Nucleosome positioning,nucleotide excision repair and photoreactivation in Saccharomyces cerevisiae

The position of nucleosomes on DNA participates in gene regulation and DNA replication. Nucleosomes can be repressors by limiting access of factors to regulatory sequences, or activators by facilitating binding of factors to exposed DNA sequences on the surface of the core histones. The formation of UV induced DNA lesions, like cyclobutane pyrimidine dimers (CPDs), is modulated by DNA bending around the core histones. Since CPDs are removed by nucleotide excision repair (NER) and photolyase repair, it is of paramount importance to understand how DNA damage and repair are tempered by the position of nucleosomes. In vitro, nucleosomes inhibit NER and photolyase repair. In vivo, nucleosomes slow down NER and considerably obstruct photoreactivation of CPDs. However, over-expression of photolyase allows repair of nucleosomal DNA in a second time scale. It is proposed that the intrinsic abilities of nucleosomes to move and transiently unwrap could facilitate damage recognition and repair in nucleosomal DNA.     

The influence of quality of primers on the formation of primer dimers in PCR

Abstract

Polymerase chain reaction (PCR) is the most commonly used method for nucleic acids amplification. PCR performance depends on several causes, among which the quality of primers is one of the main determinants affecting specificity, sensitivity and reliability of the reaction. Here, we report on the results of the detailed study devoted to the dimerization of the primers during PCR. The course and specificity of the reaction were studied on the model DNA templates as well as genomic DNA using primers that form amplifiable heterodimeric structures with different thermodynamic stability. It was confirmed that more than two 3′-overlapping nucleotides cause a considerable accumulation of primer dimers. It turned out that the presence of any DNA promotes the formation of dimers even for primers, which do not tend to nonspecific amplification in the absence of DNA. It was shown that dimerization could not be eliminated by commonly used techniques. Even the use of hot-start DNA polymerases does not prevent PD formation if primers with stable 3′-overlapping are employed. Despite several advantages of PCR with abutting primers, their close disposition has no benefits regarding the formation of PD if low-quality primers are utilized.     

An alternative to Urry's model for the gramicidin transmembrane channels

It is suggested that the conducting transmembrane channels formed by the linear gramicidins A, B and C may be head-to-head (formyl end-to-formyl end) dimers of double-stranded parallel β-helices. This possibility is not in conflict with any of the various experimental findings bearing on the molecular organization of the channels and represents a plausible alternative to Urry's model of a head-to-head dimer of single-stranded β^6.3-helices.     

Histone modification and chromatin remodeling during NER

Here we review our developments of and results with high resolution studies on global genome nucleotide excision repair (GG-NER) in Saccharomyces cerevisiae. Technologies were developed to examine NER at nucleotide resolution in yeast sequences of choice and to determine how these related to local changes in chromatin. We focused on how GG-NER relates to histone acetylation for its functioning and we identified the histone acetyltransferase Gcn5 and acetylation at lysines 9/14 of histone H3 as a major factor in enabling efficient repair. Factors influencing this Gcn5-mediated event are considered which include Rad16, a GG-NER specific SWI/SNF factor and the yeast histone variant of H2AZ (Htz1). We describe results employing primarily MFA2 as a model gene, but also those with URA3 located at subtelomeric sequences. In the latter case we also see a role for acetylation at histone H4. We then consider the development of a high resolution genome-wide approach that enables one to examine correlations between histone modifications and the NER of UV-induced cyclobutane pyrimidine dimers throughout entire yeast genome. This is an approach that will enable rapid advances in understanding the complexities of how compacted chromatin in chromosomes is processed to access DNA damage before it is returned to its pre-damaged status to maintain epigenetic codes.     

The interaction of manganese ions with DNA

We present the structure of the duplex formed by a fragment of auto-complementary DNA with the sequence d(CGTTAATTAACG). The structure was determined by X-ray crystallography. Up to date it is the first structure presenting the interaction between a DNA oligonucleotide and manganese ions. The presence of Mn²⁺ creates bonds among the N7 atom of guanines and phosphates. These bonds stabilize and determine the crystallographic network in a P3₂ space group, unusual in oligonucleotide crystals. The crystal structure observed is compared with those found in the presence of Mg²⁺, Ca²⁺ and Ni²⁺, which show different kinds of interactions. The double helices show end-to-end interactions, in a manner that the terminal guanines interact with the minor groove of the neighboring duplex, while the terminal cytosines are disordered. We have chosen this sequence since it contains a TTAA repeat. Such repeats are very rare in all genomes. We suggest that this sequence may be very susceptible to the formation of closely spaced thymine dimers.     

