Immunoglobulin recognition of synthetic and natural left-handed Z DNA conformations and sequences

The relative immunogenicities of the poly[d(G-C)] and poly[d(A-C).d(G-T)] families of helices have been determined. The specificities of the resultant immunoglobulins have been characterized for recognition of different synthetic and natural left-handed sequences and conformations. Certain modifications of poly[d(G-C)] in the sugar-phosphate backbone and cytosine C-5 potentiate the right(R)-to-left(L) (B----Z) transition under physiological conditions. The resulting polynucleotides, poly[d(G-SC)], poly[d(G-io5C)], poly[d(G-br5C)] and poly[d(G-m5C)], are also highly immunogenic. In contrast, DNAs incapable of assuming the left-handed conformation under physiological salt concentrations are weakly or non-immunogenic. These include unmodified poly[d(G-C)] as well as members of the poly[d(A-C).d(G-T)] family of sequences bearing pyrimidine C-5 substitutions (methyl, bromo, iodo). These polynucleotides undergo the R----L isomerization under more stringent ionic and thermal conditions. The specificities of purified polyclonal and monoclonal anti-Z DNA immunoglobulins (IgG) were measured by binding to radiolabeled polynucleotides, by electrophoretic analysis of IgG bound to covalent closed circular DNAs, and by immunofluorescent staining of polytene chromosomes. The salt-induced left-handed forms of poly[d(G-C)] and its derivatives (including the cytidine C-5 methyl, bromo, iodo, and N-5 aza substituted polynucleotides) and of the modified poly[d(A-C).d(G-T)] polymers are bound to varying degrees by different antibodies. The patterns of substrate recognition demonstrate the existence of several antigenic domains in left-handed DNAs, including the helix convex surface and the sugar-phosphate backbone. Substitutions in these regions can produce enhancing (required substitutions), neutral, or inhibitory effects on subsequent IgG binding. Additionally, certain modifications of either the convex surface of Z DNA at the C-5 position of cytidine (i.e. a methyl group) or of the backbone (i.e. phosphorothioate substitution) can lead to polymorphic left-handed conformations that are compatible with antibody binding when present individually but not in combination. The recognition patterns exhibited with DNA substrates from the two DNA families indicate that some, but not all, IgGs show specificity for different nucleotide sequences. The anti-Z DNA IgGs were used to probe for specific left-handed Z DNA determinants on plasmid (e.g. pBR322) or viral (e.g. simian virus 40 (SV40] DNAs and on the acid-fixed polytene chromosomes of dipteran larvae.(ABSTRACT TRUNCATED AT 400 WORDS)

Isolation of Z-DNA-containing plasmids

A purified, monoclonal antibody, specific for the left-handed Z-form of poly(dG-dC), was coupled covalently to Sephacryl S-1000 beads. Such an antibody column provides a convenient method to isolate and purify those plasmid DNAs that contain Z-DNA from a large excess of other DNAs, RNA, etc. From a library of Escherichia coli DNA, cloned into the vector plasmid pUC-8, several recombinant plasmids were isolated, which bind to this antibody. Thus, E. coli contains sequences, which in "natural" negatively supercoiled DNA, adopt a left-handed Z-DNA-like conformation.

Temperature dependence of the activity of DNA-modifying enzymes: endonucleases and DNA ligase

The activities of 17 endonucleases: the restriction endonucleases AvaI, Bam HI, EcoRI, HindIII, PstI and SalI, which cleave pBR322 DNA once: AluI, AvaII, CfoI, HaeIII, HhaI, HinfI, HpaII and TaqI, which cut pBR322 DNA several times, and three 'unspecific' nucleases (S1 nuclease, staphylococcal nuclease and DNase I from bovine pancreas) were determined between 0 degrees and 65 degrees C. The reaction was followed by the disappearance of covalently closed circular pBR322 DNA, using the alkaline ethidium fluorescence assay of Morgan et al. [Nucleic Acids Res. (1979) 7, 547-594]; the activity of T4 DNA ligase was similarly measured by the conversion of nicked circular DNA to closed circular DNA. For each enzyme, small aliquots of the same solution were incubated at different temperatures simultaneously in a temperature gradient device, resulting in a high relative precision. The experimental results are summarized by the simplest possible theoretical description, using linear or exponential kinetics and apparent activation energies Ea for the enzymatic reaction, Ei for the enzyme inactivation and Ti for the inactivation temperature. To a good approximation these three parameters suffice for describing the temperature dependence of the activity of most of the enzymes.

