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At least 847 records · Page 47Linked to original sources
PubMed2003

From DNA structure to gene expression: mediators of nuclear compartmentalization and dynamics.

Eukaryotic genomes are functionally compartmentalized into chromatin domains by their attachment to a supporting structure that has traditionally been termed the nuclear matrix. Present evidence indicates the dynamics of this entity, which requires particular properties of the elements that mediate this kind of interaction. Above all, this is enabled by the so-called 'mass binding phenomenon' by which scaffold/matrix-attachment regions (S/MARs) reversibly associate with ubiquitous factors. Recent investigations and novel techniques have shown that these contacts can be altered by modulators as well as by specific interactions with the components of enhancers and locus control regions.

Chromatin↗
PubMed1998

Complete genomic structure DNA polymorphisms, and alternative splicing of the human AF-6 gene.

In our previous work, detailed deletion mapping of ovarian cancers indicated that a 300-kb region of chromosome 6q27 was likely to contain one or more putative tumor suppressor genes associated with development of this type of cancer. DNA sequencing in the region disclosed the presence of AF-6, a gene that had been identified as the ALL-1 fusion partner involved in acute myeloid leukemias with t(6;11)(q27;q23) translocations. In the work reported here, we determined the complete genomic sequence of the AF-6 gene, including exon-intron boundaries, and found six DNA polymorphisms. One of them, an insertion/deletion polymorphism, determined the presence or absence of seven amino acids in the AF-6 product. We also identified two alternatively spliced forms of the gene; the two novel transcripts would encode additional C-terminal peptides in comparison to the reported protein. Sequencing of seven cosmid clones that covered the entire gene revealed 32 exons (not including one exon involved in the insertion/deletion polymorphism), spanning approximately 140 kb of genomic DNA. These results may contribute to an understanding of the mechanism causing chromosomal translocations in leukemic cells.

Alternative Splicing↗
PubMed1994

A new family of zinc finger proteins in petunia: structure, DNA sequence recognition, and floral organ-specific expression.

We have previously cloned a gene for a zinc finger protein (EPF1) that is expressed specifically in petals and interacts with the promoter region of the 5-enolpyruvylshikimate-3-phosphate synthase gene in petunia. In an attempt to isolate genes encoding additional factors that interact with this promoter, we cloned four novel genes encoding zinc finger proteins (EPF2-5a, EPF2-5b, EPF2-4, and EPF2-7). Sequence analyses revealed that overall similarity between the EPF1 and the EPF2 protein family, except in the zinc finger motifs and the basic amino acid cluster, was very low, suggesting that the two groups belong to different subfamilies. DNA binding specificities of EPF1, EPF2-5, and EPF2-4 were very similar, as expected from the conserved zinc finger motifs. However, EPF2-7 showed no binding to the probes tested in spite of having the conserved motifs. DNA binding studies using a series of spacing mutant probes suggested a binding mechanism in which the EPF proteins recognize spacings in target DNA. RNA gel blot analyses and histochemical analyses with a promoter and beta-glucuronidase fusion revealed that expression of the EPF2-5 gene (EPF2-5) was petal and stamen specific. Expression of the EPF2-7 gene (EPF2-7) was sepal and petal specific and localized in vascular tissues. The preferential expression in two adjacent floral organs raises the possibility that these genes are downstream transcription factors of floral homeotic genes.

Amino Acid Sequence↗
PubMed2006

Herpes simplex virus capsid structure: DNA packaging protein UL25 is located on the external surface of the capsid near the vertices.

