两种抽提乙型肝炎病毒共价闭合环状DNA方法的效果比较

乙型肝炎病毒(hepatitis B virus,HBV)作为一种嗜肝DNA病毒,在感染肝细胞后会在细胞核中形成病毒转录复制的模板和基因储存库--共价闭合环状DNA(covalently closed circular DNA, cccDNA),其持续存在是乙型肝炎慢性化和难以治愈的核心,也是此研究领域内的重点。从细胞样品中稳定抽提获取cccDNA对于保证cccDNA检测的准确性至关重要。Hirt法是一种抽提真核细胞染色体外DNA的方法,被用于HBV cccDNA的抽提,但存在操作复杂和耗时长等问题。为简化操作,有研究对Hirt法进行改良,结合硅胶膜离心柱来抽提染色体外DNA,但尚不清楚该法用于HBV cccDNA抽提与传统Hirt法的效果差异。本研究基于HBV cccDNA细胞转染系统、HBV复制细胞系及感染系统,以DNA印迹(Southern blot)和定量聚合酶链式反应(quantitative polymerase chain reaction, qPCR)作为检测评价手段,平行比较了传统Hirt-酚/氯仿法与改良Hirt-过柱法抽提HBV cccDNA的效果。结果表明,两种方法具有相当的抽提效率和抽提特异性,而改良Hirt-过柱法耗时更短,提示在进行细胞HBV cccDNA抽提时可选择改良Hirt-过柱法以提高实验效率。     

Characterization of the Aleutian disease virus genome and its intracellular forms

Aleutian disease virus (ADV) of mink is a nondefective parvovirus with a single-stranded DNA genome. We characterized the viral DNA forms found in infected cells prepared by a modified Hirt extraction procedure. Double-stranded DNA molecules corresponding in size to 4.8-kilobase-pair duplex monomers and 9.6-kilobase-pair duplex dimers were identified in agarose gels by blot hybridization to 32P-labeled ADV DNA. A rapidly reannealing ADV duplex monomer was isolated on a preparative scale and physically mapped with a series of restriction endonucleases. The map derived was similar to one derived from double-stranded ADV DNA produced by self-primed synthesis on virion DNA, but differed from restriction endonuclease maps reported for other parvovirus DNAs. The purified duplex monomer could be labeled with [32P]dCTP by nick translation and used as a probe in blot hybridization to detect ADV sequences in DNA from small numbers of infected cells. Additional studies indicated that double-stranded ADV DNA could first be detected at 24 h after infection.     

An improved method for rapid purification of covalently closed circular plasmid DNA over a wide size range

An improved method has been developed for the large-scale purification of covalently closed circular (CCC) plasmid DNA molecules of sizes ranging from 4·3 to 73 kb. This protocol uses an alkaline-lysis procedure followed by acid-phenol extraction but with several modifications to previously reported methods. The principal modification is the replacement of NaCl by MgCl₂ in the extraction buffer to improve yield and to remove chromosomal and other non-CCC plasmid DNA. Plasmid DNA can be purified in less than 1 h and used successfully in restriction enzyme analysis and cloning experiments.     

Hydroxyurea-Induced Accumulation of Short Fragments During Polyoma DNA Replication I. Characterization of Fragments

Hydroxyurea treatment of 3T6 mouse fibroblast cells infected with polyoma virus resulted within 15 min in more than a 20-fold reduction of the rate of both viral and cellular DNA synthesis. After the initial rapid inhibition, the rate of DNA synthesis remained essentially constant for at least 2 h. In the inhibited cells viral DNA accumulated as short chains with a sedimentation coefficient of about 4S (hydroxyurea fragments). A variable proportion of these fragments was released from the template strands when the viral DNA was extracted by the Hirt procedure. Reannealing experiments demonstrated that hydroxyurea fragments were polyoma-specific and probably synthesized on both parental strands at the replication forks.     

