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PubMed1979

Extrachromosomal circular ribosomal DNA in the yeast Saccharomyces carlsbergensis.

Purified ribosomal DNA from Saccharomyces carlsbergensis contains a small proportion of circular DNA molecules with a contour length of 3 micron or integral multiples thereof. Hybridization of yeast ribosomal DNA with 26 S rRNA, using the R-loop technique, reveals that these circular molecules contain sequences complementary to yeast ribosomal RNA. We suggest that these extrachromosomal rRNA genes may be intermediates in the amplification of rRNA genes in yeast.

DNA, Circular↗
PubMed1995

Characterization of fully 2'-modified oligoribonucleotide hetero- and homoduplex hybridization and nuclease sensitivity.

The nuclease stability and melting temperatures (Tm) were compared for fully modified oligoribonucleotide sequences containing 2'-fluoro, 2'-O-methyl, 2'-O-propyl and 2'-O-pentyl nucleotides. Duplexes formed between 2' modified oligoribonucleotides and RNA have typical A-form geometry as observed by circular dichroism spectroscopy. Modifications, with the exception of 2'-O-pentyl, were observed to increase the Tm of duplexes formed with complementary RNA. Modified homoduplexes showed significantly higher Tms, with the following Tm order: 2'-fluoro:2'fluoro > 2'-O-propyl:2'-O-propyl > 2'-O-methyl:2'-O- methyl > RNA:RNA > DNA:DNA. The nuclease stability of 2'-modified oligoribonucleotides was examined using snake venom phosphodiesterase (SVPD) and nuclease S1. The stability imparted by 2' modifications was observed to correlate with the size of the modification. An additional level of nuclease stability was present in oligoribonucleotides having the potential for forming secondary structure, but only for 2' modified oligoribonucleotides and not for 2'-deoxy oligoribonucleotides.

Base Sequence↗
PubMedDate not supplied

[Circular transcription map of the plasmid pBR322].

The plasmid pBR322 transcription in the isolated E. coli DNA-dependent RNA-polymerase system was studied. Transcription regions as well as transcripts orientation were defined using both the technique of "criss-cross" hybridization and the annealing of RNA-products with L- and H-strands of plasmid. Summing up obtained data together with available data on promoter localization a circular transcription map of plasmid pBR322 was constructed. Effects of heparin, ion strength and E. coli S-30 system on in vitro transcripts were also studied. The 110-long RNA transcript synthesized in Ori region of pBR322 was found to be the most sensitive to all these factors. RNA-transcripts obtained in in vitro system are able to direct protein synthesis in cell-free S-30 system.

Autoradiography↗
PubMed1985

Rapid alkaline preparation for yeast circular covalently closed DNA molecules.

The alkaline preparation of prokaryotic plasmids (Birnboim and Doly, 1979) has been here adapted to yeast. By simple denaturation and renaturation steps we recovered, from Saccharomyces cerevisiae and Schizosaccharomyces pombe, a population of nucleic acid molecules highly enriched in circular forms. In S. cerevisiae killer strains it is possible to copurify double stranded RNA molecules. The overall recovery was estimated to be 10-30% of the total circular molecules.

DNA, Circular↗
PubMed2005

Scalable recovery of plasmid DNA based on aqueous two-phase separation.

Future developments in gene therapy and DNA vaccination depend on cost-effective large-scale production of pharmaceutical-grade pDNA (plasmid DNA). Given the large amount of impurities present in the feedstock, purification processes that have high specificity and capacity at a moderate cost are required. In the present study, we describe a non-chromatographic procedure based on aqueous two-phase extraction allowing a fast and simply scalable capture step. PEG [poly(ethylene glycol)] in combination with potassium citrate or potassium phosphate was tested as phase component for extraction. By increasing either PEG or salt concentration, the partitioning of nucleic acids changed from bottom to top phase. Phase systems with a composition of 15% PEG 800 and 20% potassium phosphate at pH 7.0 showed a strong partitioning of pDNA to the bottom phase, linked to a clear decrease in open circular pDNA, while proteins, genomic DNA and RNA remain at the top or at the interphase. A great advantage of the current process is that the complete procedure of lysis, precipitation, clarification and extraction can be performed in a single vessel. The number of denatured and sheared genomic DNAs in a spiking experiment was found to be depleted by more than 99%.

Chemical Fractionation↗
PubMed1984

Nucleotide sequence of cucumber pale fruit viroid: homology to hop stunt viroid.