Torsional stress induces left-handed helical stretches in DNA of natural base sequence: circular dichroism and antibody binding

Above a threshold of torsional stress, the c.d. spectrum of covalently closed circular DNA of natural base sequence acquires a Z-like contribution and antibodies raised against Z-DNA are bound. Mapping of the antibody binding sites by electron microscopy reveals sites which correlate with stretches enriched in alternating purine-pyrimidine sequences and GC base pairs.

The activity of transcription factor IIIC1 is impaired during differentiation of F9 cells

Differentiation in vitro of mouse F9 embryonal carcinoma (EC) cells to the parietal endoderm (PE) mimics processes of development of the early mouse embryo. This differentiation is accompanied by a dramatic down-regulation of all genes transcribed by RNA polymerase III (pol III). Complementation of extracts from cells, differentiated for various time periods with purified pol III transcription factors show for the first time that TFIIIC1 can substantially restore this impaired transcription, particularly in the early stages of differentiation. At later stages (day 7) the TBP (TATA-binding protein )-TAF complex, TFIIIBbeta, may also become limiting, which can contribute to but cannot account for the reduced transcription of type 2 promoters in PE cells. Because TFIIIBbeta is not required for the expression of type 3 promoters, other components must necessarily be involved, and our results show that U6 transcription can significantly be reactivated by TFIIIC1. By employing a variant type 3 promoter construct, which essentially requires a mutant form of TBP (TBP-DR2), we show that TBP is not limiting in PE extracts. The partial purification of pol III transcription factors from PE and EC cells revealed that TFIIIC2 activity could be purified from both cell types, whereas TFIIIC1 activity was dramatically reduced in extracts from PE cells.

First commissioning results with the Grenoble test electron cyclotron resonance ion source at iThemba LABS

iThemba Laboratory for Accelerator Based Science (iThemba LABS) is a multi-disciplinary accelerator facility. One of its main activities is the operation of a separated-sector cyclotron with a K-value of 200, which provides beams of various ion species. These beams are used for fundamental nuclear physics research in the intermediate energy region, radioisotope production, and medical physics applications. Due to the requirements of nuclear physics for new ion species and higher energies, the decision was made to install a copy of the so-called Grenoble test source (GTS) at iThemba LABS. In this paper, we will report on the experimental setup and the first results obtained with the GTS2 at iThemba LABS.

Liquid metal ion source assembly for external ion injection into an electron string ion source (ESIS)

An assembly for a commercial Ga(+) liquid metal ion source in combination with an ion transportation and focusing system, a pulse high-voltage quadrupole deflector, and a beam diagnostics system has been constructed in the framework of the iThemba LABS (Cape Town, South Africa)-JINR (Dubna, Russia) collaboration. First, results on Ga(+) ion beam commissioning will be presented. Outlook of further experiments for measurements of charge breeding efficiency in the electron string ion source with the use of external injection of Ga(+) and Au(+) ion beams will be reported as well.

Beam experiments with the Grenoble test electron cyclotron resonance ion source at iThemba LABS

At iThemba Laboratory for Accelerator Based Sciences (iThemba LABS) an electron cyclotron ion source was installed and commissioned. This source is a copy of the Grenoble Test Source (GTS) for the production of highly charged ions. The source is similar to the GTS-LHC at CERN and named GTS2. A collaboration between the Accelerators and Beam Physics Group of CERN and the Accelerator and Engineering Department of iThemba LABS was proposed in which the development of high intensity argon and xenon beams is envisaged. In this paper, we present beam experiments with the GTS2 at iThemba LABS, in which the results of continuous wave and afterglow operation of xenon ion beams with oxygen as supporting gases are presented.

Preparation of a primary argon beam for the CERN fixed target physics

The fixed target experiment NA61 in the North Area of the Super Proton Synchrotron is studying phase transitions in strongly interacting matter. Up to now they used the primary beams available from the CERN accelerator complex (protons and lead ions) or fragmented beams created from the primary lead ion beam. To explore a wider range of energies and densities a request was made to provide primary argon and xenon beams. This paper describes the results of the setting up and 10 week test run of the Ar(11+) beam from the 14.5 GHz ECR ion source and the linear accelerator (Linac3) at CERN.