Effect of Phleomycin on Polyoma Virus Synthesis in Mouse Embryo Cells

The addition of phleomycin (25 mug) to primary mouse embryo cells infected with polyoma virus was found to cause 96% inhibition of the synthesis of infectious virus. When ribonucleic acid and protein synthesis was investigated in these cells by use of isotope incorporation, it was found that neither was inhibited drastically. Immunofluorescent staining studies with the use of antibody directed to the viral structural proteins showed that proteins were synthesized in the presence of the antibiotic. However, when deoxyribonucleic acid (DNA) synthesis was investigated, it was found that DNA synthesis in uninfected cells was completely inhibited within the initial 10 hr of phleomycin addition, whereas DNA synthesis in infected cells proceeded at a reduced rate. Selective DNA extraction (Hirt method) of phleomycin-treated infected cells demonstrated that synthesized viral DNA was salt-extractable, similar to that in infected control cells lacking phleomycin. This extracted DNA was further fractionated by ethidium bromide-cesium chloride density gradient equilibrium centrifugation. The phleomycin-treated preparations revealed twice as much component II (circular nicked and linear) as component I (supercoiled) DNA, whereas the DNA from normally infected control cells showed the reverse picture. It was also demonstrated that viral particles synthesized in the presence of phleomycin did not contain component I DNA. This packaged DNA was found to consist of fragments of both the host and viral types. Cells that were prelabeled with (3)H-thymidine and then treated with phleomycin demonstrated host DNA degradation. However, fragments formed from prelabeled host DNA were not encapsidated into viral particles.     

Nicking-closing enzyme is associated with SV40 DNA in vivo as a sodium dodecyl sulfate-resistant complex.

A fraction of the cellular nicking-closing (NC) enzyme cosediments with SV40 chromatin isolated after Triton X-100 treatment of infected cells nuclei. Extraction of viral DNA according to the Hirt procedure by treatment of infected cells with sodium dodecyl sulfate (SDS) followed by sedimentation in sucrose gradient to separate the DNA from the bulk of detergent also revealed NC activity associated with DNA. Reconstitution experiments showed that only prebinding of the NC enzyme to DNA protects it against irreversible inactivation by SDS. These results suggest that a fraction of the cellular NC activity is indeed associated with the viral chromosome in vivo.     

A unique subgenomic species of adenovirus 2 DNA generated under high multiplicities of infection.

We have identified a novel subgenomic viral DNA in KB cells infected with adenovirus 2 (Ad2) under high multiplicities of infection. KB cells were infected with Ad2 at multiplicities of infection greater than 100 PFU/cell. 32P-labeled viral DNA was selectively extracted by a modification of the method of Hirt (8) from the infected cells and analyzed by electrophoresis on agarose gels. In addition to full-length DNA (33 to 23 x 10(6) daltons), a unique subgenomic DNA species of about 12 to 13% (2.6 x 10(6) daltons) of full-length DNA in size was found in the infected cells. This subgenomic DNA was found to be double stranded and was not packaged inside the virus particles. This DNA could be isolated in large amounts (30 to 50% of total viral DNA) from infected cells. When cleaved with restriction endonuclease KpnI, the subgenomic DNA yielded two fragments, each corresponding to about 6% and 7% of the full-length genome in size.     

A simplified PCR-based method for the detection of Renibacterium salmoninarum utilizing preparations of rainbow trout (Oncorhynchus mykiss, Walbaum) lymphocytes.

A method for the detection of Renibacterium salmoninarum by PCR is described. A rapid, reliable procedure was developed for the extraction of DNA, which could be applied to infected kidney homogenates and head kidney lymphocyte preparations. The target for DNA amplification was a 376-bp region of the gene encoding the 57-kDa major surface antigen (MSA). The PCR was specific for R. salmoninarum and allowed the detection of 10 to 100 cells of the pathogen. Use of the PCR for the examination of experimentally infected rainbow trout showed it to be as reliable as plate culture methods for the detection of R. salmoninarum in infected kidneys.     

"Endless" viral DNA in cells infected with channel catfish virus

The state of intracellular viral DNA in cells infected with channel catfish virus has been studied by the Hirt selective extraction procedure and by restriction endonuclease digestion. The sedimentation properties and restriction patterns of viral DNA in the Hirt supernatant fraction indicate that the majority, if not all, of the DNA is in the form of linear unit-length (Mr approximately equal to 85 x 10(6)) molecules. However, restriction digests of viral DNA in the pellet fraction lacked two fragments corresponding to the molecular ends of unit-length DNA. In addition, there appeared in HpaI digests of pellet DNA a new restriction fragment interpretable as the product of fusion between the ends of unit-length molecules. The size of the new fragment requires that fusion occur in such a way that one copy of the terminally repeated sequences (Mr approximately equal to 12.3 x 10(6)) of the unit-length DNA is lost in the process. In pulse-chase experiments, radioactivity flowed from the pellet fraction to the supernatant fraction, suggesting a precursor-product relationship for these DNA species. The results are easily understood if unit-length virion DNA is generated by excision from concatemeric structures.     

