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At least 775 records · Page 43Linked to original sources
PubMed2000

Complementary DNA structure and genomic organization of Drosophila menin.

Menin is a protein product of a tumor supressor gene MEN1, mutations of which are responsible for multiple endocrine neoplasia type 1, an autosomal dominant familial cancer syndrome. We determined the nucleotide sequence of the Drosophila menin cDNA using RT-PCR and RACE, and confirmed it by direct sequencing of genomic DNA. Gene expression of Drosophila menin was detected by Northern blot analysis in adult and embryo as two types of transcripts, one identical in size to the cDNA, and the other larger but detected only in embryo. The Drosophila menin gene was composed of five exons in which the protein was encoded in exon 2 through 5, and spanned approximately 6.3 kb. The deduced amino acid (AA) sequence of Drosophila menin consisted of 751 AAs with a calculated molecular mass of 81.7 kDa, and showed 44-47% identity to human, rat, mouse and zebrafish menin over the entire length. Among the AA residue substitutions that have been reported as disease-associated missense mutations and single AA deletions, 53 out of 71 were completely conserved in Drosophila. The presence of menin ortholog in insect indicates that menin is an evolutionally conserved protein with a fundamental role in biological processes.

Amino Acid Sequence↗
PubMed2003

Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad.

The solution structure of a cyclic oligonucleotide d has been determined by two-dimensional NMR spectroscopy and restrained molecular dynamics. Under the appropriate experimental conditions, this molecule self-associates, forming a symmetric dimer stabilized by four intermolecular Watson-Crick base pairs. The resulting four-stranded structure consists of two G:C:A:T tetrads, formed by facing the minor groove side of the Watson-Crick base-pairs. Most probably, the association of the base-pairs is stabilized by coordinating a Na(+) cation. This is the first time that this novel G:C:A:T tetrad has been found in an oligonucleotide structure. This observation increases considerably the number of sequences that may adopt a four-stranded architecture. Overall, the three-dimensional structure is similar to those observed previously in other quadruplexes formed by minor groove alignment of Watson-Crick base pairs. This resemblance strongly suggests that we may be observing a general motif for DNA-DNA recognition.

Base Pairing↗
PubMed1995

DNA structure determines protein binding and transcriptional efficiency of the proenkephalin cAMP-responsive enhancer.

Two precisely arranged proenkephalin cAMP response elements (CREs) behave as a single protein binding site. The experiments described support a model in which a secondary structural change creates a new binding site, which is made up of sequences from both of the CREs. The CRE-binding protein (CREB) binds CRE-1, but binding there is entirely dependent on the presence of CRE-2. Electron spectroscopic images show that a CREB dimer occupies twice as much DNA in the proenkephalin gene as in the prodynorphin gene. The enhancer region is sensitive to P1 nuclease in a CREB concentration-dependent manner, and sensitivity is strand-specific, indicating protein-stabilized structural change. DNase I analysis shows that in the native proenkephalin gene, CREB binds both CRE-1 and CRE-2. In vivo, both CREs are occupied in the transcriptionally active proenkephalin gene, while neither is in the silent gene. Whereas CREB can bind CRE-2, mutation or elimination of either proenkephalin CRE alters response to second messengers and transcription factors. Thus, binding to CRE-2 alone is not sufficient. Specific and efficient transcription of the proenkephalin gene requires the presence of both CREs, precisely arranged to allow them to form a single protein binding site.

Animals↗
PubMed2002

Circuits and programmable self-assembling DNA structures.

Self-assembly is beginning to be seen as a practical vehicle for computation. We investigate how basic ideas on tiling can be applied to the assembly and evaluation of circuits. We suggest that these procedures can be realized on the molecular scale through the medium of self-assembled DNA tiles. One layer of self-assembled DNA tiles will be used as the program or circuit that leads to the computation of a particular Boolean expression. This layer templates the assembly of tiles, and their associations then lead to the actual evaluation involving the input data. We describe DNA motifs that can be used for this purpose; we show how the template layer can be programmed, in much the way that a general-purpose computer can run programs for a variety of applications. The molecular system that we describe is fundamentally a pair of two-dimensional layers, but it seems possible to extend this system to multiple layers.

Algorithms↗
PubMedDate not supplied

[A cytofluorometric study of the stability of secondary DNA structure in the epithelial cells in endometrial hyperplasia and cancer].

Studies were performed on epithelial cells obtained from uterine cavity in 49 women. All cases were subdivided into four groups; unaltered endometrium-9, glandular endometrial hyperplasia-10, atypical hyperplasia-4 and endometrial adenocarcinoma-30. For fluorimetric evaluation of single- and double-strand DNA specimens were dyed with acridine orange, which is known to produce red fluorescence in combination with double-strand acids. Values of coefficients alpha for single and double-strand DNA after acid hydrolysis were much higher than those before acid treatment. This study provides a deeper insight into the relation between DNA lesions and malignancy.

