Gene enrichment using antibodies to DNA/RNA hybrids : mapping the ribosomal DNA of slime mold and rat

A novel method for gene enrichment has been developed and applied to mapping the rRNA genes of two eucaryotic organisms. The method makes use of antibodies to DNA/RNA hybrids prepared by injecting rabbits with the synthetic hybrid poly(rA)•poly(dT). Antibodies which cross-react with non-hybrid nucleic acids were removed from the purified IgG fraction by adsorption on columns of DNA-Sepharose, oligo(dT)-cellulose, and poly(rA)-Sepharose. Subsequent purification of the specific DNA/RNA hybrid antibody was carried out on a column of oligo(dT)-cellulose to which poly(rA) was hybridized. Attachment of these antibodies to CNBr-activated Sepharose produced an affinity resin which specifically binds DNA/RNA hybrids.

In order to map the rDNA of the slime mold Dictyostelium discoideum, R-loops were formed using unsheared nuclear DNA and the 178 and 268 rRNAs of this organism. This mixture was passed through a column containing the affinity resin, and bound molecules containing R- loops were eluted by high salt. This purified rDN A was observed directly in the electron microscope. Evidence was obtained that there is a physical end to Dictyostelium rDN A molecules approximately 10 kilobase pairs (kbp) from the region which codes for the 268 rRNA. This finding is consistent with reports of other investigators that the rRNA genes exist as inverse repeats on extra-chromosomal molecules of DNA unattached to the remainder of the nuclear DNA in this organism.

The same general procedure was used to map the rRNA genes of the rat. Molecules of DNA which contained R-loops formed with the 188 and 288 rRNAs were enriched approximately 150- fold from total genomal rat DNA by two cycles of purification on the affinity column. Electron microscopic measurements of these molecules enabled the construction of an R-loop map of rat rDNA. Eleven of the observed molecules contained three or four R-loops or else two R-loops separated by a long spacer. These observations indicated that the rat rRNA genes are arranged as tandem repeats. The mean length of the repeating units was 37.2 kbp with a standard deviation of 1.3 kbp. These eleven molecules may represent repeating units of exactly the same length within the errors of the measurements, although a certain degree of length heterogeneity cannot be ruled out. If significantly shorter or longer repeating units exist, they are probably much less common than the 37.2 kbp unit.

The last section of the thesis describes the production of antibodies to non-histone chromosomal proteins which have been exposed to the ionic detergent sodium dodecyl sulfate (SDS). The presence of low concentrations of SDS did not seem to affect either production of antibodies or their general specificity. Also, a technique is described for the in situ immunofluorescent detection of protein antigens in polyacrylamide gels.

Sputtering of uranium

Sputtering yields for uranium metal under bombardment by 13 - 120 keV protons and by 20 - 120 keV He+ are presented. Angular distributions of the material sputtered by these ions are also given. Sputtering yields for 40 and 80 keV Ar+ were measured as well.

The technique employed to make these measurements was the detection of fission tracks in mica produced by ^(235)U sputtered onto collector foils which were subsequently exposed to a high fluence of thermal neutrons. The technique is extremely sensitive and allowed the measurement of sputtering yields less than 10^(-4) atoms per ion. It also made possible a detailed study of the emission of chunks from the uranium targets during sputtering. Mass distributions of chunks emitted during bombardment by 40 - 120 keV protons and by 80 keV argon are presented.

Comparisons are made between the experimental results and those predicted by the Sigmund theory of sputtering.

The energy spectra of uranium atoms sputtered from uranium metal and uranium dioxide targets

The energy spectra of ²³⁵U atoms sputtered from a 93% enriched ²³⁵U metal foil and a hot pressed ²³⁵U0₂ pellet by an 80 keV ⁴⁰Ar⁺ beam have been measured in the range 1 eV to 1 keV. The measurements were made using a mechanical time-of-flight spectrometer in conjunction with the fission track technique for detecting ²³⁵U. The design and construction of this spectrometer are discussed in detail, and its operation is mathematically analyzed.

The results of the experiment are discussed in the context of the random collision cascade model of sputtering. The spectrum obtained by the sputtering of the ²³⁵U metal target was found to be well described by the functional form E(E+E_b)^-2.77, where E_b = 5.4 eV. The ²³⁵U0₂ target produced a spectrum that peaked at a lower energy (~ 2 eV) and decreased somewhat more rapidly for E ≳ 100 eV.

Investigations into electronic stopping regime sputtering of uranium tetrafluoride

Yields were measured for ²³⁵U sputtered from UF₄ by ¹⁶O, ¹⁹F, and ³⁵Cl over the energy range ~.12 to 1.5 MeV/ amu sing a charge equilibrated beam in the stripped beam arrangement for all the incident ions and in the transmission arrangement for ¹⁹F and ³⁵Cl. In addition, yields were measured for ¹⁹F incident in a wide range of discrete charge states. The angular dependence of all the measured yields were consistent with cosʋ. The stripped beam and transmission data were well fit by the form (Az²eqln(BƐ)/Ɛ)⁴ (where Ɛ was the ion energy in MeV/amu and z_eq(Ɛ) was taken from Zeigler(80). The fitted values of B for the various sets of data were consistent with a constant B₀, equal to 36.3 ± 2.7, independent of incident ion. The fitted values of A show no consistent variation with incident ion although a difference can be noted between the stripped beam and transmission values, the transmission values being higher.

The incident charge data were well fit by the assumptions that the sputtering yield depended locally on a power of the incident ion charge and that the sputtering from the surface is exponentially correlated to conditions in the bulk. The equilibrated sputtering yields derived from these data are in agreement with the stripped beam yields.

In addition, to aid in the understanding of these data, the data of Hakansson(80,81a,81b) were examined and contrasted with the UF₄ results. The thermal models of Seiberling(80) and Watson(81) were discussed and compared to the data.