Structural Organization Of DNA Research Articles

Effect of Mn2+ and Ca2+ Ions on Formation of Structurally Ordered Nanoscale Complexes of DNA with Nuclear Proteins HMGB1 and H1

The structural organization of DNA in complex with linker histone H1 and non-histone chromosomal protein HMGB1 in presence of calcium and manganese ions have been studied using FTIR and UV circular dichroism spectroscopy. We have demonstrated that the presence of calcium ions leads to the formation of highly ordered DNA-H1-HMGB1 structures, while manganese ions decrease the order in the earlier reported nanoscale complexes.

Formation of Structurally Ordered Nanoscale Complexes of DNA with Nuclear Proteins HMGB1 and H1

The structural organization of DNA in complex with linker histone H1 and non-histone chromosomal protein HMGB1 have been studied using atomic force microscopy and vibrational spectroscopy. The possibility of formation ordered nanoscale DNA-protein complexes is reported.

Peculiarities of Molecular Mechanisms Involved in Modification of the Structural and Molecular Organization of the Cell Genome.

Within the framework of the previously proposed model of structural organization of DNA that supplements the Watson-Crick model and is based on a mathematical regulation - Fibonacci sequence, we suppose the existence of nucleotides without nitrogenous base and acting as linkers connecting DNA subunits.

Plastid nucleoids: evolutionary reconstruction of a DNA/protein structure with prokaryotic ancestry.

Plastid nucleoids: evolutionary reconstruction of a DNA/protein structure with prokaryotic ancestry.

Fluorescent in situ hybridization on comets: FISH comet.

The DNA in eukaryotic cells is organized into loop domains that represent basic structural and functional units of chromatin packaging. The comet assay, a sensitive method for monitoring DNA damage and repair, involves electrophoresis of nucleoids comprising supercoiled DNA attached to the nuclear matrix. Breaks in the DNA relax the supercoiling and allow DNA loops to expand, and on electrophoresis to move towards the anode, giving the appearance of a comet tail. We use fluorescent in situ hybridization (FISH) to investigate the structure of the chromatin within comet preparations and to study specific DNA sequences within comets. In this chapter we describe our FISH comets protocols, deal with some technical questions and outline the theory. FISH with comets should be useful to researchers interested in the structural organization of DNA and chromatin, the localization of DNA damage, and the kinetics of repair of damage.

Structural Organization of DNA in Chlorella Viruses

Chlorella viruses have icosahedral capsids with an internal membrane enclosing their large dsDNA genomes and associated proteins. Their genomes are packaged in the particles with a predicted DNA density of ca. 0.2 bp nm−3. Occasionally infection of an algal cell by an individual particle fails and the viral DNA is dynamically ejected from the capsid. This shows that the release of the DNA generates a force, which can aid in the transfer of the genome into the host in a successful infection. Imaging of ejected viral DNA indicates that it is intimately associated with proteins in a periodic fashion. The bulk of the protein particles detected by atomic force microscopy have a size of ∼60 kDa and two proteins (A278L and A282L) of about this size are among 6 basic putative DNA binding proteins found in a proteomic analysis of DNA binding proteins packaged in the virion. A combination of fluorescence images of ejected DNA and a bioinformatics analysis of the DNA reveal periodic patterns in the viral DNA. The periodic distribution of GC rich regions in the genome provides potential binding sites for basic proteins. This DNA/protein aggregation could be responsible for the periodic concentration of fluorescently labeled DNA observed in ejected viral DNA. Collectively the data indicate that the large chlorella viruses have a DNA packaging strategy that differs from bacteriophages; it involves proteins and share similarities to that of chromatin structure in eukaryotes.

New Molecular Systems. Peculiarities of Structural Organization of Biopolymers

We proposed a new model of DNA structure, which allows rearrangement of monomers in the polymer chain backbone according to mathematical laws. On the basis of the analysis of structural organization of DNA we concluded that rearrangements of monomers should also occur during the formation of the molecular structure of other polymers (RNA and proteins).

Histone metabolic pathways and chromatin assembly factors as proliferation markers

The structural organization of DNA into chromatin is of key importance to regulate genome function and stability. Maintenance of such an organization is thus crucial to preserve cellular identity. At each cell cycle, during S phase, this is achieved by duplication of chromatin structure in tight coordination with DNA replication. Such a coordinate process requires histone synthesis and their deposition onto DNA by chromatin assembly factors to be efficiently coupled to DNA synthesis. In this review, we highlight the intimate relationship between these chromatin-related events and DNA replication and we show how it is possible to take advantage of this coupling in order to identify cells with high replicative potential such as tumor cells. On the basis of recent data, we discuss the potential use of chromatin-associated factors as new proliferation markers of interest for cancer diagnosis and prognosis.

Structure-function relationships in replication origins of the yeast Saccharomyces cerevisiae: higher-order structural organization of DNA in regions flanking the ARS consensus sequence.