Double stranded cDNA of cucumber pale fruit viroid ( CPFV ) has been cloned by the method of Okayama and Berg (Mol.Cell.Biol.2,161-170 (1982] and the complete nucleotide sequence was established. The covalently closed circular molecules of single-stranded CPFV RNA consists of 303 nucleotides. The nucleotide sequence of CPFV was compared with the previously established sequence of hop stunt viroid (HSV), which consists of 297 nucleotides ( Ohno et al. Nucleic Acid Res.11,6185-6197 (1983]. CPFV differs from HSV in the nucleotide sequence at 16 positions which include 8 exchanges, 7 insertions and 1 deletion. Both viroids share about 95% sequence homology. Considering the pathogenic properties of both viroids together, it is concluded that CPFV is a cucumber isolate of HSV.

Base Sequence↗
PubMed1985

An in vitro system for accurate transcription initiation of chloroplast protein genes.

We have developed an homologous in vitro system from spinach chloroplasts that correctly initiates transcription of the plastid genes for the large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL) and the beta subunit of the plastid ATPase (atpB). The transcriptionally active extracts from spinach chloroplasts require circular DNA templates for specific initiation. The RNA polymerase activity is insensitive to rifampicin. The extent of transcription in vitro is a function of the extract:template ratio. The efficiency of the rbcL transcription in vitro is more than one transcript per one hundred templates per hour.

Cell-Free System↗
PubMed1990

In vitro infection of human hepatoma (HepG2) cells with hepatitis B virus.

An in vitro system for production of hepatitis B virus (HBV) was established by infection of human hepatoma (HepG2) cells. HBV particles obtained from the serum of a chronic hepatitis B surface antigen (subtype ad) carrier were used to inoculate HepG2 cells. HBV envelope and core proteins were synthesized de novo by the infected cells and secreted into the medium 3 to 6 days postinfection. Viral covalently closed circular DNA, the putative template for viral RNA transcription, accumulated in the cells with increasing time postinfection. The HBV-infected HepG2 cells were maintained for several months (HepG2-BV cell line) and continued producing viral antigens. Both HBV DNA replicative intermediates and major HBV transcripts were identified in HepG2-BV cells. Complete HBV particles, which contain HBV DNA and DNA polymerase activity and express the three antigenic specificities of the envelope (hepatitis B surface antigen, pre-S2, and pre-S1), were released into the culture supernatant. Thus, successful in vitro infection of transformed human hepatocytes raising stable HBV-producing cells was achieved for the first time. This strongly suggests that HepG2 cells have a receptor(s) for virus attachment and penetration. Such a system represents a significant advance for the study of HBV-target cell interactions as the early events of HBV infection.

Blotting, Northern↗
PubMed2004

Influence of mutations in the hepatitis B virus genome on virus replication and drug resistance--implications for novel antiviral strategies.

Persistent infection with the hepatitis B virus (HBV) represents a major health problem worldwide with over 350 million patients at risk of developing liver cirrhosis or hepatocellular carcinoma. HBV is a small, partially double-stranded DNA virus with four overlapping genes and a unique life cycle, creating an intracellular pool of covalently closed circular DNA molecules for persistence and an RNA template for replication via reverse transcription. Mutations occur frequently, and particular selection pressures, both endogenous (host immune clearance) and exogenous (vaccines and antivirals), readily select escape mutants. For example, HBeAg-negative chronic HBV infection with either basal core promoter or precore mutations is predominant in many parts of the world. Therapy of HBV infection with the nucleoside analogue lamivudine frequently leads to the selection of drug-resistant strains with polymerase mutations. Treatment options for chronic HBV infection include at present either interferon-alpha or the oral nucleos(t)ide analogues lamivudine or adefovir. However, these drugs have drawbacks, including possible serious side effects and low response rates in HBeAg-negative patients in the case of interferon or recurrence of viremia after cessation of therapy and development of escape mutants after a long period of treatment with nucleoside inhibitors. Recent advances of in vitro and in vivo models allow to study new antiviral strategies, including novel nucleoside analogues, nucleocapsid inhibitors or small interfering RNA. This review summarises the impact of clinically relevant mutations in the HBV genome on viral replication and drug sensitivity, the current status of therapy and promising future perspectives on novel drug regimens.

Animals↗
PubMed1980

Purification and characterization of nuclease beta from Ustilago maydis.

