The Preliminary Study on DNA Barcoding of Mosses——A Case of Part of Genera of Meteoriaceae

We compared the performances of the candidate loci for moss DNA barcoding and the primers used in amplifying the loci. Primers for three coded loci (matK, rps4 and rbcL a) and four non coded loci (atpB rbcL, atpF H, psbK I and trnH psbA) of the chloroplast genome, one from the mitochondrial genome (nad5), and one from the nucleus genome (ITS2) were evaluated. Seventy four samples representing 14 species belonging to five genera of Trachypodoaceae (or Meteoriaceae) were screened. All primers for matK and a pair of primers for trnH psbA failed. Low successes were encountered with the primers for atpF H and psbK I. The primers for psbK I produced several bands and the PCR products of atpF H were difficult to sequence. The powers of the remaining six loci were compared using the variability, identification success and the resolutions. It was found that ITS2 is the most promising candidate for DNA barcoding for mosses. Among the chloroplast genes, atpB rbcL exhibited the highest resolution. Although trnH psbA is very variable, it is too short to be an ideal barcode alone. Combinations of chloroplast genes were also tried and Ps of both atpB rbcL+trnH psbA and rbcL a++trnH psbA were 64% using NJ method. More additions of loci did not increase the resolution. No barcoding gap exists for all these loci. Phylogenetic analyses were carried out prior to the DNA barcoding evaluation and some taxonomic problems do exist. This study exemplifies the necessity of correct species delimitation and the adoption of both plastid and nuclear loci in plant DNA barcoding.     

The effects of DNA intercalators on chromatin of chicken red blood cells——differential extraction on nonhistone proteins

Taking advantage of the effects on DNA secondary structure of two DNA-intercalators,ethidium bromide and chloroquine,we used each of them to treat nuclei from both mature erythrocytes and reticulocytes of chicken,as an alternative approach to study the relationships between DNA secondary structure,nuclear proteins and chromatin structure.We presented results of differential extraction of nuclear proteins from nuclei with DNA-intercalators,as well as preliminary characterization of these proteins.A 45kd protein is the major component in fractions extracted by both intercalators from nuclei from either mature erythrocytes or reticulocytes and seems to be a DNA-binding protein.Furthermore,from current concepts of functional aspects of DNA conformation and structural heterogeneity in chromatin and nuclear proteins,we have discussed both the significance of our results as well as technical aspects of this approach.     

The effect of temperature on the electrochemical properties of copper—DNA membranes

The influence of temperature, electrode plate metals and protamine on the membrane potential of an electrochemically prepared copper—DNA (Cu-DNA) membrane (size, 2.5×6cm; thickness, 80μm; Cu/P molar ratio, 0.4) was investigated. The results obtained showed that the membrane potential increased with temperature as well as with increasing order of ionization tendency of the divalent metals used, and decreased with an increase of protamine bound to the membrane. These results indicated that electrons accumulated on the anode side, and positive holes formed on the cathode side, of a Cu-DNA membrane prepared by electrolysis.     

Theoretical Studies on α-Helix—DNA Interactions

Abstract

The ¹H NMR relaxation effects produced by paramagnetic Cr(III) complexes on nucleoside 5′-mono- and -triphosphates in D₂O solution at Ph′=3 were measured. The paramagnetic probes were [Cr(III)(H₂O) ₆]³⁺, [Cr(III)(H₂O)₃ (HATP)], [Cr(III)(H₂O)₃(HCTP)] and [Cr(III) (H₂O)₃(UTP)^?, while the matrix nucleotides (0.1 M) were H₂AMP, HIMP^?, and H₂ATP^2-. For the aromatic base protons, the ratios of the transverse to longitudinal paramagnetic relaxation rates (R_2p/R_1p) for the [Cr(III)(H₂O)₆]³⁺/H₂ATP^2-, [Cr(III)(H₂O)₃(HATP)]/H₂ATP^2-, [Cr(III)(H₂O)₃(HCTP)]/H₂ATP² and [Cr(III)(H₂O)₃(UTP)]^?/H₂ATP² systems were below 2.33 so the dipolar term predominates. For a given nucleotide, R_1p for the purine H(8) signal was larger than for the H(2) signal with the [Cr(III)(H₂O)₆]³⁺ probe, while R_1p for the H(2) signal was larger with all the other Cr(III) probes. Molecular mechanics computations on the [Cr(III)(H₂O)₄(HPP)(α,β)], [Cr(III)(NH₃)₄(HPP)(α,β)], [Co(III)(NH₃)₃(H₂PPP)(α,βγ)] and [Co(III)(NH₃)₄(HPP)(α,β)] complexes gave calculated energy-minimized geometries in good agreement with those reported in crystal structures. The molecular mechanics force constants found were then used to calculate the geometry of the inner sphere [Cr(III)(H₂O)₆]³⁺ and [Cr(III)(H₂O)₃(HATP)(α,βγ)] complexes as well as the structures of the outer sphere [Cr(III) (H₂O)₆]³⁺-(H₂AMP) and [Cr(III)(H₂O)₆]-(HIMP)^? species. The gas-phase structure of the [Cr(III)(H₂O)₃(HATP)(α,βγ)] complex shows the existence of a hydrogen bond interaction between a water ligand and the adenine N(7) (O…N = 2.82 Å). The structure is also stabilized by intramolecular hydrogen bonds involving the -O(2′)H group and the adenine N(3) (O…N = 2.80 Å) as well as phosphate oxygen atoms and a water molecule (O…O = 2.47 Å). The metal center has an almost regular octahedral coordination geometry.

