken cells. RAV-60 appears to be intermediate between RAV-0 and RAV-2 in its genetic composition, based on the pattern of hybridization obtained with the nucleic acids of these viruses and on the melting profiles of the various hybrid combinations. Of the three viruses tested, RAV-0 appears to have the greatest sequence homology with the viral nucleic acids of the uninfected cell. Hybridization between RAV-60 3-H-labeled complementary DNA and either DNA or RNA from the uninfected cell indicates that RAV-60 contains some nucleic acid sequences which are not present in the cell. In addition, some RAV-60 sequences which hybridize with the cell nucleic acid contain significant amounts of mismatching, as indicated by the lower thermal stability of these hybrid duplexes. Hybrid formation between these partially homologous sequences was excluded under stringent annealing conditions. The data indicate that RAV-60 is a recombinant between exogenous and endogenous viral genes.     

Detection of Chlamydia trachomatis in clinical specimens by nucleic acid spot hybridization

A nucleic acid spot hybridization assay was used to detect Chlamydia trachomatis DNA. The hybridization probes included DNA isolated from elementary bodies of lymphogranuloma venereum (LGV) strains and cloned fragments of both chromosomal and plasmid DNA. The sensitivity of the test was in the range 10 to 100 pg homologous DNA and 10 in vitro infected cells. Cross-reactivity with bacterial DNA was avoided when purified chlamydia-specific DNA fragments were used as probes. C. trachomatis was detectable in most of the clinical specimens with large amounts of infectious particles. Also some isolation-negative specimens gave a positive signal in the test.     

Optimization of excimer-forming two-probe nucleic acid hybridization method with pyrene as a fluorophore.

A previously presented homogeneous assay method, named the excimer-forming two-probe nucleic acid hybridization (ETPH) method, is based on specific excimer formation between two pyrenes attached at the neighboring terminals of two sequential probe oligonucleotides complementary to a single target. In this study, we investigated assay conditions and optimal molecular design of probes for intense excimer emission using a pyrenemethyliodoacetamide-introduced 16mer probe, a pyrene butanoic acid-introduced 16merprobe and a target 32mer. The length of the linker between the pyrene residue and the terminal sugar moiety remarkably influenced the quantum efficiency of excimer emission; the pair of linker arms of these two probes was optimal. The quantum efficiency was also dependent upon the concentrations of dimethylformamide and NaCl added to the assay solution. Spectroscopic measurements and T m analysis showed that an optimal configuration of the two pyrene residues for intense excimer emission might be affected by pyrene-pyrene interaction, pyrene-duplex interaction (intercalation/stacking) and solvent conditions as a whole. We then demonstrated the practicality of the ETPH method with the optimal hybridization conditions thus attained by determining that the concentration of 16S rRNA in extracts from Vibrio mimicus ATCC 33655 cells in exponential growth phase is 18 500 16S rRNA molecules/cell on average.     

Esterase 2-oligodeoxynucleotide conjugates as sensitive reporter for electrochemical detection of nucleic acid hybridization

A thermostable, single polypeptide chain enzyme, esterase 2 from Alicyclobacillus acidocaldarius, was covalently conjugated in a site specific manner with an oligodeoxynucleotide. The conjugate served as a reporter enzyme for electrochemical detection of DNA hybridization. Capture oligodeoxynucleotides were assembled on gold electrode via thiol-gold interaction. The esterase 2-oligodeoxynucleotide conjugates were brought to electrode surface by DNA hybridization. The p-aminophenol formed by esterase 2 catalyzed hydrolysis of p-aminophenylbutyrate was amperometrically determined. Esterase 2 reporters allows to detect approximately 1.5 x 10(-18)mol oligodeoxynucleotides/0.6 mm2 electrode, or 3 pM oligodeoxynucleotide in a volume of 0.5 microL. Chemically targeted, single site covalent attachment of esterase 2 to an oligodeoxynucleotide significantly increases the selectivity of the mismatch detection as compared to widely used, rather unspecific, streptavidin/biotin conjugated proteins. Artificial single nucleotide mismatches in a 510-nucleotide ssDNA could be reliably determined using esterase 2-oligodeoxynucleotide conjugates as a reporter.