UL25 is one of seven herpes simplex virus-encoded proteins involved specifically in DNA encapsidation. Its role appears to be to stabilize the capsid so that DNA is prevented from escaping once it has entered. To clarify the function of UL25, we have examined capsids with the goal of defining where it is located. Analysis of trypsin-treated capsids showed that UL25 is sensitive to cleavage like other proteins such as the major capsid and portal proteins that are exposed on the capsid surface. Internal proteins such as the scaffolding protein and protease were not affected under the same experimental conditions. Capsids were also examined by electron microscopy after staining with gold-labeled antibody specific for UL25. Images of stained capsids demonstrated that most labeled sites (71% in C capsids) were at capsid vertices, and most stained C capsids had label at more than one vertex. A quantitative immunoblotting method showed that the capsid contents of UL25 were 56, 20, and 75 copies per capsid in A, B, and C capsids, respectively. Finally, soluble UL25 protein was found to bind in vitro to purified capsids lacking it. The amount of bound UL25 corresponded to the amount present in B capsids, and bound UL25 was found by immunoelectron microscopy to be located predominantly at the capsid vertices. The results are interpreted to suggest that five UL25 molecules are found at or near each of the capsid vertices, where they are exposed on the capsid surface. Exposure on the surface is consistent with the view that UL25 is added to the capsid as DNA is packaged or during late stages of the packaging process.

Animals↗
PubMed1989

Fine structure DNA mapping studies of the chromosomal region harboring the genetic defect in neurofibromatosis type I.

To better map the location of the von Recklinghausen neurofibromatosis (NF1) gene, we have characterized a somatic cell hybrid designated 7AE-11. This microcell-mediated, chromosome-transfer construct harbors a centromeric segment and a neo-marked segment from the distal long arm of human chromosome 17. We have identified 269 cosmid clones with human sequences from a 7AE-11 library and, using a panel of somatic cell hybrids with a total of six chromosome 17q breakpoints, have mapped 240 of these clones on chromosome 17q. The panel included a hybrid (NF13) carrying a der(22) chromosome that was isolated from an NF1 patient with a balanced translocation, t(17;22) (q11.2;q11.2). Fifty-three of the cosmids map into a region spanning the NF13 breakpoint, as defined by the two closest flanking breakpoints (17q11.2 and 17q11.2-q12). RFLP clones from a subset of these cosmids have been mapped by linkage analysis in normal reference families, to localize the NF1 gene more precisely and to enhance the potential for genetic diagnosis of this disorder. The cosmids in the NF1 region will be an important resource for testing DNA blots of large-fragment restriction-enzyme digests from NF1 patient cell lines, to detect rearrangements in patients' DNA and to identify the 17;22 NF1 translocation breakpoint.

Animals↗
PubMed1996

Gene structure, DNA methylation, and imprinted expression of the human SNRPN gene.

The human SNRPN (small nuclear ribonucleoprotein polypeptide N) gene is one of a gene family that encode proteins involved in pre-mRNA splicing and maps to the smallest deletion region involved in the Prader-Willi syndrome (PWS) within chromosome 15q11-q13. Paternal only expression of SNRPN has previously been demonstrated by use of cell lines from PWS patients (maternal allele only) and Angelman syndrome (AS) patients (paternal allele only). We have characterized two previously unidentified 5' exons of the SNRPN gene and demonstrate that exons -1 and 0 are included in the full-length transcript. This gene is expressed in a wide range of somatic tissues and at high, approximately equal levels in all regions of the brain. Both the first exon of SNRPN (exon -1) and the putative transcription start site are embedded within a CpG island. This CpG island is extensively methylated on the repressed maternal allele and is unmethylated on the expressed paternal allele, in a wide range of fetal and adult somatic cells. This provides a quick and highly reliable diagnostic assay for PWS and AS, which is based on DNA-methylation analysis that has been tested on > 100 patients in a variety of tissues. Conversely, several CpG sites approximately 22 kb downstream of the transcription start site in intron 5 are preferentially methylated on the expressed paternal allele in somatic tissues and male germ cells, whereas these same sites are unmethylated in fetal oocytes. These findings are consistent with a key role for DNA methylation in the imprinted inheritance and subsequent gene expression of the human SNRPN gene.

Adolescent↗
PubMedDate not supplied

[Approaches to classifying bifidobacteria based on DNA structural data].