Effect of plasmid pKM101 in ultraviolet irradiated uvr+ and uvr- Escherichia coli.

The effect of plasmid pKM101 on UV irradiated excision proficient and excision deficient cells was investigated. The plasmid increased the survival of excision proficient cells while partially inhibiting thymine dimer excision. The frequency of mutations was almost unchanged. In excision deficient cells the effect of the plasmid on survival was less pronounced while cell mutability was increased. Our data indicate that the mucAB genes (carried by the plasmid) influence the two types of cells in a different way.     

Evaluation of acute corneal damage induced by 222-nm and 254-nm ultraviolet light in Sprague–Dawley rats

Two hundred twenty-two nanometres ultraviolet (UV) light produced by a krypton–chlorine excimer lamp is harmful to bacterial cells but not skin. However, the effects of 222-nm UV light exposure to the eye are not fully known. We evaluated acute corneal damage induced by 222- and 254-nm UV light in albino rats. Under deep anaesthesia, 6-week-old Sprague–Dawley albino rats were exposed to UV light. The exposure levels of corneal radiation were 30, 150, and 600?mJ/cm². Epithelial defects were detected by staining with fluorescein. Superficial punctate keratitis developed in corneas exposed to more than 150?mJ/cm² of UV light, and erosion was observed in corneas exposed to 600?mJ/cm² of UV light. Haematoxylin and eosin staining also showed corneal epithelial defects in eyes exposed to 254-nm UV light. However, no damage developed in corneas exposed to 222-nm UV light. Cyclobutane pyrimidine dimer-positive cells were observed only in normal corneas and those exposed to 254-nm UV light. Although some epithelial cells were stained weakly in normal corneas, squamous epithelial cells were stained moderately, and the epithelial layer that was detached from the cornea exposed to 600?mJ/cm² of light was stained intensely in corneas exposed to 254-nm UV light. In the current study, no corneal damage was induced by 222-nm UV light, which suggested that 222-nm UV light may not harm rat eyes within the energy range and may be useful for sterilising or preventing infection in the future.     

Effect of Hinge Region State on Interaction of Human IgG3 with the Complement System

Covalently cross-linked rod-like dimers of human myeloma IgG3 are more efficient in the inhibition of the complement system reaction than compact dimers. This correlates with an increase in the stability of C_H2 domains of the immunoglobulin in the state with the rod-like hinge region.     

UV damage to plant life in a photobiologically dynamic environment: the case of marine phytoplankton

The effect of UV-B radiation on growth of marine phytoplankton was investigated in relation to DNA damage induced by a range of biologically effective doses (BEDs). Emiliania huxleyi (Prymnesiophyceae) was chosen as a model organism of the ocean's phytoplankton because of its importance in global biogeochemical cycling of carbon and sulphur, elements that influence the world's climate as components of the trace gases carbon dioxide (CO₂) and dimethylsulfide (DMS). A marine diatom, Cyclotella, was studied for its capacity to repair the DNA damage, quantified as thymine dimers by the application of a monoclonal antibody against these photoproducts. DNA repair was shown to be complete after just a few hours of exposure to visible light; the repair rate increased with PAR intensity. E. huxleyi appeared to be most sensitive to UV-B radiation: growth was already affected above a dose of 100 J m^-2 d^-1 (biologically effective radiation, weighted with Setlow's DNA action spectrum), probably through effects on the cell cycle related to damage to nuclear DNA: mean specific growth rates were inversely correlated with thymine dimer contents in cells. Near the ocean's surface UV-B radiation conditions that induce the changes observed by us in cultures can be expected during the growing season of phytoplankton, not only in the tropics but also at higher latitudes. Nevertheles, blooms of species such as E. huxleyi are often excessive in the field. It is suggested that exposure duration of cells near the surface of the ocean can be shorter than our artificial 3 h in the laboratory due to vertical mixing, a phenomenon that is typical for the ocean's upper 50–100 m. When mixing reaches depths greater than the layer where most UV-B is attenuated, negative effects on cells through UV-A-induced inhibition of photosynthesis may prevail over DNA damage, the action spectrum of which has been shown to be limited to the UV-B part of the spectrum. Moreover, the radiation wavelengths that induce DNA damage repair (UV-A and visible) are attenuated vertically much less than UV-B. The photobiological situation in the upper ocean is much more complicated than on land, and effects of UV radiation on plankton biota can only be modelled realistically here when both the spectrally differential attenuation in the UV and visual part of the spectrum and the rate of vertical mixing are taken into account. Action spectra of both damage and repair of DNA and of photosynthesis inhibition of representative microalgal species are the second conditio sine qua non if we want to predict the effect of stratospheric ozone depletion on marine phytoplankton performance.