The structures of the two outer-sphere species reveal that the phosphate group interacts strongly with the hexa-aquochromium probe. In both complexes, the nucleotides have a similar “anti” conformation around the N(9)-C(l′) glycosidic bond. However, a very important difference characterizes the two structures. For the (HIMP)^? complex, strong hydrogen bond interactions exist between one and two water ligands and the inosine N(7) and O(6) atoms, respectively (O…O = 2.63 Å O…N = 2.72, 2.70 Å). For the H₂AMP complex, the [Cr(III) (H₂O)c]³⁺ cation does not interact with N(7) since it is far from the purine system. Hydrogen bonds occur between water ligands and phosphate oxygens. The Cr-H(8) and Cr-H(2) distances revealed by the energy-minimized geometries for the two outer sphere species were used to calculate the R_1p values for the H(8) and H(2) signals for comparison with the observed R_1p values: 0.92(c), 1.04(ob) (H(8)) and 0.06(c), 0.35(ob) (H(2)) for H₂AMP; and 3.76(c), 4.53(ob) (H(8)) and 0.16(c), 0.77(ob) s^?1 (H(2)) for HIMP^?. These results suggest that the dynamic relaxation effects can be only partially understood with molecular mechanics computations, although the success of the geometry calculations suggests that future efforts in the development of computational methods are justified.     

Effect of phosphatidylcholine vesicles on the activity of DNA polymerase-α

Summary Phosphatidylcholine vesicles stimulate the activity of the DNA polymerase- from calf thymus. This effect is dependent upon the way of addition of the Mg ions, and the extent of the ³H-dTTP incorporation is closely related to the concentration of the vesicles. A role of phospholipids on the activity of the DNA-related enzymes is suggested.     

Applications——Influence of Biology on Engineering

Examples are presented showing the way in which biological systems produce a range of functions which can be implemented in engineering, such as feedback-control of stiffness （muscles and nervous system）, the design of fault-free structures （trees） and damage-tolerant materials （wood） and high performance insulation （penguin feathers） and shock absorbers （hedgehog spines）.     

Effect of Oxidized Polyamines on the Infectivity of φX174 DNA

Oxidized spermine and oxidized spermidine inhibited markedly the infectivity of the 6 m-urea treated φX174 particle, whereas they did not inactivate the infectivity of the untreated phage particle. They also markedly inhibited the infectivity of φX174 DNA, while φX174 RF I DNA was less sensitive to these reagents. These facts suggested that oxidized polyamines could react with phage DNA.

The possible reasons of the insensitivity of phage φX174 particle and less sensitivity of φX174 RF I DNA to these reagents were discussed.     

Effect of Chloramphenicol on the DNA Synthesis of Bacteriophage ϕX174

In bacteriophage ?X174 infection, the net synthesis of replicative form DNA ceased between 15 and 20 min after infection. When 30 μg of chloramphenicol/ml was added, net RF synthesis, however, continued beyond the normal time and level of turn-off. Experiments with ?X174 mutants unable to synthesize single-stranded DNA showed that a protein synthesis was required for the cessation of net RF synthesis and the protein was synthesized between 10 and 15 min after infection.     

Studies on DNA—protein interactions in the upstream regulatory region of the human ε—globin gene promoter

The erythroid- and developmental stage-specific expression of the human ε-globin gene is controlled,in part,by the 5‘-flanking DNA sequence of this gene.In the present study,we have used DNA-protein binding assays to identify trans-acting factors which regulate the temporal expression of the human ε-globin gene during development.Using gel mobility shift assays and DNaseI footprinting assays,a nuclear protein factor (termed ε-SSF1) in the nuclear extracts from mouse haematopoietic tissues at d 11 and d 13 of gestation was identified.It could specifically bind to the positive control region (between-535 and -453bp) of the human ε-globin gene.We speculated that the ε-SSF1 might be an erythroid-and developmental stage-specific activator.In addition,we found another nuclear protein factor (terned ε-R1) in the nuclear extract from mouse fetal liver at d18 of gestation,which could strongly bind to the silencer region (between-392 and -177bp) of this gene.Therefore,we speculated that the ε-R1 might be an erythroid-and developmental stagespecific repressor.Our data suggest that both ε-SSF1 and ε-R1 might play important roles in developmental regulation of the human ε-globin gene expression during the early embryonic life.On the hand,we observed that the binding patterns of nuclear proteins from three cell lines (K562,HEL and Raji) to these regulatory regions were partially different.These results suggest that different trans-acting factors in K562,HEL and Raji cells might be responsible for activating or silencing the human ε-globin gene in three different cell lines.     