Restricted infectivity of ecotropic type C retroviruses in mouse teratocarcinoma cells: Studies on viral DNA intermediates

Replication of Gross strain N-tropic type C retrovirus was markedly restricted in a pluripotential undifferentiated embryonal cell line (PCC₄) of murine teratocarcinoma, whereas the same virus could cause productive infection in a myoblast-derived differentiated line (PCD₁) of the same tumor origin. To investigate the restriction mechanism, we compared the initial viral DNA formation in these two cell lines. Analyses by means of a modified Hirt extraction procedure and a modified Southern gel transfer method indicated that PCC₄ and PCD₁ cells supported the synthesis of viral DNA intermediates after inoculation of the Gross virus. In both cells, a linear DNA duplex (form III viral DNA) appeared at 4 hr, reached a maximal level at 8–9 hr, and declined rapidly thereafter, while two closed-circular supercoiled DNA duplexes (form I viral DNA) showed their appearance, increase and decline in the 8–24 hr period. During the period from 34 to 78 hr after virus inoculation, another burst of viral DNA synthesis occurred in PCD₁ cells, presumably due to secondary virus infection, while at this period both form III and form I viral DNAs became undetectable in PCC₄ cells. The Hirt supernatant DNAs prepared from PCD₁ and PCC₄ cells 10 hr after virus inoculation were equally infectious for NIH3T3 cells in a DNA transfection assay. Both PCD₁ and PCC₄ cells were very poor recipients for DNA transfection, although one positive result with PCD₁ cells might suggest a difference between the two cell types in this aspect. These results indicate that restriction of type C retrovirus in undifferentated embryonl carcinoma cells occurs at a step subsequent to formation and maturation of viral DNA intermediates.     

Helper-independent transformation by unintegrated Harvey sarcoma virus DNA.

We have studied the unintegrated infectious DNA of Harvey sarcoma virus (Ha-SV) and Moloney leukemia virus (Mo-MuLV). The source of infectious viral DNA was the Hirt supernatant fraction from cells acutely infected with Ha-SV and Mo-MuLV. To obtain a direct quantitative assay for infectious viral DNA, recipient mouse cells were first exposed to calcium phosphate-precipitated viral DNA and then treated with dimethyl sulfoxide. Infectivity was monitored by focus formation for Ha-SV and XC plaque formation for Mo-MuLV. The viral DNA titration pattern followed single-hit kinetics for both foci and plaques, indicating that a single molecule carried information for each function. Focus-forming and plaque-forming activity were present in different molecules, since these two biological activities could be separated from each other by agarose gel electrophoresis. The focus-forming molecule was linear DNA with a molecular weight of about 4 x 10(6) daltons. The focus-forming activity of the viral DNA was sensitive to EcoRI and resistant to XhoI restriction endonucleases, whereas the plaque-forming activity was resistant to EcoRI and sensitive to XhoI. The generation of helper-independent foci indicates that Ha-SV DNA can transform mouse cells in the absence of helper virus or its proteins.     

Integrated State of Oncornavirus DNA in Normal Chicken Cells and in Cells Transformed by Avian Myeloblastosis Virus

The covalent linkage of oncornavirus-specific DNA to chicken DNA was investigated in normal chicken embryo fibroblasts (CEF) and in virus-producing leukemic cells transformed by avian myeloblastosis virus (AMV). The virus-specific sequences present in cellular DNA fractionated by different methods were detected by DNA-RNA hybridization by using 70S AMV RNA as a probe. In CEF and in leukemic cells, the viral DNA appeared to be present only in the nucleus. After cesium chloride-ethidium bromide density equilibrium sedimentation, the viral DNA was present as linear, double-stranded molecules not separable from linear chicken DNA. After extraction by the Hirt procedure, the viral DNA precipitated with the high-molecular-weight DNA. After alkaline sucrose velocity sedimentation, the viral DNA cosedimented with the high-molecular-weight cellular DNA. The results indicate that in both types of cells studied, the oncornavirus-specific DNA sequences were linked by alkali stable bonds to nuclear cellular DNA of high molecular weight and did not appear to be present in free form of any size.     

