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At least 55 records · Page 3Linked to original sources
PubMed1999

Regulated formation of extrachromosomal circular DNA molecules during development in Xenopus laevis.

Extrachromosomal circular DNA molecules of chromosomal origin have been detected in many organisms and are thought to reflect genomic plasticity in eukaryotic cells. Here we report a developmentally regulated formation of extrachromosomal circular DNA that occurs de novo in preblastula Xenopus embryos. This specific DNA population is not detected in the male or female germ cells and is dramatically reduced in later developmental stages and in adult tissues. The activity responsible for the de novo production of extrachromosomal circles is maternally inherited, is stored in the unfertilized egg, and requires genomic DNA as a template. The formation of circular molecules does not require genomic DNA replication but both processes can occur simultaneously in the early development. The production of extrachromosomal circular DNA does not proceed at random since multimers of the tandemly repeated sequence satellite 1 were over-represented in the circle population, while other sequences (such as ribosomal DNA and JCC31 repeated sequence) were not detected. This phenomenon reveals an unexpected plasticity of the embryonic genome which is restricted to the early developmental stage.

Animals↗
PubMed1999

Chemical ligation of oligodeoxyribonucleotides on circular DNA templates.

We report the use of small circular DNA as a triplex-directing template for the highly efficient chemical ligation of oligodeoxyribonucleotides (ODNs) using cyanogen bromide (BrCN). These investigations compared the use of a linear homopyrimidine DNA template (17mer) and a circular pyrimidine-rich DNA template (44mer) for directing the chemical ligation of two homopurine ODNs (6mer + 11mer). The effects of substrate/template ratio, buffer, salt, ionic strength, pH and temperature have been examined in the BrCN activated ligation reactions. The optimal yield of 51% for ligation on the linear template was at pH 6.0, 200 mM MgCl2, 4 degreesC. In contrast, near quantitative ligation on the circular template occurred at higher pH, higher temperature, and showed less dependence on Mg2+concentration (97% yield, pH 7.5, 200 mM MgCl2, 25 degreesC). The relative observed rate of the ligation reaction was a minimum of 35 times faster on the circular DNA template relative to the linear template at pH 7.5, 200 mM MgCl2, 4 degreesC. These investigations reveal that chemical ligation of short ODNs on circularized DNA templates through triplex formation is a highly efficient process over a broad range of conditions.

Base Pairing↗
PubMed1984

Sequence repetition and genomic distribution of small polydisperse circular DNA purified from HeLa cells.

Covalently closed circular DNA molecules (cccDNA) from the human HeLa cell line were purified (96% pure by weight) by use of ATP-dependent deoxyribonuclease, and cloned into the HindIII site of phage lambda vector Charon 7. From the cccDNA library thus obtained, nine recombinants carrying mitochondrial DNA and 36 recombinants carrying small polydisperse circular (spc) DNA were picked at random for subsequent tests. The inserted fragments of spcDNA ranged in size from 0.6 to 7.6 kb with a mean length of 1.9 kb, a value which is the same as the average length of spcDNA. Analysis of the cloned spcDNA fragments revealed that (a) all the spcDNA clones investigated shared homologies with chromosomal DNA sequences, (b) all but one cloned DNA contained repetitive sequences, (c) the sequence organization could be roughly classified according to the reiteration frequency as greater than 10(5) (Alu family class), 10(4) to 10(5) (KpnI family class), 10(3) to 10(4) (mitochondrial DNA class) and less than 10(3) times per haploid genome, and (d) most of the repetitive sequences were dispersed in the genome, although some appeared clustered.

Cloning, Molecular↗
PubMed1978

A new method for the purification and identification of covalently closed circular DNA molcules.

A new technique has been developed for the rapid isolation of covalently closed circular DNA molecules. The procedure is a selective extraction based on differences in the partitioning of covalently closed circular DNA molecules and noncovalently closed species between phenol and water at acid pH and low ionic strength. Under the conditions described, linear as well as nicked circular DNA is extracted into phenol, while covalently closed circular DNA molecules remain in the water phase. The method permits the quantitative isolation of covalently closed circular DNA from either total cellular DNA or partially purified preparations, to a degree of purity comparable with buoyant density procedures.

DNA, Circular↗
PubMed1991

Electrophoretic size separations in liquified agarose of polystyrene particles and circular DNA.

Polystyrene sulfate particles of 0.37 to 1.78 mu in diameter are retarded in their electrophoretic migration in proportion to the concentration of agarose liquified above its gelling temperature. In the concentration range of 0.02 to 0.2% liquified agarose, the degree of this retardation in electrophoresis at 40 degrees C is inversely related to particle size. By contrast, mitochondrial DNA (16 kb), plasmid pBR322 DNA (4 kb) and plasmid PSA509 DNA (3 kb) exhibit under the same conditions a degree of retardation which is proportional to their size. This confirms the existence of two divergent mechanisms of size separation similarly observed in other liquid polymer media, i.e. one based on collisions with the gel fiber (molecular sieving) and one based on exclusion from the fiber network (the electrophoretic equivalent of gel permeation).

DNA, Circular↗
PubMed1995

Unwinding of closed circular DNA by the Escherichia coli RuvA and RuvB recombination/repair proteins.

The RuvA and RuvB proteins of Escherichia coli promote the branch migration of Holliday junctions during genetic recombination and the recombinational repair of damaged DNA. Using a topological assay that measures the underwinding of covalently closed duplex DNA, we find that RuvA and RuvB promote the transient unwinding of relaxed or supercoiled DNA. Detection of unwinding by RuvAB requires the presence of ATP and a non-hydrolysable ATP analogue (ATP gamma S), and was not observed in the presence of ATP or ATP gamma S alone. These results indicate that RuvAB catalyse the unwinding and rewinding of duplex DNA via an intermediate that can be stabilised by the presence a non-hydrolysable cofactor. At elevated concentrations of Mg2+ (12 to 30 mM), which are known to favour RuvB binding to DNA without the need for RuvA, RuvB protein alone promotes DNA unwinding. These results show that RuvB protein, an ATPase that forms hexameric ring structures that encircle the DNA, is directly responsible for the DNA unwinding activity exhibited by RuvAB. From these results, we propose that branch migration of Holliday junctions by RuvAB occurs by the passage of double-stranded DNA through the RuvAB complex, in a reaction coupled to transient DNA unwinding.

Adenosine Triphosphate↗
PubMed1994

The evolutionary origin of the 35 kb circular DNA of Plasmodium falciparum: new evidence supports a possible rhodophyte ancestry.

In common with other Apicomplexan parasites, Plasmodium falciparum carries two extrachromosomal DNAs, one of which, the 6 kb element, is undoubtedly mitochondrial. The second, generally referred to as the 35 kb circle, is of unknown provenance, but the nature and organization of its genetic content makes a mitochondrial association unlikely and the molecule has features reminiscent of plastid genomes. We now report the occurrence on the circle of an open reading frame specifying a predicted 470 amino acid protein that shares more than 50% identity with a gene currently known only on the plastome of red algae. This high degree of conservation confirms the 35 kb circle's plastid ancestry, and we speculate that it may have originated from the rhodoplast of an ancient red algal endosymbiont in the progenitor of the Apicomplexa.

Amino Acid Sequence↗