A brief historical review of classifications of Bifidobacteria demonstrates the difficulties in this problem, for the present-day classifications are far from being satisfactory. Based on the genotypical heterogeneity of the genus Bifidobacterium, the authors validate the possibility of raising it to the status of the family Bidobacteriaceae fam. nov. The principle of forming new genera within the frames of this hypothetical family, discussed in the paper, originates from the genomic similarity of representatives of some species of this group of microorganisms.

Bifidobacterium↗
PubMed1995

Influence of counter-ions on the crystal structures of DNA decamers: binding of [Co(NH3)6]3+ and Ba2+ to A-DNA.

A-DNA is a stable alternative right-handed double helix that is favored by certain sequences (e.g., (dG)n.(dC)n) or under low humidity conditions. Earlier A-DNA structures of several DNA oligonucleotides and RNA.DNA chimeras have revealed some conformational variation that may be the result of sequence-dependent effects or crystal packing forces. In this study, four crystal structures of three decamer oligonucleotides, d(ACCGGCCGGT), d(ACCCGCGGGT), and r(GC)d(GTATACGC) in two crystal forms (either the P6(1)22 or the P2(1)2(1)2(1) space group) have been analyzed at high resolution to provide the molecular basis of the structural difference in an experimentally consistent manner. The study reveals that molecules crystallized in the same space group have a more similar A-DNA conformation, whereas the same molecule crystallized in different space groups has different (local) conformations. This suggests that even though the local structure is influenced by the crystal packing environments, the DNA molecule adjusts to adopt an overall conformation close to canonical A-DNA. For example, the six independent CpG steps in these four structures have different base-base stacking patterns, with their helical twist angles (omega) ranging from 28 degrees to 37 degrees. Our study further reveals the structural impact of different counter-ions on the A-DNA conformers. [Co(NH3)6]3+ has three unique A-DNA binding modes. One binds at the major groove side of a GpG step at the O6/N7 sites of guanine bases via hydrogen bonds. The other two modes involve the binding of ions to phosphates, either bridging across the narrow major groove or binding between two intra-strand adjacent phosphates. Those interactions may explain the recent spectroscopic and NMR observations that [Co(NH3)6]3+ is effective in inducing the B- to A-DNA transition for DNA with (G)n sequence. Interestingly, Ba2+ binds to the same O6/N7 sites on guanine by direct coordinations.

Barium↗
PubMed1991

Paranemic structures of DNA and their role in DNA unwinding.

A DNA structure is defined as paranemic if the participating strands can be separated without mutual rotation of the opposite strands. The experimental methods employed to detect paranemic, unwound, DNA regions is described, including probing by single-strand specific nucleases (SNN), conformation-specific chemical probes, topoisomer analysis, NMR, and other physical methods. The available evidence for the following paranemic structures is surveyed: single-stranded DNA, slippage structures, cruciforms, alternating B-Z regions, triplexes (H-DNA), paranemic duplexes and RNA, protein-stabilized paranemic DNA. The problem of DNA unwinding during gene copying processes is analyzed; the possibility that extended paranemic DNA regions are transiently formed during replication, transcription, and recombination is considered, and the evidence supporting the participation of paranemic DNA forms in genes committed to or undergoing copying processes is summarized.

Animals↗
PubMed1995

Hydration patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition.