Molecular cloning of the Harvey sarcoma virus closed circular DNA intermediates: initial structural and biological characterization.

Supercoiled Harvey sarcoma virus (Ha-SV) DNA was extracted from newly infected cells by the Hirt procedure, enriched by preparative agarose gel electrophoresis, and digested with EcoRI, which cleaved the viral DNA at a unique site. The linearized Ha-SV DNA was then inserted into lambda gtWESlambda B at the EcoRI site and cloned in an approved EK2 host. Ha-SV DNA inserts from six independently derived recombinant clones have been analyzed by restriction endonuclease digestion, molecular hybridization, electron microscopy, and infectivity. Four of the Ha-SV DNA inserts were identical, contained about 6.0 kilobase pairs (kbp), and comigrated in agarose gels with the infectious, unintegrated, linear Ha-SV DNA. One insert was approximately 0.65 kbp smaller (5.35 kbp) and one was approximately 0.65 kpb larger (6.65 kpb) than the 6.0 kpb inserts. R-looping with Ha-SV RNA revealed that the small (5.35 kbp) insert contained one copy of the Ha-SV RNA. Preliminary restriction endonuclease digestion of the recombinant DNAs suggested that the middle-size inserts contained a 0.65-kbp tandem duplication of sequences present only one in the small-size insert; this duplication corresponded to the 0.65-kpb terminal duplication of the unintegrated linear Ha-SV DNA. The large-size insert apparently contained a tandem triplication of these terminally located sequences. DNA of all three sized inserts induced foci in NIH 3T3 cells, and focus-forming activity could be rescued from the transformed cells by superinfection with helper virus. Infectivity followed single-hit kinetics, suggesting that the foci were induced by a single molecule.     

Rapid purification of covalently closed circular DNAs of bacterial plasmids and animal tumor viruses

A rapid and simple purification of covalently closed circular (supercoiled) DNA from both bacterial clones (plasmids) and African green monkey cells (SV40) is presented. The method involves immediate treatment of lysed cells with sodium hydroxide, followed by neutralization and phenol extraction in high salt. After the extraction mixture is centrifuged, supercoiled DNA is found in the aqueous phase, the noncovalently closed DNA molecules form a white precipitate at the interphase, and proteins pellet. Contaminating RNA is eliminated from the aqueous phase by RNAse treatment and precipitation of the supercoiled DNA with polyethylene glycol. Residual polyethylene glycol is removed from the resuspended DNA by chloroform extraction. The purified supercoiled DNA is compatible with restriction enzymes, and is efficient at transforming both _χ1776 and HB101 bacterial hosts. Centrifugation in ethidium bromide-cesium chloride or sucrose gradients is not necessary. The method is virtually independent of the molecular size and gives good yields of supercoiled DNA. The technique is applicable to large-scale preparations and as a rapid “screening” procedure in which 20 to 30 samples can be easily purified within 5 to 6 h.     

Molecular analysis of parapoxvirus from a spotted seal Phoca largha in Japan

A spotted seal Phoca largha with nodular and scab lesions on the whole body was brought to an aquarium in Nagoya, Japan. We extracted DNA from the lesions and used the polymerase chain reaction (PCR) method for detecting orthopoxvirus and parapoxvirus DNA. Parapoxvirus but not orthopoxvirus DNA was detected. The partial nucleotide sequence of the envelope gene was determined from the PCR product, and the sequence was seen to be closely related to 2 parapoxvirus strains from spotted seals in Alaska, showing 100% identity at the amino acid level, with one nucleotide substitution. Virus-neutralizing (VN) antibody against canine distemper virus (CDV) was not detected in the serum, indicating that this individual was not infected with CDV or phocine distemper virus (PDV), which both have a high mortality rate for marine mammals. These results suggest that the lesions were caused by infection with pinniped parapoxvirus, and that the viruses spread and are maintained within the habitat range or populations of spotted seals from the Bering Sea to the Japan Sea. This is the first report of molecular analysis of parapoxvirus in marine mammals in Japan.     

Transfection of molecularly cloned Friend murine leukemia virus DNA yields a highly leukemogenic helper-independent type C virus.

