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At least 721 records · Page 40Linked to original sources
PubMed2006

Mismatch repair factor MSH2-MSH3 binds and alters the conformation of branched DNA structures predicted to form during genetic recombination.

Genetic studies in Saccharomyces cerevisiae predict that the mismatch repair (MMR) factor MSH2-MSH3 binds and stabilizes branched recombination intermediates that form during single strand annealing and gene conversion. To test this model, we constructed a series of DNA substrates that are predicted to form during these recombination events. We show in an electrophoretic mobility shift assay that S. cerevisiae MSH2-MSH3 specifically binds branched DNA substrates containing 3' single-stranded DNA and that ATP stimulates its release from these substrates. Chemical footprinting analyses indicate that MSH2-MSH3 specifically binds at the double-strand/single-strand junction of branched substrates, alters its conformation and opens up the junction. Therefore, MSH2-MSH3 binding to its substrates creates a unique nucleoprotein structure that may signal downstream steps in repair that include interactions with MMR and nucleotide excision repair factors.

Adenosine Triphosphate↗
PubMedDate not supplied

[A comparative study of the DNA structural damages and synthesis in embryos of the silkworm Bombyx mori irradiated with gamma rays at different developmental stages].

Studies have been made on formation and reparation of apurine-apyrimidine (AP) regions, monothread DNA ruptures, as well as on inhibition and recovery of DNA synthesis in gamma-irradiated 3- and 7-day embryos of the silkworm which sharply differ in their radiosensitivity. It was shown that in 3-day embryos, the number of AP regions and DNA ruptures immediately after irradiation is significantly higher than in 7-day embryos. DNA synthesis is more radiosensitive in 3-day embryos as compared to that in 7-day ones. Kinetics of postradiation recovery of regions and DNA ruptures in 3- and 7-day embryos is heterogeneous and significantly different. However, radiation inhibition and postradiation recovery of DNA synthesis in irradiated 3- and 7-day embryos are associated mainly with postradiation survival of these embryos.

Animals↗
PubMed1995

The distribution of ND genes in yeast mitochondrial genomes and the mitochondrial DNA structure of Pichia membranaefacens.

For long time, it has been believed that the yeast mitochondrial (mt) genome lacks NADH dehydrogenase subunit genes which are designated ND genes. However, our complete mtDNA sequencing of yeast Hansenula wingei led us to the first finding of seven mitochondrial ND genes. We investigated the distribution of ND genes in mtDNAs of other yeasts including Pichia membranaefaciens, Yarrowia lypolitica, Candida maltosa, Saccharomyces kluyveri and Saccharomyces exiguus. By Southern hybridization with probes of H. wingei's ND1, 2 and 5 genes, we detected positive signals on mtDNAs in P. membranaefaciens, Y. lypolitica, and C. maltosa. To confirm this, we cloned and sequenced DNA fragment of ND5 gene in P. membranaefaciens. We have discussed the sequence homology and genome structure.

Base Sequence↗
PubMed1991

Chromosome structure: DNA nucleotide sequence elements of a subset of the minichromosomes of the protozoan Trypanosoma brucei.

The genome of the protozoan Trypanosoma brucei contains a set of about 100 minichromosomes of about 50 to 150 kb in size. The small size of these chromosomes, their involvement in antigenic variation, and their mitotic stability make them ideal candidates for a structural analysis of protozoan chromosomes and their telomeres. We show that a subset of the minichromosomes is composed predominantly of simple-sequence DNA, with over 90% of the length of the minichromosome consisting of a tandem array of 177-bp repeats, indicating that these molecules have limited protein-coding capacity. Proceeding from the tip of the telomere to a chromosome internal position, a subset of the minichromosomes contained the GGGTTA telomere repeat, a 29-bp telomere-derived repeat, a region containing 74-bp G + C-rich direct repeats separated by approximately 155 bp of A + T-rich DNA that has a bent character, and 50 to 150 kb of the 177-bp repeat. Several of the minichromosome-derived telomeres did not encode protein-coding genes, indicating that the repertoire of telomeric variant cell surface glycoprotein genes is restricted to some telomeres only. The telomere organization in trypanosomes shares striking similarities to the organization of telomeres and subtelomeres in humans, yeasts, and plasmodia. An electron microscopic analysis of the minichromosomes showed that they are linear molecules without abnormal structures in the main body of the chromosome. The structure of replicating molecules indicated that minichromosomes probably have a single bidirectional origin of replication located in the body of the chromosome. We propose a model for the structure of the trypanosome minichromosomes.

Animals↗
PubMedDate not supplied

Radioadapted chicken embryo cells: challenge specificity and alterations in higher-order DNA structure.

Radioadapted chicken embryo cells (X-irradiation in ovo with 10 cGy at the 14th day of development with priming periods of 24 h) were treated in vitro by challenge doses of 14 different DNA- and/or chromatin-interactive agents, including X-rays. A decrease in the cellular damage, as measured by scheduled DNA synthesis, was only observed with X-irradiation. Sedimentation of nucleoids as well as viscosity of alkaline lysates from ethidium bromide (0.35-400 micrograms/ml)-, novobiocin (125-1800 micrograms/ml)-, and hyperthermia (30 min at 43 degrees and 45 degrees)-treated cells suggest a higher tendency of radioadapted cells to undergo positive DNA supercoiling. When DNA from adapted and non-adapted chicken embryo cells was used as substrate, neither its digestion by DNase I nor the inhibition of DNase I activity by various DNA-interactive agents was changed in primed cells. From the previous investigations as well as from the present results it is concluded that an increase of tightening of protein-DNA interactions within the nuclear matrix is a molecular determinant of the elevated radiation resistance in radioadapted chicken embryo cells.

