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At least 199 records · Page 11Linked to original sources
PubMed2001

Leishmania mexicana: the circular DNA 1 (CD1) element contains genes encoding nucleotide-binding protein.

OBJECTIVE: To determine the nucleotide sequence of cloned CD1 fragments from Leishmania mexicana and find ORFs predicted to have protein coding function. METHODS: CD1 element was separated by CHEF and recovered by agarase, and the digested CD1 fragments were cloned into pZero vector. Nucleotide sequences were determined by the dideoxy chain termination method with the automatic sequencing system ALF using the M13 universal primers. Sequences were analyzed using GCG-PCGENE computer programs. RESULTS: The sequence with 4,385 nucleotides was determined and two ORFs were considered to have protein coding function (encoding nucleotide-binding protein). CONCLUSION: Genes encoding nucleotide-binding protein were identified from the amplified CD1 element of Leishmania mexicana.

Amino Acid Sequence↗
PubMed1983

Intracellular location of small circular DNA complexes in mammalian cell lines.

For determination of the cellular location of small polydisperse circular DNA complexes, rat myoblastic L6 cells, HeLa cells, and mouse L cells were enucleated and processed by the micapress-adsorption method for electron microscopy (H. Yamagishi, T. Kunisada, and T. Tsuda, 1982, Plasmid 8, 299-306). Small circular DNA complexes from intact cells showed a heterogeneous size distribution of from 0.1 to more than 2 micron with a mean contour length of 0.6 to 0.8 micron, like that of covalently closed circular DNAs. Cells contained 400 to 1200 copies. The size distribution in the cytoplasts was narrow and the number-average length was 0.3 to 0.4 micron, whereas that in L6 karyoplasts was wide and the average length was 0.9 micron. The longer circular complexes appeared to be absent from the cytoplasts. The origin and biological functions of these complexes are discussed in relation to the cellular locations of the complexes.

Animals↗
PubMed1980

Conformational transitions in closed circular DNA molecules. II. Biological implications.

A model of regulation of gene action based on the theory of conformational transitions in closed circular DNA molecules is proposed and discussed in connection with the mechanisms of cellular differentiation. The model predicts two main types of regulation of gene action (1) the change in the topological linking number of the DNA loops leading to the change in the amount of the DNA segments present in the transcriptionally active A-form and (2) the change of some nucleotide sequences in closed superhelical DNA loops resulting in conformational transitions of some of the other sequences in the same loop. The first type of regulation may explain the mechanism of terminal differentiation of the stem cells and the changes accompanying the malignant transformation. The second one may explain the variegated position effect of the gene and determination of the stem cells during ontogenesis.

Chromatin↗
PubMed2003

Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization.

DNA cyclization is potentially the most powerful approach for systematic quantitation of sequence-dependent DNA bending and flexibility. We extend the statistical mechanics of the homogeneous DNA circle to a model that considers discrete basepairs, thus allowing for inhomogeneity, and apply the model to analysis of DNA cyclization. The theory starts from an iterative search for the minimum energy configuration of circular DNA. Thermodynamic quantities such as the J factor, which is essentially the ratio of the partition functions of circular and linear forms, are evaluated by integrating the thermal fluctuations around the configuration under harmonic approximation. Accurate analytic expressions are obtained for equilibrium configurations of homogeneous circular DNA with and without bending anisotropy. J factors for both homogeneous and inhomogeneous DNA are evaluated. Effects of curvature, helical repeat, and bending and torsional flexibility in DNA cyclization are analyzed in detail, revealing that DNA cyclization can detect as little as one degree of curvature and a few percent change in flexibility. J factors calculated by our new approach are well consistent with Monte Carlo simulations, whereas the new theory has much greater efficiency in computations. Simulation of experimental results has been demonstrated.

Algorithms↗
PubMed1992

Detection of extrachromosomal circular DNA sequences from tumor cells by an alkaline lysis, Alu-polymerase chain reaction technique.

Extrachromosomal circular DNAs ranging in size from submicroscopic molecules of approximately 100 kb to cytogenetically resolvable structures of 1000+ kb called minute and double-minute chromosomes have been shown to harbor amplified genes in primary tumor cells, tumor cell lines, and drug-resistant cells grown in vitro. The presence of these molecules in transformed and malignant cells trends to reflect genetic instability and also suggests that role in tumor progression. Using a colon carcinoma cell line, we developed a technique to detect extrachromosomal circular DNA-specific sequences by Alu-polymerase chain reaction. Circular DNA was enriched by selective alkaline denaturation of genomic DNA. We have successfully performed this procedure with a minimum of 5 x 10(5) cells. The technique does not require any prior knowledge of the sequences located on the covalent circular DNA molecules for their detection. The procedure should be useful as a routine screen of primary tumor cells for the presence of extrachromosomal circular DNA and should permit the preparation of specific probes ot aid in their detailed characterizations.

Base Sequence↗
PubMed1980

HMG proteins (1 + 2) form beaded structures when complexed with closed circular DNA.

Structures bearing a resemblance to nucleosomes can be assembled by incubating calf thymus High Mobility Group proteins (1 + 2) with closed circular DNA. These HMG proteins are capable of forming beads and inducing superhelicity when bound to DNA. However, they do not protect from nuclease digestion the discrete DNA fragments characteristic of nucleosomes. The relationship between HMGs (1 + 2) and the "primitive" histone-like DNA-packaging proteins from prokaryotes and mitochondria is discussed.

Animals↗
PubMedDate not supplied

[Intramolecular compactization of circular DNA in interaction with dansyl hydrazide trivaline leading to a formation of a new type of structure--triple rings].

Compactization of supercoiled circular plasmid pBR322 caused by interaction with synthetic oligopeptide dansyl hydrazide trivaline capable of beta-structure formation was studied by electron microscopy. The results show that at rising input peptide concentration circular DNA molecules undergo intramolecular structural transition with the formation of compact ring structures. The compact ring structures are formed by the fiber having the thickness of 60 A. The analysis of morphology of intermediate structures and the contour length measurements enable us to conclude that 60 A-fiber contains three lying side-by-side and interwound double-stranded DNA segments. Thus, the compact ring structures are addressed to as triple rings. The triple ring have one special point, where the triple region ends are locked by a duplex DNA segment. The mechanisms responsible for the triple ring formation may be of importance for DNA and chromatin compactization processes in vivo.

DNA, Circular↗
PubMed1983

Quantitative binding of covalently closed circular DNA to nitrocellulose in NaI.

A procedure for quantitatively binding covalently closed circular DNA to nitrocellulose is detailed. The procedure involves making DNA saturated with respect to Nat at 25 degrees C, denaturing the DNA by heating to 80-100 degrees C, then passing the DNA-NaI solution through a nitrocellulose membrane at 50-60 degrees C. Form I DNA remains denatured throughout the loading procedure and is quantitatively deposited on the membrane as denatured DNA. The mechanism of binding DNA to nitrocellulose in NaI appears to be different from the binding promoted by NaCl.

Collodion↗