Adenocarcinoma↗
PubMed2005

Selective interactions of perylene derivatives having different side chains with inter- and intramolecular G-quadruplex DNA structures. A correlation with telomerase inhibition.

While the importance of the aromatic core in small organic molecules, studied as G-quadruplex mediated telomerase inhibitors, appears well studied by a number of researches, the role of side chains has been less well characterized. In this paper, we have studied the ability of six perylene derivatives with different side chains to induce both inter- and intramolecular G-quadruplex structures. The distance between the aromatic core and the positive charges in the side chains emerges as a significant molecular feature in G-quadruplex formation. Furthermore, the G-quadruplex formation appears also related to drugs 'self-association', influenced by the side chains basicity. The different efficiencies of the six perylene derivatives in interacting both with inter- and intramolecular G-quadruplex structures satisfactorily correlate with telomerase inhibition in cell-free systems.

Base Sequence↗
PubMed1997

Alloplasmic wheats with Aegilops crassa cytoplasm which express photoperiod-sensitive homeotic transformations of anthers, show alterations in mitochondrial DNA structure and transcription.

Alloplasmic wheat. Triticum aestivum cv. Norin 26, with Aegilops crassa cytoplasm, shows photoperiod-sensitive cytoplasmic male sterility (PCMS). This alloplasmic line expresses pistillody of anthers only when grown in long-day conditions (> 15 h light). To assess the molecular basis of the PCMS, we carried out Southern and Northern hybridization analyses on mitochondrial DNAs and RNAs isolated from seedlings of alloplasmic lines showing various PCMS phenotypes using probes for twelve mitochondrial genes. All RFLP patterns of mitochondrial DNA from alloplasmic lines greatly differed from those of common wheat, and were slightly changed from those of the parental species, i.e., Ae. crassa. This indicates that nuclear substitutions between related plant species induce structural alterations in the mitochondrial genome. Furthermore, RFLP patterns of (cr)-N61 and FR-mutant probed with coxIII and orf25 were identical with each other, but different from those of the other alloplasmic lines, indicating that the nuclei of N61 and FR-mutant harbor some gene(s) that induces structural alterations of the mitochondrial genome in the coxIII and orf25 regions. The transcription patterns of atp6 and cob in Ae. crassa type were different from those of T. aestivum type. Furthermore, the orf25 transcript in alloplasmic wheats was about 300 nucleotides longer than that of euplasmic lines, including the Ae. crassa pure line, suggesting that transcription patterns of orf25 are associated with recovery from the PCMS phenomenon. These data clearly show the mutual cross-talk between the nuclear genome and chondriome. These observations raise the possibility that the dysfunction of mitochondria caused by the failure of a cooperative control of mitochondrial gene(s) expression influences the pathway of flower morphogenesis, especially in the process that determines organ identity.

Blotting, Northern↗
PubMedDate not supplied

[Sexual differences in a state systems of DNA structure maintenance and generation of reactive oxygen species in somatic cells of mice 101/H reparation-defective strain and manifestation of these differences after exposure to ionizing radiation].

To analyse a role of the factor of a genetic fundamentals of cells in formation of radiation-induced genome instability (RIGI) we investigated a condition of DNA pattern, content of superoxide anion-radical O2*- and a sum of reactive oxigen species (ROS) (O2*-, OH*, H2O2), and also catalase activity in bone marrow cells of male and female mice of 101/H strain in the norm and at once after chronic (10 day) exposure to 200 mGy gamma-radiation. Thus we based on conception about a significance of mechanisms of DNA repair and production of reactive oxygen species (ROS) in development of radiation-induced genome instability (RIGI), and also on the data on sex bound differences in efficiency of DNA repair in reply to impact of the genotoxic agents for male and female mice of 101/H strain. Sex connected differences in redox system of bone marrow cells were established. In males lower catalase activity was found in the norm, with considerable increase of the activity and the content of ROS after chronic irradiation with a low dose (200 mGy); at the same time a direct correlation between the ROS content and catalase activity occurred. In female, which have higher DNA repair potential, higher level of catalase activity was found in the norm, with reduction after irradiation and lower, than in male, level of O2*- content; no changes in the general ROS content, or direct correlation between the content of a superoxide anion-radical (O2*-) and the sum of ROS were observed. The detected differences between male and female the studied parameters in the norm and after irradiation indicate a connection of the studied characteristics and their changes with a sex, confirm the literature data about a significance of the factor of a genetic fundamentals of bioobject in formation of radiation-induced genome instability.

Animals↗
PubMed1976

DNA structure in sheared and unsheared chromatin.