Crystallographic studies of DNA fragments of the A and B conformations have shown that the structure and hydration of the DNA double helix depend both on the base sequence and the environment. Detailed analyses of solvent organization in DNA crystals and its role in intermolecular interactions have been reported mainly for B-DNA structures. We have determined the crystal structures of several isomorphous A-DNA octamers at resolutions from 1.8 to 2.5 A and refined them by the same procedure. Comparative analysis of five independently refined structures in terms of hydration and intermolecular interactions has been performed leading to the following findings. The A-DNA major groove is extensively hydrated and together with the hydration shells of the sugar-phosphate backbone can form an ordered network of fused polygons. The water structure of the phosphate backbone is less conserved than that of the grooves. Characteristic hydration patterns are associated with specific base sequences. The A-DNA minor groove provides sites for intermolecular contacts through hydrophobic and polar interactions. Well-ordered water molecules mediate interduplex interactions that involve either the grooves or the backbone, or both. The direct and water-mediated intermolecular interactions observed in the A-DNA crystal structures are relevant to various recognition motifs between DNA and other molecules. In particular, intermolecular interactions at the DNA minor groove are analogous to those observed in the recently reported crystal structures of complexes between the TATA-binding protein and the TATA-box.

Base Sequence↗
PubMed2000

A novel approach for analyzing the structure of DNA modified by Benzo[a]pyrene diol epoxide at single-molecule resolution.

Benzo[a]pyrene diol epoxide (BPDE) has been shown to bind specifically to the exocyclic amino group of deoxyguanosine in duplex DNA. Interestingly, this metabolite exhibits stereoselectivity in its tumorigenic and mutagenic effects. It is thought that local DNA conformation is altered at the site of the adduct, resulting in aberrant biological processes, and that in certain sequence contexts BPDE-DNA adducts induce bends in the DNA. In the work presented here, we compared DNA structural alterations of BPDE-modified DNA and unmodified DNA via tapping mode atomic force microscopy (AFM). DNA fragments 366 base pairs (bp) in length were generated by PCR from the duplicated multiple-cloning site of pBEND2 inserted into pGEM-3Zf(-), and either mock-modified or treated with BPDE to give modification levels between 1 and 5% of the nucleotides. Control or BPDE-modified DNA was adsorbed to mica and visualized in air by AFM. The contour lengths and end-to-end lengths of individual molecules were measured. The ratio of end-to-end distance to contour length was significantly smaller for modified DNA molecules than for the unmodified DNA preparation, although the frequency distributions of the contour lengths were similar for the two preparations. This suggests BPDE-DNA adducts cause significant bending of DNA molecules, confirming previous conclusions based on more indirect measurements. The average induced bend angle for BPDE-DNA adducts is estimated to be at least 30 degrees.

Benzopyrenes↗
PubMed1995

DNA analogues with nonphosphodiester backbones.

This review discusses the recent developments of DNA analogues with nonphosphodiester backbones in terms of DNA structure and antisense and antigene potential. A larger number of derivatives are now available in which the phosphodiester linkage has been replaced but the deoxyribose retained. However, only a few of these (e.g. the ones having a thioformacetal or a carboxamide linkage) appear to be good structural DNA mimics. Two successful attempts to replace the entire deoxyribose phosphate backbone have been reported, the morpholino derivatives and the peptide nucleic acids (PNA), which contain an N-(2-aminoethyl)glycine-based pseudopeptide backbone. Most information is available on the PNA, which is a very promising DNA mimic. In conclusion, the deoxyribose phosphate backbone is not essential for a potent structural DNA mimic and not even required for a helical duplex structure.

Antisense Elements (Genetics)↗
PubMed1997

Slipped structures in DNA triplet repeat sequences: entropic contributions to genetic instabilities.

Slipped DNA structures can occur in sequences with direct repeats. DNA triplet repeats, particularly (CTG)n, (CGC)n, and (GAA)n, are known to be associated with several neurological diseases. Slippage is probably the cause of expansion of the number of repeats, a process called dynamic mutation, which is known to be the cause of the diseased state. Here it is shown that the conformational entropy associated with slippage is more destabilizing for long direct repeats (300-1000 base pairs) than shorter runs (10-30 base pairs), by about 2 kcal/mol. This contributes to the greater instability of longer sequences. Entropic considerations also favor the formation of simple bulges, rather than hairpin structures. A model is presented for dynamic mutations, and experimentally testable predictions are made that will allow the model to be tested.

Base Sequence↗