A nuclease highly active on single-stranded DNA has been purified 11,200-fold from Ustilago maydis. The enzyme has a sedimentation coefficient of 4.3 S and a Stokes radius of 36 A. The native form of the enzyme appears to be a single polypeptide chain of 68,000 daltons. The enzyme is fully active in the presence of chelating agents but is strongly inhibited by nucleotides. Maximal activity is seen at pH 6. The enzyme hydrolyzes linear DNA in an exonucleotytic fashion from the 5' end liberating 3'-mononucleotides and small oligonucleotides. Degradation of DNA takes place through a distributive mode rather than a processive mode. The enzyme is also active on both single-stranded and duplex circular DNA, dephosphorylates 5'-nucleotides, and hydrolyzes RNA.

Basidiomycota↗
PubMed1996

A synthetic model for triple-helical domains in self-splicing group I introns studied by ultraviolet and circular dichroism spectroscopy.

Structural studies were performed on synthetic oligonucleotides with sequences corresponding to the P4/P6 and J3/4, J6/7 regions of the self-splicing group I intron of the bacteriophage T4 nrdB pre-mRNA, which correspond to the proposed triple-helical domain in the Tetrahymena thermophila intron. A 23-mer RNA was synthesized as a mixed ribo-deoxyribo oligonucleotide, modeling an expected base-paired region of P4 along with the J3/4 and P6 (5'-end bases of P6) regions. strand modeling the 3'-end bases of P6 and J6/7 regions, with which a triple helix may form, was synthesized as a pure oligoribonucleotide (7-mer RNA). The interactions of these oligonucleotides have been characterized by UV and circular dichroism (CD) spectroscopy. The results show that the 23-mer RNA forms a stable hairpin modeling the P4 base-paired region. Triple helix association between the 23-mer RNA hairpin and the 7-mer RNA single strand was detected by CD in the presence of Mg2+ (>5mM) but not in presence of a monovalent cation like Na+ (up to 500 mM). Studies on selected variants of both 7-mer and 23-mer RNAs were carried out. The results show that for the association of the two partner strands not only the formation of P6 helix but also triplet interactions between two strands are required. The association of the two strands in general follow a pattern predicted by comparative sequence analysis. Parallel studies on pure oligoribonucleotides having base sequence corresponding to those of the oligoribonucleotides showed no evidence of association under similar conditions, which could indicate that the 2'-hydroxyl groups of the riboses might play an important role in hydrogen bonding to form the required nucleoside triples. Molecular modeling studies on the proposed "plaited triple helix" formed by the association of the 23-mer RNA hairpin and 7-mer RNA single strand showed that the structure is sterically and energetically feasible.

Animals↗
PubMed2005

Synthesis and hybridization studies of oligonucleotides containing 1-(2-deoxy-2-alpha-C-hydroxymethyl-beta-D-ribofuranosyl)thymine (2'-alpha-hm-dT).

We report the first investigation of oligoribonucleotides containing a few 1-(2-deoxy-2-alpha-C-hydroxymethyl-beta-D-ribofuranosyl)thymine units (or 2'-hm-dT, abbreviated in this work as 'H'). Both the 2'-CH2O-phosphoramidite and 3'-O-phosphoramidite derivatives of H were synthesized and incorporated into both 2',5'-RNA and RNA chains. The hybridization properties of the modified oligonucleotides have been studied via thermal denaturation and circular dichroism studies. While 3',5'-linked H was shown previously to significantly destabilize DNA:RNA hybrids and DNA:DNA duplexes (modification in the DNA strand; DeltaT(m) approximately -3 degrees C/insert), we find that 2',5'-linked H have a smaller effect on 2',5'-RNA:RNA and RNA:RNA duplexes (DeltaT(m) = -0.3 degrees C and -1.2 degrees C, respectively). The incorporation of 3',5'-linked H into 2',5'-RNA:RNA and RNA:RNA duplexes was found to be more destabilizing (-0.7 degrees C and -3.6 degrees C, respectively). Significantly, however, the 2',5'-linked H units confer marked stability to RNA hairpins when they are incorporated into a 2',5'-linked tetraloop structure (DeltaT(m) = +1.5 degrees C/insert). These results are rationalized in terms of the compact and extended conformations of nucleotides.

Circular Dichroism↗
PubMed2003

Effect of transcription on folding of the Tetrahymena ribozyme.