In order to better understand the involvement of the DNA molecule in the replication initiation process we have characterized the structure of the DNA at Autonomously Replicating Sequences (ARSs) in Saccharomyces cerevisiae. Using a new method for anti-bent DNA analysis, which allowed us to take into account the bending contribution of each successive base plate, we have investigated the higher-order structural organization of the DNA in the region which immediately surrounds the ARS consensus sequence (ACS). We have identified left- and right-handed anti-bent DNAs which flank this consensus sequence. The data show that this organization correlates with an active ACS. Analysis of the minimum nucleotide sequence providing ARS function to plasmids reveals an example where the critical nucleotides are restricted to the ACS and the right-handed anti-bent DNA domain, although most of the origins considered contained both left- and right-handed anti-bent DNAs. Moreover, mutational analysis shows that the right-handed form is necessary in order to sustain a specific DNA conformation which is correlated with the level of plasmid maintenance. A model for the role of these individual structural components of the yeast replication origin is presented. We discuss the possible role of the right-handed anti-bent DNA domain, in conjunction with the ACS, in the process of replication initiation, and potentialities offered by the combination of left- and right-handed structural components in origin function.

DNA loop domain organization: the three-dimensional genomic code.

It is well known that aberrations in the nuclear matrix contribute to the development of cancer, but many aspects of this process remain unknown. The mammalian sperm nuclear matrix serves as a distinctive model of DNA loop domain organization by the nuclear matrix since the integrity of the DNA structure can be measured by the ability of the paternal chromosomes to participate in embryogenesis. The structure of the nuclear matrix is known to be important for normal cellular functions such as transcriptional regulation and DNA replication. Even small aberrations in DNA structural organization in the sperm cell could have disastrous consequences for the embryo if they were essential for function. Recent work from our laboratory suggests that sperm nuclei with disrupted nuclear matrix structures but intact DNA cannot participate fully in embryogenesis, suggesting that the structural organization of DNA may provide important, heritable information that is necessary for development. We term the DNA sequence together with its three-dimensional organization the "genomic code." We suggest that the sperm nucleus is an ideal model for understanding the principles of the involvement of the three-dimensional structure of DNA in normal cellular function. Finally, the implications for cancer about what we can learn using sperm DNA as a model about the "genomic code" are discussed. J. Cell. Biochem. Suppl. 35:23-26, 2000.

Significance of specific protein S-S bonds in the structural-functional organization of DNA

The role of S-S bridges of residual protein in the structural organization of DNA is investigated. The effects of various S-S splitting agents on the naturally occurring DNA-RP protein complexes isolated from various eukaryotic and prokaryotic cells are studied. It is demonstrated that, depending on the incubation conditions, thiols induce dissociation of the DNA-RP complexes to double-strand fragment-DNA subunits of varied size. It is found that the DNA-RP complexes contain specific S-S bonds that may determine different levels of DNA organization in the cromosome.

DNA Packaging and Organization in Mammalian Spermatozoa: Comparison with Somatic Cell

Mammalian sperm DNA is the most tightly compacted eukaryotic DNA, being at least sixfold more highly condensed than the DNA in mitotic chromosomes. To achieve this high degree of packaging, sperm DNA interacts with protamines to form linear, side-by-side arrays of chromatin. This differs markedly from the bulkier DNA packaging of somatic cell nuclei and mitotic chromosomes, in which the DNA is coiled around histone octamers to form nucleosomes. The overall organization of mammalian sperm DNA, however, resembles that of somatic cells in that both the linear arrays of sperm chromatin and the 30-nm solenoid filaments of somatic cell chromatin are organized into loop domains attached at their bases to a nuclear matrix. In addition to the sperm nuclear matrix, sperm nuclei contain a unique structure termed the sperm nuclear annulus to which the entire complement of DNA appears to be anchored when the nuclear matrix is disrupted during decondensation. In somatic cells, proper function of DNA is dependent upon the structural organization of the DNA by the nuclear matrix, and the structural organization of sperm DNA is likely to be just as vital to the proper functioning of the spermatozoa.

Structural organization of DNA

This chapter summarizes (a) the building blocks of nucleotides and in this context discusses separately the nucleic acid bases, the sugar and phosphate components, (b) the bond types in nucleotides, (c) the metabolism of nucleotides, (d) the lower levels of DNA structure (primary, secondary, tertiary, nucleosomal), (e) supranucleosomal organization of eukaryotic DNA, (f) chromosomes of animal cells, and (g) the temporal and spatial order of gene replication.

STRUCTURAL ORGANIZATION OF PLASTID DNA IN TWO ANOMALOUSLY PIGMENTED DINOFLAGELLATES1

ABSTRACTThe structural organization of DNA in the plastids of two anomalously pigmented dinoflagellates, Glenodinium foliaceum Stein and Gyrodinium aureolum Hulburt, was determined using the DNA‐specific fluorochrome DAPI and correlated with TEM observations. The plastids of G. foliaceum were found to possess both a peripheral DNA ring and isolated point nucleoids. This arrangement was shown to be similar to that of the diatom Asterionella formosa Hass. and may be characteristic of the Bacillariophyceae. G. aureolum exhibited a novel distribution of plastid. DNA as one or two beaded bands, whereas the plastids of the similarly pigmented haptophyte, Emiliania huxleyi (Lohm.) Hay & Mohler, possessed scattered point nucleoids. These findings support the idea that G. foliaceum harbours an endosymbiotic diatom, but suggest that the plastids of G. aureolum and E. huxleyi are unrelated. The use of plastid DNA configuration as a phylogenetic marker is considered.