Unintegrated viral DNA was isolated via the Hirt procedure from mouse fibroblasts newly infected with Friend murine leukemia virus (F-MuLV) clone 201, a biologically cloned helper virus isolated from stocks of F-MuLV complex. A physical map of the unintegrated in vivo linear viral DNA was generated for several restriction endonucleases. The supercoiled viral DNA was digested with EcoRI, which cleaved the viral DNA at a unique site. The linearized viral DNA was then inserted into lambda gtWES.lambda B at the EcoRI site and cloned in an approved EK2 host. Eight independent lambda-mouse recombinants were identified as containing F-MuLV DNA inserts by hybridization with F-MuLV 32P-labeled complementary DNA. One of the F-MuLV DNA inserts was 9.1 kilobases (kb) and had the same restriction enzyme sites as the unintegrated linear F-MuLV DNA. Six inserts were 8.5 kb; each lacked a single copy of the terminally redundant sequences of the unintegrated linear viral DNA. One insert was 8.2 kb and contained a 0.9-kb deletion. After digestion with EcoRI, one recombinant DNA preparation containing an 8.5-kb insert was infectious for NIH 3T3 cells. Undigested recombinant DNA was not infectious. The infectivity of the EcoRI-digested DNA followed multihit kinetics, indicating that more than one molecule was required to register as an infectious unit. The virus isolated from this transfection (F-MuLV-57) was NB-ecotropic, helper-independent, and formed XC plaques. Inoculation of this virus into newborn NIH Swiss mice induced leukemia and splenomegaly in greater than 90% of animals within 3 to 4 weeks. The gross and microscopic abnormalities induced by F-MuLV clone 57 were identical to those seen with the original parent stocks of F-MuLV clone 201. These results indicate that this helper-independent F-MuLV can induce a rapid nonthymic leukemia in the absence of the spleen focus-forming virus.     

PCR amplification of crude microbial DNA extracted from soil

A rapid, inexpensive, large-scale DNA extraction method involving minimal purification hasbeen developed that is applicable to various soil types. DNA was extracted from 100 g of soilusing direct lysis with glass beads and sodium dodecyl sulphate (SDS) followed by polyethyleneglycol precipitation, potassium acetate precipitation, phenol extraction and isopropanolprecipitation. The crude extract could be used in PCR directed at high-copy number (bacterialsmall subunit rRNA) and single-copy (fungal β-tubulin) genes.     

Multimeric forms of herpes simplex virus type 2 glycoproteins.

Molecular clones of closed circular DNA molecules of a mink cell focus-inducing murine leukemia virus (MCF-13 MuLV) were generated. Closed circular DNA molecules isolated from a Hirt extraction of recently infected NIH/3T3 cells were inserted at their unique EcoRI site into lambda gtWES.lambda B. Restriction endonuclease analysis of inserts of two clones indicated that they represented intact MCF-13 MuLV genomes. One viral insert contained two large terminal repeat sequences, and the other contained only one. A 300-base-pair DNA fragment located in the envelope region of the MCF-13 MuLV genome was determined to be related to xenotropic MuLV sequences.     

一种简便、快速从病毒感染鱼、虾组织中制备PCR模板的方法

以虹彩病毒(iridovirus)感染大黄鱼的脾组织、对虾白斑杆状病毒(whitespotsyndromebaculovirus,WSBV)感染中国对虾的肌肉组织为材料,采用一种简便、快速的方法获得了可满足病毒PCR检测的高质量模板DNA,分别以针对虹彩病毒、WSBV的特异性引物进行PCR扩增,均能有效扩增出预期的条带。与常规DNA病毒模板制备方法相比,具有简便、快速、提取率高、无污染等优点,尤其适用于水产动物病毒PCR检测试剂盒的商品化开发及生产实际应用。     

Methods for microbial DNA extraction from soil for PCR amplification

Amplification of DNA from soil is often inhibited by co-purified contaminants. A rapid, inexpensive, large-scale DNA extraction method involving minimal purification has been developed that is applicable to various soil types (1). DNA is also suitable for PCR amplification using various DNA targets. DNA was extracted from 100g of soil using direct lysis with glass beads and SDS followed by potassium acetate precipitation, polyethylene glycol precipitation, phenol extraction and isopropanol precipitation. This method was compared to other DNA extraction methods with regard to DNA purity and size.