Sequential formation of RNA interactions during transcription can bias the folding pathway and ultimately determine the functional state of a transcript. The kinetics of cotranscriptional folding of the Tetrahymena L-21 ribozyme was compared with refolding of full-length transcripts under the same conditions. Sequential folding after transcription by phage T7 or Escherichia coli polymerase is only twice as fast as refolding, and the yield of native RNA is the same. By contrast, a greater fraction of circularly permuted variants folded correctly at early times during transcription than during refolding. Hybridization of complementary oligonucleotides suggests that cotranscriptional folding enables a permuted RNA beginning at G303 to escape non-native interactions in P3 and P9. We propose that base pairing of upstream sequences during transcription elongation favors branched secondary structures that increase the probability of forming the native ribozyme structure.

Animals↗
PubMed1989

Extrahepatic replication of woodchuck hepatitis virus in chronic infection.

We describe studies of woodchuck hepatitis virus nucleic acids in liver and other tissues of chronically infected woodchucks, using Southern and Northern blot hybridization techniques. Single-stranded and covalently closed circular replicative DNA molecules were distinguished from partly double-stranded virus genomes. In most animals the liver contained more virus than any other organ, but all extrahepatic organs studied (spleen, thymus, pancreas, and kidney) contained viral DNA and significant amounts of viral RNA. In the spleen, partly double-stranded virus genomes were present at higher levels than in any other organ but liver, but nonetheless replicative intermediates were not detected. The observation of RNA transcripts in the absence of detectable covalently closed circular DNA template suggests that a small proportion of cells in extrahepatic tissues are infected with WHV.

Animals↗
PubMed1991

Mutations affecting hepadnavirus plus-strand DNA synthesis dissociate primer cleavage from translocation and reveal the origin of linear viral DNA.

Hepadnaviruses replicate their circular DNA genomes via reverse transcription of an RNA intermediate. The initial product of reverse transcription, minus-strand DNA, contains two copies of a short direct repeat (DR) sequence, termed DR1 and DR2. Plus-strand DNA synthesis initiates at DR2 on minus-strand DNA, using as a primer a short, DR1-containing oligoribonucleotide derived by cleavage and translocation from the 5' end of pregenomic RNA. To clarify the sequence requirements for plus-strand primer cleavage and translocation, we have constructed mutants of the duck hepatitis B virus bearing base changes in or around the DR1 sequence in the primer. A point mutation at the terminal nucleotide of DR1 has a striking phenotype: normal levels of duplex viral DNA are produced, but nearly all of the DNA is linear rather than circular. Mapping of the 5' end of plus-strand DNA reveals that primer cleavage occurs with normal efficiency and accuracy, but the primer is not translocated to DR2; rather, it is extended in situ to generate duplex linear DNA. Other mutations just 3' to DR1 similarly affect primer translocation, although with differing efficiencies. Linear DNA found in wild-type virus preparations has the same fine structure as the mutant linears described above. These results indicate that (i) plus-strand primer cleavage and translocation are distinct steps that can be dissociated by mutation, (ii) lesions in sequences not included in the primer can severely inhibit primer translocation, and (iii) elongation of such untranslocated primers is responsible for the variable quantities of linear DNA that are found in all hepadnaviral stocks.

Animals↗
PubMed1989

A photoreversible phytochrome affinity column chromatography for putative phytochrome receptor studies.

Using a photoreversible phytochrome affinity column, we have isolated a small RNA molecule that binds to the affinity column. The RNA was identified by a A260/A280 ratio of 2.0, hypochromicity, orcinol, ribonuclease A and DNase tests. Agarose gel electrophoresis and circular dichroic spectral characteristics also indicate it to be a small RNA molecule. The successful preparation of a photoreversible phytochrome affinity column, the possible usage of the column and the significance of the RNA binding have been discussed.

Chromatography, Affinity↗
PubMed1995

Inhibition of duck hepatitis B virus DNA replication by antiviral chemotherapy with ganciclovir-nalidixic acid.

The aim of this study was to examine the effects of ganciclovir and nalidixic acid either alone or in combination on duck hepatitis B virus DNA replication in vivo with particular reference to production of viral supercoiled DNA and RNA. The most effective antiviral response was observed in the livers of ducks treated by the combination therapy for 28 days, which resulted in a substantial decrease in the amounts of viral supercoiled DNA, relaxed circular and single-stranded DNA, and also viral RNA. This combination treatment was not hepatotoxic over the study period.

Animals↗