Animals↗
PubMed1996

Differential association of HMG1 and linker histones B4 and H1 with dinucleosomal DNA: structural transitions and transcriptional repression.

We examined the structural and functional consequences of incorporating either histone H1, histone B4 or HMG1 into a synthetic dinucleosome containing two 5S rRNA genes. We found that all three proteins bind to linker DNA, stabilizing an additional 20 bp from micrococcal nuclease digestion and restrict nucleosome mobility. Histone H1 has the highest-affinity interaction with the dinucleosome; histone B4 and HMG1 associate with significantly reduced affinities. We found that histone H1 binds to the dinucleosome template with a dissociation constant (KD) of 7.4 nM, whereas the KD is 45 nM for histone B4 and 300 nM for HMG1. The KDs for the interaction of these proteins with naked DNA are 18 nM for H1, 80 nM for B4 and 300 nM for HMG1. The differences in association of these proteins with the dinucleosome are reflected in the efficiency with which the different proteins repress transcription from the 5S rRNA genes. Thus, although all three proteins can contribute to the organization of chromatin, the stability of the structures they assemble will vary. Our results provide a molecular explanation for the transcriptional promiscuity of Xenopus early embryonic chromatin, which is enriched in HMG1 and linker histone B4, but deficient in histone H1.

Animals↗
PubMed2005

Crystal structure and DNA binding functions of ERCC1, a subunit of the DNA structure-specific endonuclease XPF-ERCC1.

Human XPF-ERCC1 is a DNA endonuclease that incises a damaged DNA strand on the 5' side of a lesion during nucleotide excision repair and has additional role(s) in homologous recombination and DNA interstrand crosslink repair. We show that a truncated form of XPF lacking the N-terminal helicase-like domain in complex with ERCC1 exhibits a structure-specific endonuclease activity with similar specificity to that of full-length XPF-ERCC1. Two domains of ERCC1, a central domain and a C-terminal tandem helix-hairpin-helix (HhH2) dimerization domain, bind to ssDNA. The central domain of ERCC1 binds ssDNA/dsDNA junctions with a defined polarity, preferring a 5' single-stranded overhang. The XPF-ERCC1 HhH2 domain heterodimer contains two independent ssDNA-binding surfaces, which are revealed by a crystal structure of the protein complex. A crystal structure of the central domain of ERCC1 shows its fold is strikingly similar to that of the nuclease domains of the archaeal Mus81/XPF homologs, despite very low sequence homology. A groove lined with basic and aromatic residues on the surface of ERCC1 has apparently been adapted to interact with ssDNA. On the basis of these crystallographic and biochemical studies, we propose a model in which XPF-ERCC1 recognizes a branched DNA substrate by binding the two ssDNA arms with the two HhH2 domains of XPF and ERCC1 and by binding the 5'-ssDNA arm with the central domain of ERCC1.

Animals↗
PubMed1984

DNA structural variations in the E. coli tyrT promoter.

X-ray studies have established that the structure of a right-handed, Watson-Crick double helix can change from place to place along its length as a function of base sequence. The base pairs transmit deformations out to the phosphate backbone, where they can then be recognized by proteins and other DNA-binding reagents. Here we have examined at single-bond resolution the interactions of three commonly used nucleases (DNAase I, DNAase II, and copper-phenanthroline) with a DNA of natural origin, the 160 bp tyrT promoter. All three of these reagents seem sensitive to DNA backbone geometry rather than base sequence per se. Their sequence-dependent patterns of cleavage provide evidence for structural polymorphism of several sorts: global variation in helix groove width, global variation in radial asymmetry, and local variation in phosphate accessibility. These findings explain how sequence zones of a certain base composition, or purine-pyrimidine asymmetry, can influence the recognition of DNA by protein molecules.

Base Sequence↗
PubMed2002

Further insight in the photochemistry of DNA: structure of a 2-imidazolone (5-4) pyrimidone adduct derived from the mutagenic pyrimidine (6-4) pyrimidone photolesion by UV irradiation.

Pyrimidine (6-4) pyrimidone photoproducts represent one of the major mutagenic and carcinogenic class of DNA damage produced by UV exposure. At present, besides their conversion to their Dewar valence isomer, (6-4) photoproducts are generally believed to be photostable, and the observed biological properties of Paterno-Büchi-derived photoproducts are, thus far, exclusively attributed to these two types of compounds. Using a model system (2) relevant to DNA photochemistry, we have observed that the 5'-base moiety of the (6-4) thymine dimer 3, under far-UV radiation, is able to undergo a ring contraction leading to a 2-oxoimidazoline, 1. This unprecedented secondary photochemical reaction constitutes the first report of a major photomodification affecting (6-4) photoproducts and strongly questions the biological stability of the (6-4) adducts under UV light with 2-imidazolone (5-4) pyrimidone adducts being possibly another source of endogenous DNA damage.

DNA↗