Effects of glutathione on chromium‐induced DNA. Crosslinking and DNA polymerase arrest

Hexavalent chromium (Cr (VI)) is reduced intracellularly to Cr (V), Cr (IV) and Cr (III) by ascorbate (Asc), cysteine and glutathione (GSH). These metabolites induce a spectrum of genomic DNA damage resulting in the inhibition of DNA replication. Our previous studies have shown that treatment of DNA with Cr (III) or Cr (VI) plus Asc results in the formation of DNACrDNA crosslinks (CrDDC) and guaninespecific arrests of both prokaryotic and mammalian DNA polymerases. GSH not only acts as a reductant of Cr (VI) but also becomes crosslinked to DNA by Cr, thus, the focus of the present study was to examine the role of GSH in Crinduced DNA damage and polymerase arrests. Coincubation of Cr (III) with plasmid DNA in the presence of GSH led to the crosslinking of GSH to DNA. GSH cotreatment with Cr (III) also led to a decrease in the degree of Crinduced DNA interstrand crosslinks relative to Cr (III) alone, without affecting total Cr DNA binding. DNA polymerase arrests were observed following treatment of DNA with Cr (III) alone, but were markedly reduced when GSH was added to the reaction mixture. Preformed polymerasearresting lesions (CrDDC) were not removed by subsequent addition of GSH. Treatment of DNA with Cr (VI), in the presence of GSH, resulted in crosslinking of GSH to DNA, but failed to produce detectable DNA interstrand crosslinks or polymerase arrests. The inhibitory effect of GSH on Crinduced polymerase arrest was further confirmed in human genomic DNA using quantitative PCR (QPCR) analysis. Treatment of genomic DNA with Cr (III) resulted in a marked inhibition of the amplification of a 1.6 kb target fragment of the p53 gene by Taq polymerase. This was almost completely prevented by cotreatment with GSH and Cr (III). These results indicate that Crinduced DNA interstrand crosslinks, and not DNACrGSH crosslinks, are the principal lesions responsible for blocking DNA replication. Moreover, the formation of DNACrGSH crosslinks may actually preclude the formation of the polymerase arresting lesions.     

Organization of the variant domains of α satellite DNA on human chromosome 21

The de novo creation of long, homogeneous, satellite DNA domains was postulated previously to occur by saltatory amplification. In this paper, pulsed field gel electrophoresis analysis of the α satellite DNA block organization of the human chromosome 21 supports this hypothesis. Double-dimension electrophoresis indicated that the variant copies of the basic α satellite repeat of chromosome 21 are organized in a single 3,150 Kblong domain. It was also established that the other satellite DNAs found in man (β, II, and III) are organized independently of the α satellite DNA block of the same chromosome. Presented at the NATO Advanced Research Workshop onGenome Organization and Evolution, Spetsai, Greece, 16–22 September 1992     

The effects ofγ-irradiation on the hydration characteristics of DNA and polynucleotides

Summary The effects of-irradiation and changes in the macromolecular structure on the water proton resonance spectra observed in frozen and liquid solutions have been compared for the DNA and polynucleotide solutions, using H₂O or mixed H₂O/D₂O solvents. The results indicate that in order to obtain information concerning the role of hydration water in mediating the overall radiation damage, the NMR studies must be performed in the frozen state.Member of the Euratom biology division     

Lack of DNA polymerase μ affects the kinetics of DNA double-strand break repair and impacts on cellular senescence

The specialised DNA polymerase μ (pol μ) affects a sub-class of immunoglobulin genes rearrangements and haematopoietic development in vivo. These effects appear linked to double-strand breaks (DSBs) repair, but it is still unclear how and to what extent pol μ intervenes in this process. Using high-resolution quantitative imaging of DNA damage in irradiated wild-type and pol μ^?/? mouse embryonic fibroblasts (MEFs) we show that lack of pol μ results in delayed DSB repair kinetics and in persistent DNA damage. DNA damage triggers cellular senescence, and this response is thought to suppress cancer. Independent investigations either report or not a proliferative decline for MEFs lacking pol μ. Here we show pronounced senescence in pol μ^?/? MEFs, associated with high levels of the tumor-suppressor p16^INK4A and the DNA damage response kinase CHK2. Importantly, cellular senescence is induced by culture stress and exacerbated by low doses of irradiation in pol μ^?/? MEFs. We also found that low doses of irradiation provoke delayed immortalisation in MEFs lacking pol μ. Pol μ^?/? MEFs thus exhibit a robust anti-proliferative defence in response to irreparable DNA damage. These findings indicate that sub-optimal DSB repair, due to the absence of an auxiliary DNA damage repair factor, can impact on cell fitness and thereby on cell fate.