Shearing chromatin, by either sonication or vortex homogenization, introduces significant structural artifacts. These may be detected by the anomalously large increase in the number of ethidium bromide binding sites and the large alteration of the circular dichroism spectra of chromatin. Structural alterations are also suggested by the disappearance of differential light scattering after shearing.

Binding Sites↗
PubMed1993

A gene for cytochrome c oxidase subunit II in duck mitochondrial DNA: structural features and sequence evolution.

The gene encoding cytochrome c oxidase subunit II (COXII) was amplified by polymerase chain reaction (PCR) using mitochondrial DNAs (mtDNAs) isolated from two genera of domesticated ducks, Anas platyrhnchos and Cairina muschata, and their intergeneric and intrageneric hybrids as templates. Comparison of the nucleotide sequences from the two different duck lineages shows that they have approximately 91% homology. The nucleotide substitution pattern in the duck COXII gene reveals a high transition/transversion ratio (8.8:1.0) while 93.2% of the nucleotide substitutions are silent. The duck COXII, which uses GUG as the initiation codon, contains 228 amino acid residues. Comparison of the deduced COXII amino acid sequences in duck, chicken, Xenopus laevis, mouse, bovine and human reveals five highly conserved domains. The evolutionary conservation of the primary structure of COXII implies its functional importance.

Amino Acid Sequence↗
PubMed2005

A near-infrared Fourier transform Raman spectroscopy of epidermal keratinocytes: changes in the protein-DNA structure following malignant transformation.

We report here the use of near-infrared (NIR) Fourier transform (FT) Raman spectroscopy to analyze normal human epidermal keratinocytes prior to and following malignant transformation. Our analysis indicates specific Raman spectral differences between immortalized (HPK1A) and malignant ras transformed (HPK1A-ras) cells. In addition, striking spectral differences are seen in the DNA isolated from these cells and particularly in the 843/810 cm(-1) ratio with values of 1.6 +/- 0.13 in HPK1A cells and 0.68 +/- 0.09 in HPK1A-ras cells (mean +/- S.D., n = 12, P < 0.001) indicating specific alterations in the backbone conformation markers following malignant transformation. Subsequently, we analysed the effect of a strong inhibitor of keratinocyte growth, the Vitamin D analog EB1089, on the Raman spectra of intact cells and on the 843/810 cm(-1) ratio in the DNA isolated from both cell lines. Specific changes were observed in intact cells in the 1300-750 cm(-1) region. Furthermore, the 843/810 cm(-1) ratio of isolated DNA from HPK1A cells was not affected by EB1089 but significantly increased in DNA isolated from HPK1A-ras cells so much that it became closer to the value observed for HPK1A cells (1.07 +/- 0.10). Our data suggest that Raman analysis of DNA and in particular the 843/810 cm(-1) ratio can provide useful indices of malignant transformation and efficacy of anticancer agents.

Calcitriol↗
PubMed1984

Base-stacking interactions in double-helical DNA structures: experiment versus theory.

Atom-atom potential energy calculations have been undertaken for deriving stacking energies in double-helical structures. A comparison between the energy patterns of A- and B-type double-helical fragments determined by single-crystal X-ray diffraction methods versus idealized uniform models based on fibre diffraction data shows that the van der Waals stacking energy is largely sensitive to local changes in the relative orientation of adjacent base pairs. The sequence-dependent conformational variability observed in the high-resolution structures appears to be a consequence of the equipartitioning of the stacking energy along the double helix. The large energy variations expected for a uniform structure are dampened considerably in the observed structures by means of local changes in conformational features such as helix rotation and roll angles between base pairs.

DNA↗
PubMed1993

Mapping and positioning DNA-binding proteins along genomic DNA. Structure of D. melanogaster ribosomal 'Alu-repeats' and 1.688 satellite chromatin.

Chromatin structure of so-called 'Alu-repeat' in D. melanogaster ribosomal non-transcribed spacer that contains sequences homologous to the promoter of ribosomal genes has been studied. Using the 'protein image' hybridization assay based on UV-light-induced DNA-protein crosslinking and 2-D gel retardation electrophoresis, two proteins of the molecular mass of 50 kD (rABP50) and 70 kD (rABP70), associated with 'Alu-repeat' DNA have been found. Exo III mapping of crosslinking sites and DNase I footprinting have provided a detailed map of H1, rABP50 and rABP70 contacts within the 'Alu-repeat' and H1 and a non-histone protein contacts on satellite DNA. These data indicate precise positioning of non-histone proteins, histone H1 and nucleosomes within genomic regions studied and account for the presence of unusual 240 bp long nucleosomal particles in 'Alu-repeats'. The same approach can be adapted for successive mapping and positioning proteins on genomic DNA.

Animals↗